RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux kishi13 3.2.0-95-highbank #135-Ubuntu SMP PREEMPT Tue Nov 10 14:26:08 UTC 2015 armv7l Buildd toolchain package versions: launchpad-buildd_137 python-lpbuildd_137 sbuild_0.65.2-1ubuntu2~ubuntu12.04.1~ppa7 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.7 python-debian_0.1.27ubuntu1~ubuntu12.04.1~ppa2. Syncing the system clock with the buildd NTP service... 27 Jan 23:15:58 ntpdate[8832]: adjust time server 10.211.37.1 offset 0.000125 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8905283', '/home/buildd/filecache-default/bdf524d1fbccc9606fe3cb203c365489d3f7f335'] Unpacking chroot for build PACKAGEBUILD-8905283 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8905283'] Mounting chroot for build PACKAGEBUILD-8905283 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8905283', 'deb http://ftpmaster.internal/ubuntu xenial main universe', 'deb http://ftpmaster.internal/ubuntu xenial-security main universe', 'deb http://ftpmaster.internal/ubuntu xenial-updates main universe', 'deb http://ftpmaster.internal/ubuntu xenial-proposed main universe'] Overriding sources.list in build-PACKAGEBUILD-8905283 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8905283', 'armhf'] Updating debian chroot for build PACKAGEBUILD-8905283 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:3 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:4 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:5 http://ftpmaster.internal xenial/main armhf Packages [1451 kB] Get:6 http://ftpmaster.internal xenial/universe armhf Packages [7043 kB] Get:7 http://ftpmaster.internal xenial/main Translation-en [854 kB] Get:8 http://ftpmaster.internal xenial/universe Translation-en [4826 kB] Get:9 http://ftpmaster.internal xenial-security/main armhf Packages [28 B] Get:10 http://ftpmaster.internal xenial-security/universe armhf Packages [28 B] Get:11 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:12 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:13 http://ftpmaster.internal xenial-updates/main armhf Packages [28 B] Get:14 http://ftpmaster.internal xenial-updates/universe armhf Packages [28 B] Get:15 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:17 http://ftpmaster.internal xenial-proposed/main armhf Packages [37.0 kB] Get:18 http://ftpmaster.internal xenial-proposed/universe armhf Packages [369 kB] Get:19 http://ftpmaster.internal xenial-proposed/main Translation-en [27.5 kB] Get:20 http://ftpmaster.internal xenial-proposed/universe Translation-en [196 kB] Fetched 15.4 MB in 19s (809 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'apt-get autoremove' to remove them. The following packages will be REMOVED: perl-modules* The following NEW packages will be installed: init-system-helpers libapt-pkg5.0 libisl15 libperl5.22 libprocps4 perl-modules-5.22 The following packages will be upgraded: advancecomp apt apt-transport-https base-files base-passwd binutils bsdutils cpp cpp-5 debconf debianutils diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv grep hostname init initscripts libapparmor1 libasan2 libasn1-8-heimdal libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap2 libcap2-bin libcc1-0 libcomerr2 libcurl3-gnutls libdbus-1-3 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfdisk1 libffi6 libgcc-5-dev libgcc1 libgcrypt20 libgmp10 libgnutls-deb0-28 libgomp1 libgpg-error0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhx509-5-heimdal libidn11 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libmpfr4 libncurses5 libncursesw5 libnih-dbus1 libnih1 libp11-kit0 libpcre3 libpng12-0 libroken18-heimdal librtmp1 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libusb-0.1-4 libuuid1 libwind0-heimdal linux-libc-dev lsb-base make mount multiarch-support ncurses-base ncurses-bin openssl perl perl-base pkg-create-dbgsym pkgbinarymangler procps systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 121 upgraded, 6 newly installed, 1 to remove and 0 not upgraded. Need to get 112 MB of archives. After this operation, 255 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files armhf 9.4ubuntu3 [69.6 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils armhf 1:2.27.1-1ubuntu3 [48.9 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main debianutils armhf 4.7 [84.4 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main diffutils armhf 1:3.3-3 [143 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main dpkg armhf 1.18.4ubuntu1 [1989 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libc6-dev armhf 2.21-0ubuntu5 [1585 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial/main libc-dev-bin armhf 2.21-0ubuntu5 [58.6 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev armhf 4.4.0-1.15 [797 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 armhf 1:2.24-12 [11.7 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libc-bin armhf 2.21-0ubuntu5 [984 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 armhf 5.3.1-7ubuntu1 [49.9 kB] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 armhf 5.3.1-7ubuntu1 [6020 B] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 armhf 5.3.1-7ubuntu1 [244 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base armhf 5.3.1-7ubuntu1 [16.6 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 armhf 1:5.3.1-7ubuntu1 [39.0 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 armhf 5.3.1-7ubuntu1 [88.6 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 armhf 0.16.1-1 [406 kB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 armhf 5.3.1-7ubuntu1 [23.7 MB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 armhf 5.3.1-7ubuntu1 [25.8 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial-proposed/main binutils armhf 2.26-2ubuntu1 [2335 kB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 armhf 5.3.1-7ubuntu1 [25.3 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 armhf 5.3.1-7ubuntu1 [23.8 MB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev armhf 5.3.1-7ubuntu1 [475 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev armhf 5.3.1-7ubuntu1 [1462 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 armhf 5.3.1-7ubuntu1 [350 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 armhf 2:6.1.0+dfsg-2 [184 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main libmpfr4 armhf 3.1.3-2 [169 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main libc6 armhf 2.21-0ubuntu5 [3903 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs armhf 1.42.13-1ubuntu1 [177 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs armhf 1.42.13-1ubuntu1 [754 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main findutils armhf 4.6.0-2 [266 kB] Get:32 http://ftpmaster.internal/ubuntu/ xenial-proposed/main grep armhf 2.22-1 [139 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main hostname armhf 3.16ubuntu2 [10.9 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial-proposed/main init-system-helpers all 1.26ubuntu2 [31.2 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils armhf 2.88dsf-59.3ubuntu1 [20.7 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main perl-modules-5.22 all 5.22.1-4 [2648 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main libperl5.22 armhf 5.22.1-4 [2681 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main perl armhf 5.22.1-4 [238 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main perl-base armhf 5.22.1-4 [1178 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial-proposed/main init armhf 1.26ubuntu2 [3850 B] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 armhf 2.27.1-1ubuntu3 [54.6 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 armhf 2.27.1-1ubuntu3 [14.1 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 armhf 2.27.1-1ubuntu3 [95.3 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 armhf 2.27.1-1ubuntu3 [127 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.3ubuntu1 [18.2 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main initscripts armhf 2.88dsf-59.3ubuntu1 [24.9 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main util-linux armhf 2.27.1-1ubuntu3 [795 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 armhf 228-4ubuntu1 [50.4 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main udev armhf 228-4ubuntu1 [946 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 armhf 228-4ubuntu1 [180 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main systemd armhf 228-4ubuntu1 [3096 kB] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main libpcre3 armhf 2:8.38-1ubuntu1 [205 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 armhf 2.4-3build1 [47.8 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 armhf 6.0+20151024-2ubuntu1 [66.0 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 armhf 6.0+20151024-2ubuntu1 [75.1 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 armhf 6.0+20151024-2ubuntu1 [95.6 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 armhf 2:3.3.10-4ubuntu2 [29.6 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main procps armhf 2:3.3.10-4ubuntu2 [208 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main libapparmor1 armhf 2.10-0ubuntu11 [25.0 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.5-1ubuntu2 [3884 B] Get:62 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 armhf 1:2.4.5-1ubuntu2 [33.3 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 armhf 2.27.1-1ubuntu3 [102 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main libseccomp2 armhf 2.2.3-2ubuntu3 [28.5 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin armhf 1:2.24-12 [20.1 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20160110 [13.5 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main mount armhf 2.27.1-1ubuntu3 [116 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin armhf 6.0+20151024-2ubuntu1 [131 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main tar armhf 1.28-2.1 [181 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main libapt-pkg5.0 armhf 1.1.10 [624 kB] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main apt armhf 1.1.10 [938 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main gpgv armhf 1.4.19-6ubuntu1 [135 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libusb-0.1-4 armhf 2:0.1.12-28 [15.5 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial/main gnupg armhf 1.4.19-6ubuntu1 [564 kB] Get:75 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 armhf 0.198ubuntu1 [5956 B] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main base-passwd armhf 3.5.39 [50.5 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv armhf 228-4ubuntu1 [15.5 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 armhf 1.10.6-1ubuntu1 [141 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libnih-dbus1 armhf 1.0.3-4.3ubuntu1 [13.4 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libnih1 armhf 1.0.3-4.3ubuntu1 [45.4 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 armhf 1.42.13-1ubuntu1 [64.9 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 armhf 2:1.02.110-1ubuntu3 [139 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 armhf 1.21-1 [30.0 kB] Get:85 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 armhf 1.6.4-5 [301 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 armhf 2.4-2 [163 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3build1 [6594 B] Get:88 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 armhf 2.4-3build1 [68.7 kB] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libss2 armhf 1.42.13-1ubuntu1 [68.4 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main multiarch-support armhf 2.21-0ubuntu5 [7184 B] Get:91 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 armhf 3.2.1-4 [16.2 kB] Get:92 http://ftpmaster.internal/ubuntu/ xenial/main libp11-kit0 armhf 0.23.2-3 [91.2 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 armhf 4.7-3 [37.4 kB] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 armhf 3.3.20-1ubuntu1 [461 kB] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 armhf 1.2.54-1ubuntu1 [106 kB] Get:96 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsqlite3-0 armhf 3.10.2-1 [336 kB] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 armhf 1.0.2e-1ubuntu1 [711 kB] Get:98 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 armhf 1.13.2+dfsg-4 [98.6 kB] Get:99 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 armhf 1.13.2+dfsg-4 [230 kB] Get:100 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 armhf 1.13.2+dfsg-4 [26.7 kB] Get:101 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 armhf 1.13.2+dfsg-4 [77.9 kB] Get:102 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 armhf 1.5.9-8ubuntu1 [9192 B] Get:103 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 armhf 1.32-3ubuntu1 [42.2 kB] Get:104 http://ftpmaster.internal/ubuntu/ xenial/main libroken18-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [34.1 kB] Get:105 http://ftpmaster.internal/ubuntu/ xenial/main libasn1-8-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [138 kB] Get:106 http://ftpmaster.internal/ubuntu/ xenial/main libhcrypto4-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [75.7 kB] Get:107 http://ftpmaster.internal/ubuntu/ xenial/main libheimbase1-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [24.0 kB] Get:108 http://ftpmaster.internal/ubuntu/ xenial/main libwind0-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [47.3 kB] Get:109 http://ftpmaster.internal/ubuntu/ xenial/main libhx509-5-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [88.5 kB] Get:110 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-26-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [164 kB] Get:111 http://ftpmaster.internal/ubuntu/ xenial/main libheimntlm0-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [13.4 kB] Get:112 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi3-heimdal armhf 1.7~git20150920+dfsg-4ubuntu1 [78.5 kB] Get:113 http://ftpmaster.internal/ubuntu/ xenial/main libldap-2.4-2 armhf 2.4.42+dfsg-2ubuntu1 [139 kB] Get:114 http://ftpmaster.internal/ubuntu/ xenial/main librtmp1 armhf 2.4+20151223.gitfa8646d-1 [49.4 kB] Get:115 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libcurl3-gnutls armhf 7.47.0-1ubuntu1 [158 kB] Get:116 http://ftpmaster.internal/ubuntu/ xenial/main apt-transport-https armhf 1.1.10 [22.6 kB] Get:117 http://ftpmaster.internal/ubuntu/ xenial/main openssl armhf 1.0.2e-1ubuntu1 [486 kB] Get:118 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp armhf 1.20-1 [134 kB] Get:119 http://ftpmaster.internal/ubuntu/ xenial/main cpp armhf 4:5.2.1-16ubuntu2 [27.6 kB] Get:120 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup armhf 2:1.02.110-1ubuntu3 [61.1 kB] Get:121 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.4ubuntu1 [584 kB] Get:122 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.4ubuntu1 [195 kB] Get:123 http://ftpmaster.internal/ubuntu/ xenial/main make armhf 4.1-5 [137 kB] Get:124 http://ftpmaster.internal/ubuntu/ xenial/main gcc armhf 4:5.2.1-16ubuntu2 [5242 B] Get:125 http://ftpmaster.internal/ubuntu/ xenial/main g++ armhf 4:5.2.1-16ubuntu2 [1502 B] Get:126 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:127 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 129 [43.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 112 MB in 15s (7237 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11455 files and directories currently installed.) Preparing to unpack .../base-files_9.4ubuntu3_armhf.deb ... Unpacking base-files (9.4ubuntu3) over (7.2ubuntu11) ... Setting up base-files (9.4ubuntu3) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... Installing new version of config file /etc/lsb-release ... 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Unpacking libgcc1:armhf (1:5.3.1-7ubuntu1) over (1:5.2.1-22ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgcc1:armhf (1:5.3.1-7ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11466 files and directories currently installed.) Preparing to unpack .../libubsan0_5.3.1-7ubuntu1_armhf.deb ... Unpacking libubsan0:armhf (5.3.1-7ubuntu1) over (5.2.1-22ubuntu2) ... 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Setting up init-system-helpers (1.26ubuntu2) ... dpkg: perl-modules: dependency problems, but removing anyway as you requested: perl depends on perl-modules (>= 5.20.2-6). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11451 files and directories currently installed.) Removing perl-modules (5.20.2-6) ... Purging configuration files for perl-modules (5.20.2-6) ... (Reading database ... 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Installing new version of config file /etc/init.d/mountall.sh ... Processing triggers for systemd (225-1ubuntu9) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12026 files and directories currently installed.) Preparing to unpack .../util-linux_2.27.1-1ubuntu3_armhf.deb ... Unpacking util-linux (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Setting up util-linux (2.27.1-1ubuntu3) ... Processing triggers for systemd (225-1ubuntu9) ... (Reading database ... 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12032 files and directories currently installed.) Preparing to unpack .../systemd_228-4ubuntu1_armhf.deb ... Unpacking systemd (228-4ubuntu1) over (225-1ubuntu9) ... Setting up systemd (228-4ubuntu1) ... Installing new version of config file /etc/pam.d/systemd-user ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/system.conf ... addgroup: The group `systemd-journal' already exists as a system group. Exiting. Removing obsolete conffile /etc/X11/xinit/xinitrc.d/50-systemd-user.sh ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12029 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.38-1ubuntu1_armhf.deb ... Unpacking libpcre3:armhf (2:8.38-1ubuntu1) over (2:8.35-7.1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libpcre3:armhf (2:8.38-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12029 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3build1_armhf.deb ... Unpacking libselinux1:armhf (2.4-3build1) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:armhf (2.4-3build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12029 files and directories currently installed.) Preparing to unpack .../libtinfo5_6.0+20151024-2ubuntu1_armhf.deb ... Unpacking libtinfo5:armhf (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libtinfo5:armhf (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12029 files and directories currently installed.) Preparing to unpack .../libncurses5_6.0+20151024-2ubuntu1_armhf.deb ... Unpacking libncurses5:armhf (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:armhf (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Unpacking libapparmor1:armhf (2.10-0ubuntu11) over (2.10-0ubuntu6) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapparmor1:armhf (2.10-0ubuntu11) ... Processing triggers for systemd (228-4ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12038 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a2.4.5-1ubuntu2_all.deb ... Unpacking libaudit-common (1:2.4.5-1ubuntu2) over (1:2.4.2-1ubuntu1) ... Setting up libaudit-common (1:2.4.5-1ubuntu2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12038 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.4.5-1ubuntu2_armhf.deb ... Unpacking libaudit1:armhf (1:2.4.5-1ubuntu2) over (1:2.4.2-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libaudit1:armhf (1:2.4.5-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12038 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu3_armhf.deb ... Unpacking libmount1:armhf (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libmount1:armhf (2.27.1-1ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... 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Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12062 files and directories currently installed.) Preparing to unpack .../gpgv_1.4.19-6ubuntu1_armhf.deb ... Unpacking gpgv (1.4.19-6ubuntu1) over (1.4.18-7ubuntu1) ... Setting up gpgv (1.4.19-6ubuntu1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../systemd-sysv_228-4ubuntu1_armhf.deb ... Unpacking systemd-sysv (228-4ubuntu1) over (225-1ubuntu9) ... Setting up systemd-sysv (228-4ubuntu1) ... (Reading database ... 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Unpacking libnih1:armhf (1.0.3-4.3ubuntu1) over (1.0.3-4ubuntu27) ... Preparing to unpack .../libcomerr2_1.42.13-1ubuntu1_armhf.deb ... Unpacking libcomerr2:armhf (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libcomerr2:armhf (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.110-1ubuntu3_armhf.deb ... Unpacking libdevmapper1.02.1:armhf (2:1.02.110-1ubuntu3) over (2:1.02.99-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libdevmapper1.02.1:armhf (2:1.02.110-1ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.21-1_armhf.deb ... Unpacking libgpg-error0:armhf (1.21-1) over (1.19-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgpg-error0:armhf (1.21-1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.4-5_armhf.deb ... Unpacking libgcrypt20:armhf (1.6.4-5) over (1.6.3-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgcrypt20:armhf (1.6.4-5) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libsepol1_2.4-2_armhf.deb ... Unpacking libsepol1:armhf (2.4-2) over (2.3-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsepol1:armhf (2.4-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.4-3build1_all.deb ... Unpacking libsemanage-common (2.4-3build1) over (2.3-1build2) ... Setting up libsemanage-common (2.4-3build1) ... Installing new version of config file /etc/selinux/semanage.conf ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.4-3build1_armhf.deb ... Unpacking libsemanage1:armhf (2.4-3build1) over (2.3-1build2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsemanage1:armhf (2.4-3build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../libss2_1.42.13-1ubuntu1_armhf.deb ... Unpacking libss2:armhf (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libss2:armhf (1.42.13-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12061 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.21-0ubuntu5_armhf.deb ... Unpacking multiarch-support (2.21-0ubuntu5) over (2.21-0ubuntu4) ... Setting up multiarch-support (2.21-0ubuntu5) ... (Reading database ... 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Unpacking libgssapi3-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) over (1.6~rc2+dfsg-10ubuntu1) ... Preparing to unpack .../libldap-2.4-2_2.4.42+dfsg-2ubuntu1_armhf.deb ... Unpacking libldap-2.4-2:armhf (2.4.42+dfsg-2ubuntu1) over (2.4.41+dfsg-1ubuntu2) ... Preparing to unpack .../librtmp1_2.4+20151223.gitfa8646d-1_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d-1) over (2.4+20150115.gita107cef-1build1) ... Preparing to unpack .../libcurl3-gnutls_7.47.0-1ubuntu1_armhf.deb ... Unpacking libcurl3-gnutls:armhf (7.47.0-1ubuntu1) over (7.43.0-1ubuntu2) ... Preparing to unpack .../apt-transport-https_1.1.10_armhf.deb ... Unpacking apt-transport-https (1.1.10) over (1.0.10.2ubuntu1) ... Preparing to unpack .../openssl_1.0.2e-1ubuntu1_armhf.deb ... Unpacking openssl (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu1) ... Preparing to unpack .../advancecomp_1.20-1_armhf.deb ... Unpacking advancecomp (1.20-1) over (1.19-1) ... Preparing to unpack .../cpp_4%3a5.2.1-16ubuntu2_armhf.deb ... 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Unpacking pkgbinarymangler (129) over (122) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libc-dev-bin (2.21-0ubuntu5) ... Setting up linux-libc-dev:armhf (4.4.0-1.15) ... Setting up libc6-dev:armhf (2.21-0ubuntu5) ... Setting up libgomp1:armhf (5.3.1-7ubuntu1) ... Setting up libatomic1:armhf (5.3.1-7ubuntu1) ... Setting up libasan2:armhf (5.3.1-7ubuntu1) ... Setting up libubsan0:armhf (5.3.1-7ubuntu1) ... Setting up libgmp10:armhf (2:6.1.0+dfsg-2) ... Setting up libisl15:armhf (0.16.1-1) ... Setting up libmpfr4:armhf (3.1.3-2) ... Setting up cpp-5 (5.3.1-7ubuntu1) ... Setting up libcc1-0:armhf (5.3.1-7ubuntu1) ... Setting up binutils (2.26-2ubuntu1) ... Setting up libgcc-5-dev:armhf (5.3.1-7ubuntu1) ... Setting up gcc-5 (5.3.1-7ubuntu1) ... Setting up libstdc++-5-dev:armhf (5.3.1-7ubuntu1) ... Setting up g++-5 (5.3.1-7ubuntu1) ... Setting up perl-modules-5.22 (5.22.1-4) ... Setting up libperl5.22:armhf (5.22.1-4) ... Setting up perl (5.22.1-4) ... Setting up libprocps4:armhf (2:3.3.10-4ubuntu2) ... Setting up procps (2:3.3.10-4ubuntu2) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up udev (228-4ubuntu1) ... Installing new version of config file /etc/init.d/udev ... addgroup: The group `input' already exists as a system group. Exiting. Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Removing obsolete conffile /etc/init.d/lvm2 ... Setting up apt (1.1.10) ... Installing new version of config file /etc/apt/apt.conf.d/01-vendor-ubuntu ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt ... Installing new version of config file /etc/kernel/postinst.d/apt-auto-removal ... usermod: no changes Setting up libdbus-1-3:armhf (1.10.6-1ubuntu1) ... Setting up libnih1:armhf (1.0.3-4.3ubuntu1) ... Setting up libnih-dbus1:armhf (1.0.3-4.3ubuntu1) ... Setting up libffi6:armhf (3.2.1-4) ... Setting up libp11-kit0:armhf (0.23.2-3) ... Setting up libtasn1-6:armhf (4.7-3) ... Setting up libgnutls-deb0-28:armhf (3.3.20-1ubuntu1) ... Setting up libpng12-0:armhf (1.2.54-1ubuntu1) ... Setting up libsqlite3-0:armhf (3.10.2-1) ... Setting up libssl1.0.0:armhf (1.0.2e-1ubuntu1) ... Setting up libkrb5support0:armhf (1.13.2+dfsg-4) ... Setting up libk5crypto3:armhf (1.13.2+dfsg-4) ... Setting up libkeyutils1:armhf (1.5.9-8ubuntu1) ... Setting up libkrb5-3:armhf (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:armhf (1.13.2+dfsg-4) ... Setting up libidn11:armhf (1.32-3ubuntu1) ... Setting up libroken18-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libasn1-8-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libhcrypto4-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libheimbase1-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libwind0-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libhx509-5-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libkrb5-26-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libheimntlm0-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libgssapi3-heimdal:armhf (1.7~git20150920+dfsg-4ubuntu1) ... Setting up libldap-2.4-2:armhf (2.4.42+dfsg-2ubuntu1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d-1) ... Setting up libcurl3-gnutls:armhf (7.47.0-1ubuntu1) ... Setting up apt-transport-https (1.1.10) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up dmsetup (2:1.02.110-1ubuntu3) ... Setting up libdpkg-perl (1.18.4ubuntu1) ... Setting up make (4.1-5) ... Setting up dpkg-dev (1.18.4ubuntu1) ... Setting up gcc (4:5.2.1-16ubuntu2) ... Setting up g++ (4:5.2.1-16ubuntu2) ... Setting up pkg-create-dbgsym (0.70) ... Setting up pkgbinarymangler (129) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-4ubuntu1) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8905283', 'armhf', 'xenial-proposed', '-c', 'chroot:autobuild', '--arch=armhf', '--dist=xenial-proposed', '--purge=never', '--nolog', 'pymol_1.7.2.1-2.2.dsc'] Initiating build PACKAGEBUILD-8905283 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 3.2.0-95-highbank #135-Ubuntu SMP PREEMPT Tue Nov 10 14:26:08 UTC 2015 armv7l sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on kishi13.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ pymol 1.7.2.1-2.2 (armhf) 27 Jan 2016 23:19 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: pymol Version: 1.7.2.1-2.2 Source Version: 1.7.2.1-2.2 Distribution: xenial-proposed Machine Architecture: armhf Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/pymol-_S1jkh/pymol-1.7.2.1' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/pymol-_S1jkh' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8905283/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── pymol_1.7.2.1-2.2.dsc exists in .; copying to chroot Check architectures ─────────────────── Check dependencies ────────────────── Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/«BUILDDIR»/resolver-wxeYi6/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Packages [527 B] Ign:4 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Packages [527 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install core build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 0 B/772 B of archives. After this operation, 0 B of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-core-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-wxeYi6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [772 B] debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12057 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>> 7.0.50~), freeglut3-dev, libfreetype6-dev, libglew1.5-dev, libpng-dev, python, python-dev, python-numpy, dh-python, texlive-latex-base, tk-dev Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, init, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:5.2), g++ (>= 4:5.2), make, dpkg-dev (>= 1.17.11), debhelper (>> 7.0.50~), freeglut3-dev, libfreetype6-dev, libglew1.5-dev, libpng-dev, python, python-dev, python-numpy, dh-python, texlive-latex-base, tk-dev dpkg-deb: building package 'sbuild-build-depends-pymol-dummy' in '/«BUILDDIR»/resolver-3L895I/apt_archive/sbuild-build-depends-pymol-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Sources [483 B] Get:5 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Packages [753 B] Ign:4 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Sources [483 B] Get:5 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Packages [753 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install pymol build dependencies (apt-based resolver) │ └──────────────────────────────────────────────────────────────────────────────┘ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libapt-pkg4.16 libisl13 libprocps3 udev Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: autotools-dev bsdmainutils debhelper dh-python dh-strip-nondeterminism file fontconfig-config fonts-dejavu-core freeglut3 freeglut3-dev gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libblas-common libblas3 libbsd0 libcups2 libcupsfilters1 libcupsimage2 libdrm-amdgpu1 libdrm-dev libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2 libdrm-omap1 libdrm-radeon1 libdrm-tegra0 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgfortran3 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglew-dev libglew1.13 libglib2.0-0 libglu1-mesa libglu1-mesa-dev libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu55 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblapack3 liblcms2-2 libllvm3.6v5 libmagic1 libmpdec2 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng12-dev libpoppler57 libpotrace0 libptexenc1 libpthread-stubs0-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libsm-dev libsm6 libsynctex1 libtcl8.6 libtexlua52 libtexluajit2 libtiff5 libtimedate-perl libtk8.6 libunistring0 libx11-6 libx11-data libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxft-dev libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxxf86vm-dev libxxf86vm1 libzzip-0-13 man-db mesa-common-dev mime-support pkg-config po-debconf poppler-data python python-dev python-minimal python-numpy python2.7 python2.7-dev python2.7-minimal python3 python3-minimal python3.5 python3.5-minimal t1utils tcl tcl-dev tcl8.6 tcl8.6-dev tex-common texlive-base texlive-binaries texlive-latex-base tk tk-dev tk8.6 tk8.6-dev ucf x11-common x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev x11proto-xf86vidmode-dev xdg-utils xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc autopoint groff cups-common glew-utils fonts-droid texlive-lang-cjk libice-doc liblcms2-utils libsm-doc libxcb-doc libxext-doc libxt-doc less www-browser libmail-box-perl poppler-utils ghostscript fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum python-doc python-tk gfortran python-nose python-numpy-dbg python-numpy-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv python3.5-venv python3.5-doc tcl-doc tcl-tclreadline tcl8.6-doc xpdf-reader | pdf-viewer perl-tk gv | postscript-viewer tk-doc tk8.6-doc gvfs-bin Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libtxc-dxtn-s2tc0 | libtxc-dxtn0 libglib2.0-data shared-mime-info xdg-user-dirs libx11-doc xml-core libmail-sendmail-perl lmodern ruby texlive-latex-base-doc xterm | x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autotools-dev bsdmainutils debhelper dh-python dh-strip-nondeterminism file fontconfig-config fonts-dejavu-core freeglut3 freeglut3-dev gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasprintf0v5 libavahi-client3 libavahi-common-data libavahi-common3 libblas-common libblas3 libbsd0 libcups2 libcupsfilters1 libcupsimage2 libdrm-amdgpu1 libdrm-dev libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2 libdrm-omap1 libdrm-radeon1 libdrm-tegra0 libdrm2 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libgfortran3 libgl1-mesa-dev libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglew-dev libglew1.13 libglib2.0-0 libglu1-mesa libglu1-mesa-dev libgraphite2-3 libgs9 libgs9-common libharfbuzz-icu0 libharfbuzz0b libice-dev libice6 libicu55 libijs-0.35 libjbig0 libjbig2dec0 libjpeg-turbo8 libjpeg8 libkpathsea6 liblapack3 liblcms2-2 libllvm3.6v5 libmagic1 libmpdec2 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpng12-dev libpoppler57 libpotrace0 libptexenc1 libpthread-stubs0-dev libpython-dev libpython-stdlib libpython2.7 libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.5-minimal libpython3.5-stdlib libsm-dev libsm6 libsynctex1 libtcl8.6 libtexlua52 libtexluajit2 libtiff5 libtimedate-perl libtk8.6 libunistring0 libx11-6 libx11-data libx11-dev libx11-xcb-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri2-0-dev libxcb-dri3-0 libxcb-dri3-dev libxcb-glx0 libxcb-glx0-dev libxcb-present-dev libxcb-present0 libxcb-randr0 libxcb-randr0-dev libxcb-render0 libxcb-render0-dev libxcb-shape0 libxcb-shape0-dev libxcb-sync-dev libxcb-sync1 libxcb-xfixes0 libxcb-xfixes0-dev libxcb1 libxcb1-dev libxdamage-dev libxdamage1 libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes-dev libxfixes3 libxft-dev libxft2 libxi6 libxml2 libxmu6 libxpm4 libxrender-dev libxrender1 libxshmfence-dev libxshmfence1 libxss-dev libxss1 libxt-dev libxt6 libxxf86vm-dev libxxf86vm1 libzzip-0-13 man-db mesa-common-dev mime-support pkg-config po-debconf poppler-data python python-dev python-minimal python-numpy python2.7 python2.7-dev python2.7-minimal python3 python3-minimal python3.5 python3.5-minimal sbuild-build-depends-pymol-dummy t1utils tcl tcl-dev tcl8.6 tcl8.6-dev tex-common texlive-base texlive-binaries texlive-latex-base tk tk-dev tk8.6 tk8.6-dev ucf x11-common x11proto-core-dev x11proto-damage-dev x11proto-dri2-dev x11proto-fixes-dev x11proto-gl-dev x11proto-input-dev x11proto-kb-dev x11proto-render-dev x11proto-scrnsaver-dev x11proto-xext-dev x11proto-xf86vidmode-dev xdg-utils xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 201 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB/111 MB of archives. After this operation, 432 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-pymol-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-3L895I/apt_archive ./ sbuild-build-depends-pymol-dummy 0.invalid.0 [998 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main armhf libmpdec2 armhf 2.4.1-1 [67.7 kB] Get:3 http://ftpmaster.internal/ubuntu xenial/main armhf libpython3.5-minimal armhf 3.5.1-5 [518 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main armhf libexpat1 armhf 2.1.0-7 [52.4 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main armhf python3.5-minimal armhf 3.5.1-5 [1298 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main armhf python3-minimal armhf 3.5.1-1ubuntu2 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main armhf mime-support all 3.59ubuntu1 [31.0 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main armhf libpython3.5-stdlib armhf 3.5.1-5 [2071 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main armhf python3.5 armhf 3.5.1-5 [154 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main armhf libpython3-stdlib armhf 3.5.1-1ubuntu2 [6858 B] Get:11 http://ftpmaster.internal/ubuntu xenial/main armhf dh-python all 2.20151103ubuntu1 [74.4 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main armhf python3 armhf 3.5.1-1ubuntu2 [8710 B] Get:13 http://ftpmaster.internal/ubuntu xenial/main armhf libxau6 armhf 1:1.0.8-1 [7324 B] Get:14 http://ftpmaster.internal/ubuntu xenial/main armhf libxdmcp6 armhf 1:1.1.2-1.1 [9620 B] Get:15 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb1 armhf 1.11.1-1ubuntu1 [36.4 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main armhf libx11-data all 2:1.6.3-1ubuntu2 [113 kB] Get:17 http://ftpmaster.internal/ubuntu xenial/main armhf libx11-6 armhf 2:1.6.3-1ubuntu2 [514 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main armhf libxext6 armhf 2:1.3.3-1 [25.1 kB] Get:19 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf groff-base armhf 1.22.3-6 [1037 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main armhf bsdmainutils armhf 9.0.6ubuntu1 [169 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main armhf libpipeline1 armhf 1.4.1-2 [21.0 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main armhf man-db armhf 2.7.5-1 [836 kB] Get:23 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm2 armhf 2.4.66-2 [24.7 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/main armhf libglapi-mesa armhf 11.1.1-1ubuntu2 [35.2 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/main armhf libx11-xcb1 armhf 2:1.6.3-1ubuntu2 [8868 B] Get:26 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-dri2-0 armhf 1.11.1-1ubuntu1 [6640 B] Get:27 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-dri3-0 armhf 1.11.1-1ubuntu1 [4996 B] Get:28 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-glx0 armhf 1.11.1-1ubuntu1 [19.2 kB] Get:29 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-present0 armhf 1.11.1-1ubuntu1 [5222 B] Get:30 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-sync1 armhf 1.11.1-1ubuntu1 [7864 B] Get:31 http://ftpmaster.internal/ubuntu xenial/main armhf libxdamage1 armhf 1:1.1.4-2 [6490 B] Get:32 http://ftpmaster.internal/ubuntu xenial/main armhf libxfixes3 armhf 1:5.0.1-2 [9820 B] Get:33 http://ftpmaster.internal/ubuntu xenial/main armhf libxshmfence1 armhf 1.2-1 [4848 B] Get:34 http://ftpmaster.internal/ubuntu xenial/main armhf libxxf86vm1 armhf 1:1.1.4-1 [9770 B] Get:35 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-amdgpu1 armhf 2.4.66-2 [14.7 kB] Get:36 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-freedreno1 armhf 2.4.66-2 [13.7 kB] Get:37 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-nouveau2 armhf 2.4.66-2 [14.8 kB] Get:38 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-radeon1 armhf 2.4.66-2 [19.3 kB] Get:39 http://ftpmaster.internal/ubuntu xenial/main armhf libelf1 armhf 0.165-3 [40.4 kB] Get:40 http://ftpmaster.internal/ubuntu xenial/main armhf libbsd0 armhf 0.8.1-1 [48.4 kB] Get:41 http://ftpmaster.internal/ubuntu xenial/main armhf libedit2 armhf 3.1-20150325-1ubuntu1 [62.3 kB] Get:42 http://ftpmaster.internal/ubuntu xenial/main armhf libllvm3.6v5 armhf 1:3.6.2-3ubuntu1 [7545 kB] Get:43 http://ftpmaster.internal/ubuntu xenial/main armhf libgl1-mesa-dri armhf 11.1.1-1ubuntu2 [3031 kB] Get:44 http://ftpmaster.internal/ubuntu xenial/main armhf libgl1-mesa-glx armhf 11.1.1-1ubuntu2 [114 kB] Get:45 http://ftpmaster.internal/ubuntu xenial/main armhf libxi6 armhf 2:1.7.6-1 [24.5 kB] Get:46 http://ftpmaster.internal/ubuntu xenial/main armhf freeglut3 armhf 2.8.1-2 [61.8 kB] Get:47 http://ftpmaster.internal/ubuntu xenial/main armhf fonts-dejavu-core all 2.35-1 [1039 kB] Get:48 http://ftpmaster.internal/ubuntu xenial/main armhf ucf all 3.0033 [52.9 kB] Get:49 http://ftpmaster.internal/ubuntu xenial/main armhf fontconfig-config all 2.11.1-0ubuntu6 [48.7 kB] Get:50 http://ftpmaster.internal/ubuntu xenial/main armhf libfreetype6 armhf 2.5.2-4ubuntu2 [265 kB] Get:51 http://ftpmaster.internal/ubuntu xenial/main armhf libfontconfig1 armhf 2.11.1-0ubuntu6 [110 kB] Get:52 http://ftpmaster.internal/ubuntu xenial/main armhf libgraphite2-3 armhf 1.2.4-3ubuntu1 [44.1 kB] Get:53 http://ftpmaster.internal/ubuntu xenial/main armhf x11-common all 1:7.7+12ubuntu1 [22.4 kB] Get:54 http://ftpmaster.internal/ubuntu xenial/main armhf libice6 armhf 2:1.0.9-1 [32.7 kB] Get:55 http://ftpmaster.internal/ubuntu xenial/main armhf libjpeg-turbo8 armhf 1.4.2-0ubuntu2 [87.3 kB] Get:56 http://ftpmaster.internal/ubuntu xenial/main armhf liblcms2-2 armhf 2.6-3ubuntu2 [114 kB] Get:57 http://ftpmaster.internal/ubuntu xenial/main armhf libsm6 armhf 2:1.2.2-1 [13.9 kB] Get:58 http://ftpmaster.internal/ubuntu xenial/main armhf libunistring0 armhf 0.9.3-5.2ubuntu1 [250 kB] Get:59 http://ftpmaster.internal/ubuntu xenial/main armhf libxrender1 armhf 1:0.9.9-0ubuntu1 [15.7 kB] Get:60 http://ftpmaster.internal/ubuntu xenial/main armhf libxft2 armhf 2.3.2-1 [30.5 kB] Get:61 http://ftpmaster.internal/ubuntu xenial/main armhf libxpm4 armhf 1:3.5.11-1 [28.6 kB] Get:62 http://ftpmaster.internal/ubuntu xenial/main armhf libxss1 armhf 1:1.2.2-1 [7652 B] Get:63 http://ftpmaster.internal/ubuntu xenial/main armhf libzzip-0-13 armhf 0.13.62-3 [22.2 kB] Get:64 http://ftpmaster.internal/ubuntu xenial/main armhf poppler-data all 0.4.7-7 [1495 kB] Get:65 http://ftpmaster.internal/ubuntu xenial/main armhf libpython2.7-minimal armhf 2.7.11-3 [334 kB] Get:66 http://ftpmaster.internal/ubuntu xenial/main armhf python2.7-minimal armhf 2.7.11-3 [1040 kB] Get:67 http://ftpmaster.internal/ubuntu xenial/main armhf python-minimal armhf 2.7.11-1 [28.2 kB] Get:68 http://ftpmaster.internal/ubuntu xenial/main armhf libpython2.7-stdlib armhf 2.7.11-3 [1833 kB] Get:69 http://ftpmaster.internal/ubuntu xenial/main armhf python2.7 armhf 2.7.11-3 [217 kB] Get:70 http://ftpmaster.internal/ubuntu xenial/main armhf libpython-stdlib armhf 2.7.11-1 [7640 B] Get:71 http://ftpmaster.internal/ubuntu xenial/main armhf python armhf 2.7.11-1 [137 kB] Get:72 http://ftpmaster.internal/ubuntu xenial/main armhf libjbig0 armhf 2.1-3.1 [24.3 kB] Get:73 http://ftpmaster.internal/ubuntu xenial/main armhf libmagic1 armhf 1:5.25-2ubuntu1 [211 kB] Get:74 http://ftpmaster.internal/ubuntu xenial/main armhf file armhf 1:5.25-2ubuntu1 [20.9 kB] Get:75 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libasprintf0v5 armhf 0.19.7-2ubuntu1 [6344 B] Get:76 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf gettext-base armhf 0.19.7-2ubuntu1 [44.6 kB] Get:77 http://ftpmaster.internal/ubuntu xenial/main armhf libglib2.0-0 armhf 2.47.5-1 [977 kB] Get:78 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libicu55 armhf 55.1-7 [7420 kB] Get:79 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libxml2 armhf 2.9.3+dfsg1-1 [602 kB] Get:80 http://ftpmaster.internal/ubuntu xenial/main armhf autotools-dev all 20150820.1 [39.8 kB] Get:81 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf gettext armhf 0.19.7-2ubuntu1 [1023 kB] Get:82 http://ftpmaster.internal/ubuntu xenial/main armhf intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:83 http://ftpmaster.internal/ubuntu xenial/main armhf po-debconf all 1.0.19 [234 kB] Get:84 http://ftpmaster.internal/ubuntu xenial/main armhf libarchive-zip-perl all 1.56-2 [84.1 kB] Get:85 http://ftpmaster.internal/ubuntu xenial/main armhf libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:86 http://ftpmaster.internal/ubuntu xenial/main armhf libtimedate-perl all 2.3000-2 [37.5 kB] Get:87 http://ftpmaster.internal/ubuntu xenial/main armhf dh-strip-nondeterminism all 0.014-1 [5596 B] Get:88 http://ftpmaster.internal/ubuntu xenial/main armhf debhelper all 9.20160115ubuntu2 [740 kB] Get:89 http://ftpmaster.internal/ubuntu xenial/main armhf xorg-sgml-doctools all 1:1.11-1 [12.9 kB] Get:90 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-core-dev all 7.0.28-0ubuntu2 [250 kB] Get:91 http://ftpmaster.internal/ubuntu xenial/main armhf libxau-dev armhf 1:1.0.8-1 [9438 B] Get:92 http://ftpmaster.internal/ubuntu xenial/main armhf libxdmcp-dev armhf 1:1.1.2-1.1 [23.7 kB] Get:93 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-input-dev all 2.3.1-1 [118 kB] Get:94 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-kb-dev all 1.0.7-0ubuntu1 [224 kB] Get:95 http://ftpmaster.internal/ubuntu xenial/main armhf xtrans-dev all 1.3.5-1 [70.5 kB] Get:96 http://ftpmaster.internal/ubuntu xenial/main armhf libpthread-stubs0-dev armhf 0.3-4 [4084 B] Get:97 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb1-dev armhf 1.11.1-1ubuntu1 [70.7 kB] Get:98 http://ftpmaster.internal/ubuntu xenial/main armhf libx11-dev armhf 2:1.6.3-1ubuntu2 [583 kB] Get:99 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-omap1 armhf 2.4.66-2 [6444 B] Get:100 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-exynos1 armhf 2.4.66-2 [9500 B] Get:101 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-tegra0 armhf 2.4.66-2 [5806 B] Get:102 http://ftpmaster.internal/ubuntu xenial/main armhf libdrm-dev armhf 2.4.66-2 [165 kB] Get:103 http://ftpmaster.internal/ubuntu xenial/main armhf mesa-common-dev armhf 11.1.1-1ubuntu2 [454 kB] Get:104 http://ftpmaster.internal/ubuntu xenial/main armhf libx11-xcb-dev armhf 2:1.6.3-1ubuntu2 [9698 B] Get:105 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-dri3-dev armhf 1.11.1-1ubuntu1 [5704 B] Get:106 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-randr0 armhf 1.11.1-1ubuntu1 [13.6 kB] Get:107 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-render0 armhf 1.11.1-1ubuntu1 [10.9 kB] Get:108 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-render0-dev armhf 1.11.1-1ubuntu1 [15.1 kB] Get:109 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-randr0-dev armhf 1.11.1-1ubuntu1 [17.7 kB] Get:110 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-xfixes0 armhf 1.11.1-1ubuntu1 [8714 B] Get:111 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-shape0 armhf 1.11.1-1ubuntu1 [5510 B] Get:112 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-shape0-dev armhf 1.11.1-1ubuntu1 [6842 B] Get:113 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-xfixes0-dev armhf 1.11.1-1ubuntu1 [11.1 kB] Get:114 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-sync-dev armhf 1.11.1-1ubuntu1 [9770 B] Get:115 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-present-dev armhf 1.11.1-1ubuntu1 [6654 B] Get:116 http://ftpmaster.internal/ubuntu xenial/main armhf libxshmfence-dev armhf 1.2-1 [3558 B] Get:117 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-dri2-0-dev armhf 1.11.1-1ubuntu1 [8186 B] Get:118 http://ftpmaster.internal/ubuntu xenial/main armhf libxcb-glx0-dev armhf 1.11.1-1ubuntu1 [25.5 kB] Get:119 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-xext-dev all 7.3.0-1 [212 kB] Get:120 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-fixes-dev all 1:5.0-2ubuntu2 [14.2 kB] Get:121 http://ftpmaster.internal/ubuntu xenial/main armhf libxfixes-dev armhf 1:5.0.1-2 [9828 B] Get:122 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-damage-dev all 1:1.2.1-2 [8286 B] Get:123 http://ftpmaster.internal/ubuntu xenial/main armhf libxdamage-dev armhf 1:1.1.4-2 [4680 B] Get:124 http://ftpmaster.internal/ubuntu xenial/main armhf libxext-dev armhf 2:1.3.3-1 [77.8 kB] Get:125 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-xf86vidmode-dev all 2.3.1-2 [6116 B] Get:126 http://ftpmaster.internal/ubuntu xenial/main armhf libxxf86vm-dev armhf 1:1.1.4-1 [12.7 kB] Get:127 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-dri2-dev all 2.8-2 [12.6 kB] Get:128 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-gl-dev all 1.4.17-1 [17.9 kB] Get:129 http://ftpmaster.internal/ubuntu xenial/main armhf libgl1-mesa-dev armhf 11.1.1-1ubuntu2 [4418 B] Get:130 http://ftpmaster.internal/ubuntu xenial/main armhf libglu1-mesa armhf 9.0.0-2.1 [134 kB] Get:131 http://ftpmaster.internal/ubuntu xenial/main armhf libglu1-mesa-dev armhf 9.0.0-2.1 [170 kB] Get:132 http://ftpmaster.internal/ubuntu xenial/main armhf libxt6 armhf 1:1.1.5-0ubuntu1 [130 kB] Get:133 http://ftpmaster.internal/ubuntu xenial/main armhf libice-dev armhf 2:1.0.9-1 [39.6 kB] Get:134 http://ftpmaster.internal/ubuntu xenial/main armhf libsm-dev armhf 2:1.2.2-1 [14.8 kB] Get:135 http://ftpmaster.internal/ubuntu xenial/main armhf libxt-dev armhf 1:1.1.5-0ubuntu1 [367 kB] Get:136 http://ftpmaster.internal/ubuntu xenial/main armhf freeglut3-dev armhf 2.8.1-2 [115 kB] Get:137 http://ftpmaster.internal/ubuntu xenial/main armhf libavahi-common-data armhf 0.6.32~rc+dfsg-1ubuntu2 [21.9 kB] Get:138 http://ftpmaster.internal/ubuntu xenial/main armhf libavahi-common3 armhf 0.6.32~rc+dfsg-1ubuntu2 [18.5 kB] Get:139 http://ftpmaster.internal/ubuntu xenial/main armhf libavahi-client3 armhf 0.6.32~rc+dfsg-1ubuntu2 [21.7 kB] Get:140 http://ftpmaster.internal/ubuntu xenial/main armhf libblas-common armhf 3.6.0-2ubuntu2 [5344 B] Get:141 http://ftpmaster.internal/ubuntu xenial/main armhf libblas3 armhf 3.6.0-2ubuntu2 [103 kB] Get:142 http://ftpmaster.internal/ubuntu xenial/main armhf libcups2 armhf 2.1.2-2 [169 kB] Get:143 http://ftpmaster.internal/ubuntu xenial/main armhf libjpeg8 armhf 8c-2ubuntu8 [2202 B] Get:144 http://ftpmaster.internal/ubuntu xenial/main armhf libtiff5 armhf 4.0.6-1 [128 kB] Get:145 http://ftpmaster.internal/ubuntu xenial/main armhf libcupsfilters1 armhf 1.8.1-1 [74.2 kB] Get:146 http://ftpmaster.internal/ubuntu xenial/main armhf libcupsimage2 armhf 2.1.2-2 [14.2 kB] Get:147 http://ftpmaster.internal/ubuntu xenial/main armhf libexpat1-dev armhf 2.1.0-7 [104 kB] Get:148 http://ftpmaster.internal/ubuntu xenial/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-2ubuntu4 [161 kB] Get:149 http://ftpmaster.internal/ubuntu xenial/main armhf libpng12-dev armhf 1.2.54-1ubuntu1 [174 kB] Get:150 http://ftpmaster.internal/ubuntu xenial/main armhf libfreetype6-dev armhf 2.5.2-4ubuntu2 [582 kB] Get:151 http://ftpmaster.internal/ubuntu xenial/main armhf pkg-config armhf 0.29-2ubuntu2 [41.4 kB] Get:152 http://ftpmaster.internal/ubuntu xenial/main armhf libfontconfig1-dev armhf 2.11.1-0ubuntu6 [625 kB] Get:153 http://ftpmaster.internal/ubuntu xenial/main armhf libgfortran3 armhf 5.3.1-7ubuntu1 [164 kB] Get:154 http://ftpmaster.internal/ubuntu xenial/main armhf libglew1.13 armhf 1.13.0-2 [121 kB] Get:155 http://ftpmaster.internal/ubuntu xenial/main armhf libglew-dev armhf 1.13.0-2 [118 kB] Get:156 http://ftpmaster.internal/ubuntu xenial/main armhf libijs-0.35 armhf 0.35-11 [14.1 kB] Get:157 http://ftpmaster.internal/ubuntu xenial/main armhf libjbig2dec0 armhf 0.12+20150918-1 [48.0 kB] Get:158 http://ftpmaster.internal/ubuntu xenial/main armhf libpaper1 armhf 1.1.24+nmu4ubuntu1 [13.0 kB] Get:159 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf libgs9-common all 9.16~dfsg~0-0ubuntu4 [2936 kB] Get:160 http://ftpmaster.internal/ubuntu xenial/main armhf libgs9 armhf 9.16~dfsg~0-0ubuntu3 [1782 kB] Get:161 http://ftpmaster.internal/ubuntu xenial/main armhf libharfbuzz0b armhf 1.0.1-1build2 [122 kB] Get:162 http://ftpmaster.internal/ubuntu xenial/main armhf libharfbuzz-icu0 armhf 1.0.1-1build2 [4866 B] Get:163 http://ftpmaster.internal/ubuntu xenial/main armhf libkpathsea6 armhf 2015.20150524.37493-7build4 [46.4 kB] Get:164 http://ftpmaster.internal/ubuntu xenial/main armhf liblapack3 armhf 3.6.0-2ubuntu2 [1500 kB] Get:165 http://ftpmaster.internal/ubuntu xenial/main armhf libpaper-utils armhf 1.1.24+nmu4ubuntu1 [8000 B] Get:166 http://ftpmaster.internal/ubuntu xenial/main armhf libpixman-1-0 armhf 0.33.6-1 [158 kB] Get:167 http://ftpmaster.internal/ubuntu xenial/main armhf libpoppler57 armhf 0.38.0-0ubuntu1 [650 kB] Get:168 http://ftpmaster.internal/ubuntu xenial/main armhf libpotrace0 armhf 1.13-2 [15.1 kB] Get:169 http://ftpmaster.internal/ubuntu xenial/main armhf libptexenc1 armhf 2015.20150524.37493-7build4 [32.3 kB] Get:170 http://ftpmaster.internal/ubuntu xenial/main armhf libpython2.7 armhf 2.7.11-3 [935 kB] Get:171 http://ftpmaster.internal/ubuntu xenial/main armhf libpython2.7-dev armhf 2.7.11-3 [27.1 MB] Get:172 http://ftpmaster.internal/ubuntu xenial/main armhf libpython-dev armhf 2.7.11-1 [7710 B] Get:173 http://ftpmaster.internal/ubuntu xenial/main armhf libsynctex1 armhf 2015.20150524.37493-7build4 [34.9 kB] Get:174 http://ftpmaster.internal/ubuntu xenial/main armhf libtcl8.6 armhf 8.6.4+dfsg-3 [769 kB] Get:175 http://ftpmaster.internal/ubuntu xenial/main armhf libtexlua52 armhf 2015.20150524.37493-7build4 [68.5 kB] Get:176 http://ftpmaster.internal/ubuntu xenial/main armhf libtexluajit2 armhf 2015.20150524.37493-7build4 [172 kB] Get:177 http://ftpmaster.internal/ubuntu xenial/main armhf libtk8.6 armhf 8.6.4+dfsg-3 [616 kB] Get:178 http://ftpmaster.internal/ubuntu xenial/main armhf libxmu6 armhf 2:1.1.2-2 [38.3 kB] Get:179 http://ftpmaster.internal/ubuntu xenial/main armhf libxaw7 armhf 2:1.0.13-1 [141 kB] Get:180 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-render-dev all 2:0.11.1-2 [20.1 kB] Get:181 http://ftpmaster.internal/ubuntu xenial/main armhf libxrender-dev armhf 1:0.9.9-0ubuntu1 [21.7 kB] Get:182 http://ftpmaster.internal/ubuntu xenial/main armhf libxft-dev armhf 2.3.2-1 [40.4 kB] Get:183 http://ftpmaster.internal/ubuntu xenial/main armhf x11proto-scrnsaver-dev all 1.2.2-1 [25.0 kB] Get:184 http://ftpmaster.internal/ubuntu xenial/main armhf libxss-dev armhf 1:1.2.2-1 [12.1 kB] Get:185 http://ftpmaster.internal/ubuntu xenial/main armhf python2.7-dev armhf 2.7.11-3 [277 kB] Get:186 http://ftpmaster.internal/ubuntu xenial/main armhf python-dev armhf 2.7.11-1 [1174 B] Get:187 http://ftpmaster.internal/ubuntu xenial-proposed/main armhf python-numpy armhf 1:1.10.4-2ubuntu1 [1568 kB] Get:188 http://ftpmaster.internal/ubuntu xenial/main armhf t1utils armhf 1.39-2 [47.2 kB] Get:189 http://ftpmaster.internal/ubuntu xenial/main armhf tcl8.6 armhf 8.6.4+dfsg-3 [14.1 kB] Get:190 http://ftpmaster.internal/ubuntu xenial/main armhf tcl armhf 8.6.0+9 [5142 B] Get:191 http://ftpmaster.internal/ubuntu xenial/main armhf tcl8.6-dev armhf 8.6.4+dfsg-3 [797 kB] Get:192 http://ftpmaster.internal/ubuntu xenial/main armhf tcl-dev armhf 8.6.0+9 [5680 B] Get:193 http://ftpmaster.internal/ubuntu xenial/main armhf tex-common all 6.04 [545 kB] Get:194 http://ftpmaster.internal/ubuntu xenial/main armhf xdg-utils all 1.1.0~rc3+git20150907-1ubuntu3 [58.1 kB] Get:195 http://ftpmaster.internal/ubuntu xenial/main armhf texlive-binaries armhf 2015.20150524.37493-7build4 [7048 kB] Get:196 http://ftpmaster.internal/ubuntu xenial/main armhf texlive-base all 2015.20160117-1 [18.2 MB] Get:197 http://ftpmaster.internal/ubuntu xenial/main armhf texlive-latex-base all 2015.20160117-1 [875 kB] Get:198 http://ftpmaster.internal/ubuntu xenial/main armhf tk8.6 armhf 8.6.4+dfsg-3 [12.0 kB] Get:199 http://ftpmaster.internal/ubuntu xenial/main armhf tk armhf 8.6.0+9 [3178 B] Get:200 http://ftpmaster.internal/ubuntu xenial/main armhf tk8.6-dev armhf 8.6.4+dfsg-3 [621 kB] Get:201 http://ftpmaster.internal/ubuntu xenial/main armhf tk-dev armhf 8.6.0+9 [2976 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 111 MB in 7s (14.9 MB/s) Selecting previously unselected package libmpdec2:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12057 files and directories currently installed.) Preparing to unpack .../libmpdec2_2.4.1-1_armhf.deb ... Unpacking libmpdec2:armhf (2.4.1-1) ... Selecting previously unselected package libpython3.5-minimal:armhf. Preparing to unpack .../libpython3.5-minimal_3.5.1-5_armhf.deb ... Unpacking libpython3.5-minimal:armhf (3.5.1-5) ... Selecting previously unselected package libexpat1:armhf. 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13008 files and directories currently installed.) Preparing to unpack .../python3_3.5.1-1ubuntu2_armhf.deb ... Unpacking python3 (3.5.1-1ubuntu2) ... Selecting previously unselected package libxau6:armhf. Preparing to unpack .../libxau6_1%3a1.0.8-1_armhf.deb ... Unpacking libxau6:armhf (1:1.0.8-1) ... Selecting previously unselected package libxdmcp6:armhf. Preparing to unpack .../libxdmcp6_1%3a1.1.2-1.1_armhf.deb ... Unpacking libxdmcp6:armhf (1:1.1.2-1.1) ... Selecting previously unselected package libxcb1:armhf. Preparing to unpack .../libxcb1_1.11.1-1ubuntu1_armhf.deb ... Unpacking libxcb1:armhf (1.11.1-1ubuntu1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../libx11-data_2%3a1.6.3-1ubuntu2_all.deb ... Unpacking libx11-data (2:1.6.3-1ubuntu2) ... Selecting previously unselected package libx11-6:armhf. Preparing to unpack .../libx11-6_2%3a1.6.3-1ubuntu2_armhf.deb ... Unpacking libx11-6:armhf (2:1.6.3-1ubuntu2) ... Selecting previously unselected package libxext6:armhf. Preparing to unpack .../libxext6_2%3a1.3.3-1_armhf.deb ... Unpacking libxext6:armhf (2:1.3.3-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-6_armhf.deb ... Unpacking groff-base (1.22.3-6) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_armhf.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../libpipeline1_1.4.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.4.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_armhf.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libdrm2:armhf. Preparing to unpack .../libdrm2_2.4.66-2_armhf.deb ... Unpacking libdrm2:armhf (2.4.66-2) ... Selecting previously unselected package libglapi-mesa:armhf. Preparing to unpack .../libglapi-mesa_11.1.1-1ubuntu2_armhf.deb ... Unpacking libglapi-mesa:armhf (11.1.1-1ubuntu2) ... Selecting previously unselected package libx11-xcb1:armhf. Preparing to unpack .../libx11-xcb1_2%3a1.6.3-1ubuntu2_armhf.deb ... Unpacking libx11-xcb1:armhf (2:1.6.3-1ubuntu2) ... Selecting previously unselected package libxcb-dri2-0:armhf. Preparing to unpack .../libxcb-dri2-0_1.11.1-1ubuntu1_armhf.deb ... Unpacking libxcb-dri2-0:armhf (1.11.1-1ubuntu1) ... Selecting previously unselected package libxcb-dri3-0:armhf. Preparing to unpack .../libxcb-dri3-0_1.11.1-1ubuntu1_armhf.deb ... Unpacking libxcb-dri3-0:armhf (1.11.1-1ubuntu1) ... Selecting previously unselected package libxcb-glx0:armhf. Preparing to unpack .../libxcb-glx0_1.11.1-1ubuntu1_armhf.deb ... Unpacking libxcb-glx0:armhf (1.11.1-1ubuntu1) ... Selecting previously unselected package libxcb-present0:armhf. Preparing to unpack .../libxcb-present0_1.11.1-1ubuntu1_armhf.deb ... Unpacking libxcb-present0:armhf (1.11.1-1ubuntu1) ... Selecting previously unselected package libxcb-sync1:armhf. Preparing to unpack .../libxcb-sync1_1.11.1-1ubuntu1_armhf.deb ... Unpacking libxcb-sync1:armhf (1.11.1-1ubuntu1) ... Selecting previously unselected package libxdamage1:armhf. Preparing to unpack .../libxdamage1_1%3a1.1.4-2_armhf.deb ... Unpacking libxdamage1:armhf (1:1.1.4-2) ... Selecting previously unselected package libxfixes3:armhf. 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Selecting previously unselected package libdrm-radeon1:armhf. Preparing to unpack .../libdrm-radeon1_2.4.66-2_armhf.deb ... Unpacking libdrm-radeon1:armhf (2.4.66-2) ... Selecting previously unselected package libelf1:armhf. Preparing to unpack .../libelf1_0.165-3_armhf.deb ... Unpacking libelf1:armhf (0.165-3) ... Selecting previously unselected package libbsd0:armhf. Preparing to unpack .../libbsd0_0.8.1-1_armhf.deb ... Unpacking libbsd0:armhf (0.8.1-1) ... Selecting previously unselected package libedit2:armhf. Preparing to unpack .../libedit2_3.1-20150325-1ubuntu1_armhf.deb ... Unpacking libedit2:armhf (3.1-20150325-1ubuntu1) ... Selecting previously unselected package libllvm3.6v5:armhf. Preparing to unpack .../libllvm3.6v5_1%3a3.6.2-3ubuntu1_armhf.deb ... Unpacking libllvm3.6v5:armhf (1:3.6.2-3ubuntu1) ... Selecting previously unselected package libgl1-mesa-dri:armhf. Preparing to unpack .../libgl1-mesa-dri_11.1.1-1ubuntu2_armhf.deb ... Unpacking libgl1-mesa-dri:armhf (11.1.1-1ubuntu2) ... Selecting previously unselected package libgl1-mesa-glx:armhf. Preparing to unpack .../libgl1-mesa-glx_11.1.1-1ubuntu2_armhf.deb ... Unpacking libgl1-mesa-glx:armhf (11.1.1-1ubuntu2) ... Selecting previously unselected package libxi6:armhf. Preparing to unpack .../libxi6_2%3a1.7.6-1_armhf.deb ... Unpacking libxi6:armhf (2:1.7.6-1) ... Selecting previously unselected package freeglut3:armhf. Preparing to unpack .../freeglut3_2.8.1-2_armhf.deb ... Unpacking freeglut3:armhf (2.8.1-2) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../fonts-dejavu-core_2.35-1_all.deb ... Unpacking fonts-dejavu-core (2.35-1) ... Selecting previously unselected package ucf. Preparing to unpack .../archives/ucf_3.0033_all.deb ... Moving old data out of the way Unpacking ucf (3.0033) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../fontconfig-config_2.11.1-0ubuntu6_all.deb ... Unpacking fontconfig-config (2.11.1-0ubuntu6) ... Selecting previously unselected package libfreetype6:armhf. Preparing to unpack .../libfreetype6_2.5.2-4ubuntu2_armhf.deb ... Unpacking libfreetype6:armhf (2.5.2-4ubuntu2) ... Selecting previously unselected package libfontconfig1:armhf. Preparing to unpack .../libfontconfig1_2.11.1-0ubuntu6_armhf.deb ... Unpacking libfontconfig1:armhf (2.11.1-0ubuntu6) ... Selecting previously unselected package libgraphite2-3:armhf. Preparing to unpack .../libgraphite2-3_1.2.4-3ubuntu1_armhf.deb ... Unpacking libgraphite2-3:armhf (1.2.4-3ubuntu1) ... Selecting previously unselected package x11-common. Preparing to unpack .../x11-common_1%3a7.7+12ubuntu1_all.deb ... Unpacking x11-common (1:7.7+12ubuntu1) ... Selecting previously unselected package libice6:armhf. Preparing to unpack .../libice6_2%3a1.0.9-1_armhf.deb ... Unpacking libice6:armhf (2:1.0.9-1) ... Selecting previously unselected package libjpeg-turbo8:armhf. 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Setting up libpython3-stdlib:armhf (3.5.1-1ubuntu2) ... Setting up libxau6:armhf (1:1.0.8-1) ... Setting up libxdmcp6:armhf (1:1.1.2-1.1) ... Setting up libxcb1:armhf (1.11.1-1ubuntu1) ... Setting up libx11-data (2:1.6.3-1ubuntu2) ... Setting up libx11-6:armhf (2:1.6.3-1ubuntu2) ... Setting up libxext6:armhf (2:1.3.3-1) ... Setting up groff-base (1.22.3-6) ... Setting up bsdmainutils (9.0.6ubuntu1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libpipeline1:armhf (1.4.1-2) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libdrm2:armhf (2.4.66-2) ... Setting up libglapi-mesa:armhf (11.1.1-1ubuntu2) ... Setting up libx11-xcb1:armhf (2:1.6.3-1ubuntu2) ... Setting up libxcb-dri2-0:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-dri3-0:armhf (1.11.1-1ubuntu1) ... 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Setting up libgl1-mesa-glx:armhf (11.1.1-1ubuntu2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/mesa/ld.so.conf to provide /etc/ld.so.conf.d/arm-linux-gnueabihf_GL.conf (arm-linux-gnueabihf_gl_conf) in auto mode Setting up libxi6:armhf (2:1.7.6-1) ... Setting up freeglut3:armhf (2.8.1-2) ... Setting up fonts-dejavu-core (2.35-1) ... Setting up ucf (3.0033) ... Setting up fontconfig-config (2.11.1-0ubuntu6) ... Setting up libfreetype6:armhf (2.5.2-4ubuntu2) ... Setting up libfontconfig1:armhf (2.11.1-0ubuntu6) ... Setting up libgraphite2-3:armhf (1.2.4-3ubuntu1) ... Setting up x11-common (1:7.7+12ubuntu1) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libice6:armhf (2:1.0.9-1) ... Setting up libjpeg-turbo8:armhf (1.4.2-0ubuntu2) ... Setting up liblcms2-2:armhf (2.6-3ubuntu2) ... Setting up libsm6:armhf (2:1.2.2-1) ... Setting up libunistring0:armhf (0.9.3-5.2ubuntu1) ... Setting up libxrender1:armhf (1:0.9.9-0ubuntu1) ... Setting up libxft2:armhf (2.3.2-1) ... Setting up libxpm4:armhf (1:3.5.11-1) ... Setting up libxss1:armhf (1:1.2.2-1) ... Setting up libzzip-0-13:armhf (0.13.62-3) ... Setting up poppler-data (0.4.7-7) ... Setting up libpython2.7-stdlib:armhf (2.7.11-3) ... Setting up python2.7 (2.7.11-3) ... Setting up libpython-stdlib:armhf (2.7.11-1) ... Setting up python (2.7.11-1) ... Setting up libjbig0:armhf (2.1-3.1) ... Setting up libmagic1:armhf (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up libasprintf0v5:armhf (0.19.7-2ubuntu1) ... Setting up gettext-base (0.19.7-2ubuntu1) ... Setting up libglib2.0-0:armhf (2.47.5-1) ... No schema files found: doing nothing. Setting up libicu55:armhf (55.1-7) ... Setting up libxml2:armhf (2.9.3+dfsg1-1) ... Setting up autotools-dev (20150820.1) ... Setting up gettext (0.19.7-2ubuntu1) ... 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Setting up libxcb-dri3-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-randr0:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-render0:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-render0-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-randr0-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-xfixes0:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-shape0:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-shape0-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-xfixes0-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-sync-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-present-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxshmfence-dev:armhf (1.2-1) ... Setting up libxcb-dri2-0-dev:armhf (1.11.1-1ubuntu1) ... Setting up libxcb-glx0-dev:armhf (1.11.1-1ubuntu1) ... Setting up x11proto-xext-dev (7.3.0-1) ... Setting up x11proto-fixes-dev (1:5.0-2ubuntu2) ... Setting up libxfixes-dev:armhf (1:5.0.1-2) ... Setting up x11proto-damage-dev (1:1.2.1-2) ... Setting up libxdamage-dev:armhf (1:1.1.4-2) ... Setting up libxext-dev:armhf (2:1.3.3-1) ... Setting up x11proto-xf86vidmode-dev (2.3.1-2) ... Setting up libxxf86vm-dev:armhf (1:1.1.4-1) ... Setting up x11proto-dri2-dev (2.8-2) ... Setting up x11proto-gl-dev (1.4.17-1) ... Setting up libgl1-mesa-dev:armhf (11.1.1-1ubuntu2) ... Setting up libglu1-mesa:armhf (9.0.0-2.1) ... Setting up libglu1-mesa-dev:armhf (9.0.0-2.1) ... Setting up libxt6:armhf (1:1.1.5-0ubuntu1) ... Setting up libice-dev:armhf (2:1.0.9-1) ... Setting up libsm-dev:armhf (2:1.2.2-1) ... Setting up libxt-dev:armhf (1:1.1.5-0ubuntu1) ... Setting up freeglut3-dev:armhf (2.8.1-2) ... Setting up libavahi-common-data:armhf (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-common3:armhf (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libavahi-client3:armhf (0.6.32~rc+dfsg-1ubuntu2) ... Setting up libblas-common (3.6.0-2ubuntu2) ... Setting up libblas3 (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libcups2:armhf (2.1.2-2) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libtiff5:armhf (4.0.6-1) ... Setting up libcupsfilters1:armhf (1.8.1-1) ... Setting up libcupsimage2:armhf (2.1.2-2) ... Setting up libexpat1-dev:armhf (2.1.0-7) ... Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-2ubuntu4) ... Setting up libpng12-dev:armhf (1.2.54-1ubuntu1) ... Setting up libfreetype6-dev:armhf (2.5.2-4ubuntu2) ... Setting up pkg-config (0.29-2ubuntu2) ... Setting up libfontconfig1-dev:armhf (2.11.1-0ubuntu6) ... Setting up libgfortran3:armhf (5.3.1-7ubuntu1) ... Setting up libglew1.13:armhf (1.13.0-2) ... Setting up libglew-dev:armhf (1.13.0-2) ... Setting up libijs-0.35:armhf (0.35-11) ... Setting up libjbig2dec0 (0.12+20150918-1) ... Setting up libpaper1:armhf (1.1.24+nmu4ubuntu1) ... Creating config file /etc/papersize with new version Setting up libgs9-common (9.16~dfsg~0-0ubuntu4) ... update-alternatives: using /usr/share/ghostscript/9.16 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9 (9.16~dfsg~0-0ubuntu3) ... Setting up libharfbuzz0b:armhf (1.0.1-1build2) ... Setting up libharfbuzz-icu0:armhf (1.0.1-1build2) ... Setting up libkpathsea6:armhf (2015.20150524.37493-7build4) ... Setting up liblapack3 (3.6.0-2ubuntu2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libpaper-utils (1.1.24+nmu4ubuntu1) ... Setting up libpixman-1-0:armhf (0.33.6-1) ... Setting up libpoppler57:armhf (0.38.0-0ubuntu1) ... Setting up libpotrace0 (1.13-2) ... Setting up libptexenc1:armhf (2015.20150524.37493-7build4) ... Setting up libpython2.7:armhf (2.7.11-3) ... Setting up libpython2.7-dev:armhf (2.7.11-3) ... Setting up libpython-dev:armhf (2.7.11-1) ... Setting up libsynctex1:armhf (2015.20150524.37493-7build4) ... Setting up libtcl8.6:armhf (8.6.4+dfsg-3) ... Setting up libtexlua52:armhf (2015.20150524.37493-7build4) ... Setting up libtexluajit2:armhf (2015.20150524.37493-7build4) ... Setting up libtk8.6:armhf (8.6.4+dfsg-3) ... Setting up libxmu6:armhf (2:1.1.2-2) ... Setting up libxaw7:armhf (2:1.0.13-1) ... Setting up x11proto-render-dev (2:0.11.1-2) ... Setting up libxrender-dev:armhf (1:0.9.9-0ubuntu1) ... Setting up libxft-dev (2.3.2-1) ... Setting up x11proto-scrnsaver-dev (1.2.2-1) ... Setting up libxss-dev:armhf (1:1.2.2-1) ... Setting up python2.7-dev (2.7.11-3) ... Setting up python-dev (2.7.11-1) ... Setting up python-numpy (1:1.10.4-2ubuntu1) ... Setting up t1utils (1.39-2) ... Setting up tcl8.6 (8.6.4+dfsg-3) ... Setting up tcl (8.6.0+9) ... Setting up tcl8.6-dev:armhf (8.6.4+dfsg-3) ... Setting up tcl-dev:armhf (8.6.0+9) ... Setting up tex-common (6.04) ... update-language: texlive-base not installed and configured, doing nothing! Setting up xdg-utils (1.1.0~rc3+git20150907-1ubuntu3) ... Setting up texlive-binaries (2015.20150524.37493-7build4) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up tk8.6 (8.6.4+dfsg-3) ... Setting up tk (8.6.0+9) ... Setting up tk8.6-dev:armhf (8.6.4+dfsg-3) ... Setting up tk-dev:armhf (8.6.0+9) ... Processing triggers for tex-common (6.04) ... update-language: texlive-base not installed and configured, doing nothing! texlive-base is not ready, skipping fmtutil-sys --all call Setting up texlive-base (2015.20160117-1) ... /usr/bin/tl-paper: setting paper size for dvips to a4. /usr/bin/tl-paper: setting paper size for dvipdfmx to a4. /usr/bin/tl-paper: setting paper size for xdvi to a4. /usr/bin/tl-paper: setting paper size for pdftex to a4. Processing triggers for tex-common (6.04) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up texlive-latex-base (2015.20160117-1) ... Processing triggers for tex-common (6.04) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Setting up python3 (3.5.1-1ubuntu2) ... Setting up debhelper (9.20160115ubuntu2) ... Setting up dh-python (2.20151103ubuntu1) ... Setting up dh-strip-nondeterminism (0.014-1) ... Setting up sbuild-build-depends-pymol-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-4ubuntu1) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.2.0-95-highbank armhf (armv7l) Toolchain package versions: binutils_2.26-2ubuntu1 dpkg-dev_1.18.4ubuntu1 g++-5_5.3.1-7ubuntu1 gcc-5_5.3.1-7ubuntu1 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.3.1-7ubuntu1 libstdc++6_5.3.1-7ubuntu1 linux-libc-dev_4.4.0-1.15 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.10 apt-transport-https_1.1.10 autotools-dev_20150820.1 base-files_9.4ubuntu3 base-passwd_3.5.39 bash_4.3-14ubuntu1 binutils_2.26-2ubuntu1 bsdmainutils_9.0.6ubuntu1 bsdutils_1:2.27.1-1ubuntu3 build-essential_12.1ubuntu2 bzip2_1.0.6-8 ca-certificates_20150426ubuntu1 coreutils_8.23-4ubuntu2 cpp_4:5.2.1-16ubuntu2 cpp-5_5.3.1-7ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20160115ubuntu2 debianutils_4.7 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libwind0-heimdal_1.7~git20150920+dfsg-4ubuntu1 libx11-6_2:1.6.3-1ubuntu2 libx11-data_2:1.6.3-1ubuntu2 libx11-dev_2:1.6.3-1ubuntu2 libx11-xcb-dev_2:1.6.3-1ubuntu2 libx11-xcb1_2:1.6.3-1ubuntu2 libxau-dev_1:1.0.8-1 libxau6_1:1.0.8-1 libxaw7_2:1.0.13-1 libxcb-dri2-0_1.11.1-1ubuntu1 libxcb-dri2-0-dev_1.11.1-1ubuntu1 libxcb-dri3-0_1.11.1-1ubuntu1 libxcb-dri3-dev_1.11.1-1ubuntu1 libxcb-glx0_1.11.1-1ubuntu1 libxcb-glx0-dev_1.11.1-1ubuntu1 libxcb-present-dev_1.11.1-1ubuntu1 libxcb-present0_1.11.1-1ubuntu1 libxcb-randr0_1.11.1-1ubuntu1 libxcb-randr0-dev_1.11.1-1ubuntu1 libxcb-render0_1.11.1-1ubuntu1 libxcb-render0-dev_1.11.1-1ubuntu1 libxcb-shape0_1.11.1-1ubuntu1 libxcb-shape0-dev_1.11.1-1ubuntu1 libxcb-sync-dev_1.11.1-1ubuntu1 libxcb-sync1_1.11.1-1ubuntu1 libxcb-xfixes0_1.11.1-1ubuntu1 libxcb-xfixes0-dev_1.11.1-1ubuntu1 libxcb1_1.11.1-1ubuntu1 libxcb1-dev_1.11.1-1ubuntu1 libxdamage-dev_1:1.1.4-2 libxdamage1_1:1.1.4-2 libxdmcp-dev_1:1.1.2-1.1 libxdmcp6_1:1.1.2-1.1 libxext-dev_2:1.3.3-1 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policyrcd-script-zg2_0.1-2 poppler-data_0.4.7-7 procps_2:3.3.10-4ubuntu2 python_2.7.11-1 python-dev_2.7.11-1 python-minimal_2.7.11-1 python-numpy_1:1.10.4-2ubuntu1 python2.7_2.7.11-3 python2.7-dev_2.7.11-3 python2.7-minimal_2.7.11-3 python3_3.5.1-1ubuntu2 python3-minimal_3.5.1-1ubuntu2 python3.5_3.5.1-5 python3.5-minimal_3.5.1-5 readline-common_6.3-8ubuntu1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pymol-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-4ubuntu1 systemd-sysv_228-4ubuntu1 sysv-rc_2.88dsf-59.3ubuntu1 sysvinit-utils_2.88dsf-59.3ubuntu1 t1utils_1.39-2 tar_1.28-2.1 tcl_8.6.0+9 tcl-dev_8.6.0+9 tcl8.6_8.6.4+dfsg-3 tcl8.6-dev_8.6.4+dfsg-3 tex-common_6.04 texlive-base_2015.20160117-1 texlive-binaries_2015.20150524.37493-7build4 texlive-latex-base_2015.20160117-1 tk_8.6.0+9 tk-dev_8.6.0+9 tk8.6_8.6.4+dfsg-3 tk8.6-dev_8.6.4+dfsg-3 tzdata_2015g-1 ubuntu-keyring_2012.05.19 ucf_3.0033 udev_228-4ubuntu1 util-linux_2.27.1-1ubuntu3 x11-common_1:7.7+12ubuntu1 x11proto-core-dev_7.0.28-0ubuntu2 x11proto-damage-dev_1:1.2.1-2 x11proto-dri2-dev_2.8-2 x11proto-fixes-dev_1:5.0-2ubuntu2 x11proto-gl-dev_1.4.17-1 x11proto-input-dev_2.3.1-1 x11proto-kb-dev_1.0.7-0ubuntu1 x11proto-render-dev_2:0.11.1-2 x11proto-scrnsaver-dev_1.2.2-1 x11proto-xext-dev_7.3.0-1 x11proto-xf86vidmode-dev_2.3.1-2 xdg-utils_1.1.0~rc3+git20150907-1ubuntu3 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.1.1alpha+20120614-2ubuntu2 zlib1g_1:1.2.8.dfsg-2ubuntu4 zlib1g-dev_1:1.2.8.dfsg-2ubuntu4 ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build │ └──────────────────────────────────────────────────────────────────────────────┘ Unpack source ───────────── gpgv: Signature made Fri Jan 22 10:13:11 2016 UTC using RSA key ID 4E9F5DD9 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./pymol_1.7.2.1-2.2.dsc dpkg-source: info: extracting pymol in pymol-1.7.2.1 dpkg-source: info: unpacking pymol_1.7.2.1.orig.tar.bz2 dpkg-source: info: unpacking pymol_1.7.2.1-2.2.debian.tar.xz dpkg-source: info: applying 02_test-suite.patch dpkg-source: info: applying 03_povray.patch dpkg-source: info: applying 22_fix_pymol_import.patch dpkg-source: info: applying 27_fix_pymol_path_in_setup.patch dpkg-source: info: applying 28_no_data_install_in_python_path.patch dpkg-source: info: applying 29_fix_path_to_splash.patch dpkg-source: info: applying 31_fix_format-security.patch Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=4 HOME=/home/buildd LANG=C LANGUAGE=en_GB: LOGNAME=buildd MAIL=/var/mail/buildd OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games PWD=/«PKGBUILDDIR» SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«PKGBUILDDIR»' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package pymol dpkg-buildpackage: source version 1.7.2.1-2.2 dpkg-buildpackage: source distribution unstable dpkg-source --before-build pymol-1.7.2.1 dpkg-buildpackage: host architecture armhf fakeroot debian/rules clean dh clean --with python2 --parallel dh_testdir -O--parallel debian/rules override_dh_auto_clean make[1]: Entering directory '/«PKGBUILDDIR»' [ ! -f Makefile ] || /usr/bin/make distclean dh_auto_clean -Spython_distutils python setup.py clean -a running clean 'build/lib.linux-armv7l-2.7' does not exist -- can't clean it 'build/bdist.linux-armv7l' does not exist -- can't clean it 'build/scripts-2.7' does not exist -- can't clean it find . -name \*.pyc -exec rm {} \+ make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_clean make[1]: Entering directory '/«PKGBUILDDIR»' rm -f -r build test/tmp test/cmp generated dh_clean debian/pymol.launch debian/pymol-ref-card.* \ Rules.make create_shadertext.pyc make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules build-arch dh build-arch --with python2 --parallel dh_testdir -a -O--parallel dh_update_autotools_config -a -O--parallel debian/rules override_dh_auto_configure make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_configure -Spython_distutils make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_auto_build make[1]: Entering directory '/«PKGBUILDDIR»' dh_auto_build -Spython_distutils python setup.py build --force running build running build_py creating build/lib.linux-armv7l-2.7 creating build/lib.linux-armv7l-2.7/pymol creating build/lib.linux-armv7l-2.7/pymol/embed creating build/lib.linux-armv7l-2.7/pymol/embed/epymol copying modules/pymol/embed/epymol/__init__.py -> build/lib.linux-armv7l-2.7/pymol/embed/epymol creating build/lib.linux-armv7l-2.7/chempy creating build/lib.linux-armv7l-2.7/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-armv7l-2.7/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-armv7l-2.7/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-armv7l-2.7/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-armv7l-2.7/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-armv7l-2.7/chempy/tinker creating build/lib.linux-armv7l-2.7/pmg_tk creating build/lib.linux-armv7l-2.7/pmg_tk/skins creating build/lib.linux-armv7l-2.7/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/demo creating build/lib.linux-armv7l-2.7/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-armv7l-2.7/pmg_tk/startup copying modules/pmg_tk/startup/remote_pdb_load.py -> build/lib.linux-armv7l-2.7/pmg_tk/startup creating build/lib.linux-armv7l-2.7/pymol/opengl creating build/lib.linux-armv7l-2.7/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl/glu creating build/lib.linux-armv7l-2.7/pmg_wx copying modules/pmg_wx/__init__.py -> build/lib.linux-armv7l-2.7/pmg_wx creating build/lib.linux-armv7l-2.7/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-armv7l-2.7/chempy/fast creating build/lib.linux-armv7l-2.7/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-armv7l-2.7/chempy/fragments copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins creating build/lib.linux-armv7l-2.7/web copying modules/web/__init__.py -> build/lib.linux-armv7l-2.7/web copying modules/web/pymolhttpd.py -> build/lib.linux-armv7l-2.7/web copying modules/pymol/embed/__init__.py -> build/lib.linux-armv7l-2.7/pymol/embed creating build/lib.linux-armv7l-2.7/pymol/contrib copying modules/pymol/contrib/__init__.py -> build/lib.linux-armv7l-2.7/pymol/contrib creating build/lib.linux-armv7l-2.7/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl/glut creating build/lib.linux-armv7l-2.7/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-armv7l-2.7/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-armv7l-2.7/pymol2 copying modules/pymol2/make_cmd2.py -> build/lib.linux-armv7l-2.7/pymol2 creating build/lib.linux-armv7l-2.7/web/examples copying modules/web/examples/justhttpd.py -> build/lib.linux-armv7l-2.7/web/examples copying modules/web/examples/__init__.py -> build/lib.linux-armv7l-2.7/web/examples copying modules/pmg_tk/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-armv7l-2.7/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-armv7l-2.7/pmg_tk creating build/lib.linux-armv7l-2.7/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-armv7l-2.7/pmg_tk/skins/normal creating build/lib.linux-armv7l-2.7/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-armv7l-2.7/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-armv7l-2.7/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-armv7l-2.7/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-armv7l-2.7/chempy/champ creating build/lib.linux-armv7l-2.7/pymol/embed/wxpymol copying modules/pymol/embed/wxpymol/__init__.py -> build/lib.linux-armv7l-2.7/pymol/embed/wxpymol creating build/lib.linux-armv7l-2.7/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-armv7l-2.7/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-armv7l-2.7/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-armv7l-2.7/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-armv7l-2.7/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-armv7l-2.7/pymol/plugins creating build/lib.linux-armv7l-2.7/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl/gl copying modules/pymol/povray.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/cmd.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/internal.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/__init__.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/locking.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/commanding.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/vfont.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/util.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/xray.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/checking.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/controlling.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/headering.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/creating.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/menu.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/viewing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/parsing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/xwin.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/feedingback.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/gui.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/fitting.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/externing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/completing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/selecting.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/constants.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/keyboard.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/moving.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/editor.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/exporting.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/computing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/monitoring.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/preset.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/movie.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/api.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/selector.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/importing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/wizarding.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/helping.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/shortcut.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/m4x.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/parser.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/editing.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/experimenting.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/querying.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/rpc.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/keywords.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/colorramping.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/invocation.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/cgo.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/callback.py -> build/lib.linux-armv7l-2.7/pymol copying modules/pymol/setting.py -> build/lib.linux-armv7l-2.7/pymol creating build/lib.linux-armv7l-2.7/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-armv7l-2.7/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-armv7l-2.7/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-armv7l-2.7/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-armv7l-2.7/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-armv7l-2.7/chempy/bmin copying modules/chempy/arc.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/lst.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/__init__.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/brick.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/map.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/charge.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/dictdb.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/cif.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/models.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/pkl.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/hetatm.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/place.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/cpv.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/sdf.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/water_amber.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/water_residues.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/mmd.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/pdb.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/cex.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/neighbor.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/solvate.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/bonds.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/protein.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/io.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/mol.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/gamess1.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/mass.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/cc1.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/xyz.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/mol2.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/mae.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/gms.py -> build/lib.linux-armv7l-2.7/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-armv7l-2.7/chempy creating build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-armv7l-2.7/pymol/wizard copying modules/pymol/opengl/__init__.py -> build/lib.linux-armv7l-2.7/pymol/opengl running build_ext building 'pymol._cmd' extension creating build/temp.linux-armv7l-2.7 creating build/temp.linux-armv7l-2.7/ov creating build/temp.linux-armv7l-2.7/ov/src creating build/temp.linux-armv7l-2.7/layer0 creating build/temp.linux-armv7l-2.7/layer1 creating build/temp.linux-armv7l-2.7/layer2 creating build/temp.linux-armv7l-2.7/layer3 creating build/temp.linux-armv7l-2.7/layer4 creating build/temp.linux-armv7l-2.7/layer5 creating build/temp.linux-armv7l-2.7/modules creating build/temp.linux-armv7l-2.7/modules/cealign creating build/temp.linux-armv7l-2.7/modules/cealign/src creating build/temp.linux-armv7l-2.7/build creating build/temp.linux-armv7l-2.7/build/generated creating build/temp.linux-armv7l-2.7/contrib creating build/temp.linux-armv7l-2.7/contrib/uiuc creating build/temp.linux-armv7l-2.7/contrib/uiuc/plugins creating build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin creating build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVContext.c -o build/temp.linux-armv7l-2.7/ov/src/OVContext.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Match.c -o build/temp.linux-armv7l-2.7/layer0/Match.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Parse.c -o build/temp.linux-armv7l-2.7/layer0/Parse.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/PConv.c -o build/temp.linux-armv7l-2.7/layer1/PConv.o -ffast-math -funroll-loops -O3 -fcommon ov/src/OVContext.c: In function 'OVContext_Del': ov/src/OVContext.c:21:13: warning: variable 'heap' set but not used [-Wunused-but-set-variable] OVHeap *heap = I->heap; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVLexicon.c -o build/temp.linux-armv7l-2.7/ov/src/OVLexicon.o -ffast-math -funroll-loops -O3 -fcommon layer0/Parse.c: In function 'ParseFloat3List': layer0/Parse.c:173:10: warning: array subscript has type 'char' [-Wchar-subscripts] buf[blen] = 0; ^ ov/src/OVLexicon.c: In function 'OVLexicon_BorrowFromCString': ov/src/OVLexicon.c:360:11: warning: variable 'cur_index' set but not used [-Wunused-but-set-variable] ov_word cur_index = 0; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVHeap.c -o build/temp.linux-armv7l-2.7/ov/src/OVHeap.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/ov_utility.c -o build/temp.linux-armv7l-2.7/ov/src/ov_utility.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Sphere.c -o build/temp.linux-armv7l-2.7/layer0/Sphere.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVOneToAny.c -o build/temp.linux-armv7l-2.7/ov/src/OVOneToAny.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Debug.c -o build/temp.linux-armv7l-2.7/layer0/Debug.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVHeapArray.c -o build/temp.linux-armv7l-2.7/ov/src/OVHeapArray.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Pixmap.c -o build/temp.linux-armv7l-2.7/layer0/Pixmap.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Isosurf.c -o build/temp.linux-armv7l-2.7/layer0/Isosurf.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVRandom.c -o build/temp.linux-armv7l-2.7/ov/src/OVRandom.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c ov/src/OVOneToOne.c -o build/temp.linux-armv7l-2.7/ov/src/OVOneToOne.o -ffast-math -funroll-loops -O3 -fcommon layer0/Isosurf.c: In function 'IsosurfNewFromPyList': layer0/Isosurf.c:168:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/os_gl.c -o build/temp.linux-armv7l-2.7/layer0/os_gl.o -ffast-math -funroll-loops -O3 -fcommon layer0/Isosurf.c: In function 'IsofieldGetCorners': layer0/Isosurf.c:2211:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Basis.c -o build/temp.linux-armv7l-2.7/layer1/Basis.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUTHel10.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel10.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Triangle.c -o build/temp.linux-armv7l-2.7/layer0/Triangle.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Ray.c -o build/temp.linux-armv7l-2.7/layer1/Ray.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Map.c -o build/temp.linux-armv7l-2.7/layer0/Map.o -ffast-math -funroll-loops -O3 -fcommon layer0/Triangle.c: In function 'TriangleBuildLast': layer0/Triangle.c:1511:7: warning: variable 'both_active' set but not used [-Wunused-but-set-variable] int both_active; ^ In file included from layer1/Ray.c:44:0: layer1/Basis.c: In function 'ConeLineToSphereCapped': layer1/Basis.c:846:11: warning: variable 'base2orig_len' set but not used [-Wunused-but-set-variable] float base2orig_len, base2orig_len_sq; ^ layer1/Basis.c: In function 'BasisHitShadow': layer1/Basis.c:2361:7: warning: variable 'check_interior_flag' set but not used [-Wunused-but-set-variable] int check_interior_flag; ^ layer1/Basis.c:2360:7: warning: variable 'excl_trans_flag' set but not used [-Wunused-but-set-variable] int excl_trans_flag; ^ layer1/Ray.c: In function 'RayRenderG3d': layer1/Ray.c:967:36: warning: variable 'scale_z' set but not used [-Wunused-but-set-variable] register float scale_x, scale_y, scale_z; ^ layer1/Ray.c: In function 'RayRenderIDTF': layer1/Ray.c:2132:11: warning: variable 'mesh_start' set but not used [-Wunused-but-set-variable] int mesh_start = 0; ^ layer1/Ray.c: In function 'RayRenderPOV': layer1/Ray.c:2445:28: warning: variable 'bkrd_bottom' set but not used [-Wunused-but-set-variable] float *bkrd, *bkrd_top, *bkrd_bottom; ^ layer1/Ray.c:2445:17: warning: variable 'bkrd_top' set but not used [-Wunused-but-set-variable] float *bkrd, *bkrd_top, *bkrd_bottom; ^ layer1/Ray.c:2443:7: warning: variable 'fogRangeFlag' set but not used [-Wunused-but-set-variable] int fogRangeFlag = false; ^ layer1/Ray.c:2442:7: warning: variable 'fogFlag' set but not used [-Wunused-but-set-variable] int fogFlag = false; ^ layer1/Ray.c: In function 'RayRender': layer1/Ray.c:6122:15: warning: variable 'dc' set but not used [-Wunused-but-set-variable] int dc = 0; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/MyPNG.c -o build/temp.linux-armv7l-2.7/layer0/MyPNG.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Word.c -o build/temp.linux-armv7l-2.7/layer0/Word.o -ffast-math -funroll-loops -O3 -fcommon In file included from layer1/Ray.c:24:0: layer1/Basis.c: In function 'BasisMakeMap': layer0/Err.h:27:27: warning: 'tempRef' may be used uninitialized in this function [-Wmaybe-uninitialized] #define ErrChkPtr(G,p) {if(!p) ErrPointer(G,__FILE__,__LINE__);} ^ In file included from layer1/Ray.c:44:0: layer1/Basis.c:2871:17: note: 'tempRef' was declared here register int *tempRef; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Raw.c -o build/temp.linux-armv7l-2.7/layer0/Raw.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Deferred.c -o build/temp.linux-armv7l-2.7/layer0/Deferred.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Seq.c -o build/temp.linux-armv7l-2.7/layer1/Seq.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Block.c -o build/temp.linux-armv7l-2.7/layer0/Block.o -ffast-math -funroll-loops -O3 -fcommon layer1/Seq.c: In function 'SeqDrag': layer1/Seq.c:182:16: warning: variable 'col' set but not used [-Wunused-but-set-variable] CSeqCol *col; ^ layer1/Seq.c: In function 'SeqRelease': layer1/Seq.c:213:16: warning: variable 'col' set but not used [-Wunused-but-set-variable] CSeqCol *col; ^ layer1/Seq.c: In function 'SeqClick': layer1/Seq.c:267:16: warning: variable 'col' set but not used [-Wunused-but-set-variable] CSeqCol *col; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Util.c -o build/temp.linux-armv7l-2.7/layer0/Util.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/MemoryCache.c -o build/temp.linux-armv7l-2.7/layer0/MemoryCache.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Tracker.c -o build/temp.linux-armv7l-2.7/layer0/Tracker.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/PyMOLObject.c -o build/temp.linux-armv7l-2.7/layer1/PyMOLObject.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Feedback.c -o build/temp.linux-armv7l-2.7/layer0/Feedback.o -ffast-math -funroll-loops -O3 -fcommon layer1/PyMOLObject.c: In function 'ObjectMotion': layer1/PyMOLObject.c:384:13: warning: variable 'zero_flag' set but not used [-Wunused-but-set-variable] int zero_flag = -1; ^ layer1/PyMOLObject.c: In function 'ObjectStateFromPyList': layer1/PyMOLObject.c:1469:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll = 0; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Vector.c -o build/temp.linux-armv7l-2.7/layer0/Vector.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Tetsurf.c -o build/temp.linux-armv7l-2.7/layer0/Tetsurf.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Movie.c -o build/temp.linux-armv7l-2.7/layer1/Movie.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Texture.c -o build/temp.linux-armv7l-2.7/layer0/Texture.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Field.c -o build/temp.linux-armv7l-2.7/layer0/Field.o -ffast-math -funroll-loops -O3 -fcommon layer1/Ray.c: In function 'RayTraceThread': layer1/Ray.c:3478:25: warning: 'back_mask' may be used uninitialized in this function [-Wmaybe-uninitialized] bkrd_value = back_mask | ^ layer0/Field.c: In function 'FieldNewFromPyList': layer0/Field.c:126:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer0/Field.c:125:16: warning: variable 'n_elem' set but not used [-Wunused-but-set-variable] unsigned int n_elem; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Matrix.c -o build/temp.linux-armv7l-2.7/layer0/Matrix.o -ffast-math -funroll-loops -O3 -fcommon layer0/Matrix.c: In function 'MatrixFitRMSTTTf': layer0/Matrix.c:1180:18: warning: variable 'ix' set but not used [-Wunused-but-set-variable] int iters, ix, iy, iz, unchanged = 0; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/View.c -o build/temp.linux-armv7l-2.7/layer1/View.o -ffast-math -funroll-loops -O3 -fcommon layer1/View.c: In function 'matrix_interpolate': layer1/View.c:657:23: warning: variable 'center' set but not used [-Wunused-but-set-variable] float p0[3], p1[3], center[3]; ^ layer1/View.c:657:16: warning: variable 'p1' set but not used [-Wunused-but-set-variable] float p0[3], p1[3], center[3]; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Crystal.c -o build/temp.linux-armv7l-2.7/layer0/Crystal.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/MemoryDebug.c -o build/temp.linux-armv7l-2.7/layer0/MemoryDebug.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Err.c -o build/temp.linux-armv7l-2.7/layer0/Err.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/Queue.c -o build/temp.linux-armv7l-2.7/layer0/Queue.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Shaker.c -o build/temp.linux-armv7l-2.7/layer1/Shaker.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Extrude.c -o build/temp.linux-armv7l-2.7/layer1/Extrude.o -ffast-math -funroll-loops -O3 -fcommon layer1/Shaker.c: In function 'ShakerGetPyra': layer1/Shaker.c:73:16: warning: variable 't0' set but not used [-Wunused-but-set-variable] float av[3], t0[3]; ^ layer1/Shaker.c: In function 'ShakerDoPyra': layer1/Shaker.c:94:16: warning: variable 't0' set but not used [-Wunused-but-set-variable] float av[3], t0[3], push[3]; ^ layer1/Extrude.c: In function 'ExtrudeCGOSurfaceVariableTube': layer1/Extrude.c:1124:14: warning: variable 'stop' set but not used [-Wunused-but-set-variable] int start, stop; ^ layer1/Extrude.c:1124:7: warning: variable 'start' set but not used [-Wunused-but-set-variable] int start, stop; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/CGO.c -o build/temp.linux-armv7l-2.7/layer1/CGO.o -ffast-math -funroll-loops -O3 -fcommon layer1/CGO.c: In function 'CGONewFromPyList': layer1/CGO.c:329:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer1/CGO.c: In function 'CGOFromFloatArray': layer1/CGO.c:530:7: warning: variable 'c' set but not used [-Wunused-but-set-variable] int c; ^ layer1/CGO.c: In function 'CGOCombineBeginEnd': layer1/CGO.c:1935:11: warning: variable 'pickColorValsUC' set but not used [-Wunused-but-set-variable] uchar *pickColorValsUC; ^ layer1/CGO.c:1881:6: warning: unused variable 'ncolors' [-Wunused-variable] int ncolors = 0; ^ layer1/CGO.c: In function 'CGOCountNumVerticesForScreen': layer1/CGO.c:2313:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] while(op = (CGO_MASK & CGO_read_int(pc))) { ^ layer1/CGO.c: In function 'OptimizePointsToVBO': layer1/CGO.c:2642:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:2645:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:2649:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:2657:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBufferData returns err=%d\n"); ^ layer1/CGO.c:2671:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:2682:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBufferData returns err=%d\n"); ^ layer1/CGO.c:2688:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:2699:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: OptimizePointsToVBO() glBufferData returns err=%d\n"); ^ layer1/CGO.c:2450:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] short err = 0; ^ layer1/CGO.c: In function 'CGOProcessCGOtoArrays': layer1/CGO.c:2730:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] short err = 0; ^ layer1/CGO.c: In function 'CGOProcessScreenCGOtoArrays': layer1/CGO.c:3012:8: warning: variable 'has_texcoord' set but not used [-Wunused-but-set-variable] short has_texcoord = false; ^ layer1/CGO.c:2966:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] short err = 0; ^ layer1/CGO.c: In function 'CGOOptimizeToVBONotIndexedWithReturnedData': layer1/CGO.c:3220:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:3224:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3232:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3236:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3248:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3252:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3264:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3268:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3275:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3505:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:3509:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3517:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3521:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3533:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3537:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3549:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBONotIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3141:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] short err = 0; ^ layer1/CGO.c: In function 'CGOOptimizeToVBOIndexedWithColorImpl': layer1/CGO.c:3890:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:3893:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:3897:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3905:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3909:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3921:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3925:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3937:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3941:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3949:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3953:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:3960:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:4200:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:4203:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:4207:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4215:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:4219:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4231:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:4235:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4247:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:4251:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4259:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeToVBOIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c:3631:9: warning: variable 'err' set but not used [-Wunused-but-set-variable] short err = 0; ^ layer1/CGO.c: In function 'CGOOptimizeGLSLCylindersToVBOIndexedImpl': layer1/CGO.c:4621:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:4624:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:4628:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4661:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBufferData returns err=%d\n"); ^ layer1/CGO.c:4667:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4671:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeGLSLCylindersToVBO() glBufferData returns err=%d\n"); ^ layer1/CGO.c: In function 'CGOOptimizeSpheresToVBONonIndexedImpl': layer1/CGO.c:4932:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:4935:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:4939:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:4963:4: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeSpheresToVBONonIndexed() glBufferData returns err=%d\n"); ^ layer1/CGO.c: In function 'CGOSimplify': layer1/CGO.c:5171:11: warning: variable 'pickColorValsUC' set but not used [-Wunused-but-set-variable] uchar *pickColorValsUC; ^ layer1/CGO.c: In function 'CGOOptimizeTextures': layer1/CGO.c:5385:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:5389:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:5392:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5400:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBufferData returns err=%d\n"); ^ layer1/CGO.c:5405:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5412:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBufferData returns err=%d\n"); ^ layer1/CGO.c:5416:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5423:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeTextures() glBufferData returns err=%d\n") ^ layer1/CGO.c: In function 'CGOOptimizeLabels': layer1/CGO.c:5582:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() BEFORE glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:5586:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:5589:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5597:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n"); ^ layer1/CGO.c:5602:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5609:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n"); ^ layer1/CGO.c:5613:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5620:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n") ^ layer1/CGO.c:5624:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:5631:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeLabels() glBufferData returns err=%d\n") ^ layer1/CGO.c: In function 'CGOExpandDrawTextures': layer1/CGO.c:5679:30: warning: variable 'onvals' set but not used [-Wunused-but-set-variable] int nvals = narrays*nverts, onvals; ^ layer1/CGO.c: In function 'CGORenderRay': layer1/CGO.c:6220:42: warning: variable 'pickColorVals' set but not used [-Wunused-but-set-variable] float *normalVals = 0, *colorVals = 0, *pickColorVals; ^ layer1/CGO.c: In function 'CGO_gl_draw_buffers_indexed': layer1/CGO.c:6662:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("beginning of CGO_gl_draw_buffers_indexed returns err=%d\n"); ^ layer1/CGO.c:6788:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("CGO_gl_draw_buffers_indexed: before glDrawElements returns err=%d\n"); ^ layer1/CGO.c:6790:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("CGO_gl_draw_buffers_indexed: after glDrawElements returns err=%d\n"); ^ layer1/CGO.c:6835:1: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("CGO_gl_draw_buffers_indexed: end returns err=%d\n"); ^ layer1/CGO.c: In function 'CGO_gl_draw_label': layer1/CGO.c:7136:50: warning: variable 'textExtent' set but not used [-Wunused-but-set-variable] float worldPos[4], screenMin[3], screenMax[3], textExtent[4]; ^ layer1/CGO.c:7136:36: warning: variable 'screenMax' set but not used [-Wunused-but-set-variable] float worldPos[4], screenMin[3], screenMax[3], textExtent[4]; ^ layer1/CGO.c:7136:22: warning: variable 'screenMin' set but not used [-Wunused-but-set-variable] float worldPos[4], screenMin[3], screenMax[3], textExtent[4]; ^ layer1/CGO.c: In function 'CGO_gl_draw_texture': layer1/CGO.c:7177:50: warning: variable 'textExtent' set but not used [-Wunused-but-set-variable] float worldPos[4], screenMin[3], screenMax[3], textExtent[4]; ^ layer1/CGO.c:7177:36: warning: variable 'screenMax' set but not used [-Wunused-but-set-variable] float worldPos[4], screenMin[3], screenMax[3], textExtent[4]; ^ layer1/CGO.c:7177:22: warning: variable 'screenMin' set but not used [-Wunused-but-set-variable] float worldPos[4], screenMin[3], screenMax[3], textExtent[4]; ^ layer1/CGO.c: In function 'CGORenderGLPicking': layer1/CGO.c:7697:73: warning: variable 'pbnd' set but not used [-Wunused-but-set-variable] int nverts = CGO_get_int(pc+3), v, pl, idx = -1, pidx, bnd = -1, pbnd; ^ layer1/CGO.c:7697:57: warning: variable 'pidx' set but not used [-Wunused-but-set-variable] int nverts = CGO_get_int(pc+3), v, pl, idx = -1, pidx, bnd = -1, pbnd; ^ layer1/CGO.c: In function 'CGOSimpleCone': layer1/CGO.c:8765:15: warning: variable 'nub2' set but not used [-Wunused-but-set-variable] float nub1, nub2; ^ layer1/CGO.c:8765:9: warning: variable 'nub1' set but not used [-Wunused-but-set-variable] float nub1, nub2; ^ In file included from layer1/CGO.c:24:0: layer1/CGO.c: In function 'CGOGetSizeWithoutStops': layer1/CGO.h:35:26: warning: value computed is not used [-Wunused-value] #define CGO_read_int(p) (*((int*)((p)++))) ^ layer1/CGO.c:9045:5: note: in expansion of macro 'CGO_read_int' CGO_read_int(pc); ^ layer1/CGO.c: In function 'CGOChangeShadersTo': layer1/CGO.c:9567:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] while(op = (CGO_MASK & CGO_read_int(pc))) { ^ layer1/CGO.c: In function 'CGOOptimizeScreenTexturesAndPolygons': layer1/CGO.c:9685:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glGenBuffers returns err=%d\n"); ^ layer1/CGO.c:9689:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:9697:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBufferData returns err=%d\n"); ^ layer1/CGO.c:9701:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:9709:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBufferData returns err=%d\n"); ^ layer1/CGO.c:9713:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBindBuffer returns err=%d\n"); ^ layer1/CGO.c:9724:2: warning: suggest parentheses around assignment used as truth value [-Wparentheses] CHECK_GL_ERROR_OK("ERROR: CGOOptimizeScreenTexturesAndPolygons() glBufferData returns err=%d\n"); ^ In file included from layer0/OOMac.h:21:0, from layer1/Extrude.c:25: layer1/Extrude.c: In function 'ExtrudeCGOSurfaceTube': layer0/Err.h:29:43: warning: 'TN' may be used uninitialized in this function [-Wmaybe-uninitialized] #define CHECKOK(ok, var) ok &= var ? true : false; ^ layer1/Extrude.c:690:47: note: 'TN' was declared here float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN; ^ layer1/CGO.c: In function 'CGO_gl_draw_buffers': layer1/CGO.c:6649:5: warning: 'shaderPrg' may be used uninitialized in this function [-Wmaybe-uninitialized] CShaderPrg_Disable(shaderPrg); ^ In file included from layer0/OOMac.h:21:0, from layer1/Extrude.c:25: layer1/Extrude.c: In function 'ExtrudeCGOSurfacePolygon': layer0/Err.h:29:43: warning: 'TN' may be used uninitialized in this function [-Wmaybe-uninitialized] #define CHECKOK(ok, var) ok &= var ? true : false; ^ layer1/Extrude.c:1390:47: note: 'TN' was declared here float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN; ^ layer1/CGO.c: In function 'CGO_gl_draw_arrays': layer1/CGO.c:6510:12: warning: 'vertexVals' may be used uninitialized in this function [-Wmaybe-uninitialized] float *vertexVals; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Symmetry.c -o build/temp.linux-armv7l-2.7/layer1/Symmetry.o -ffast-math -funroll-loops -O3 -fcommon In file included from layer0/OOMac.h:21:0, from layer1/Extrude.c:25: layer1/Extrude.c: In function 'ExtrudeCGOSurfaceStrand': layer0/Err.h:29:43: warning: 'TN' may be used uninitialized in this function [-Wmaybe-uninitialized] #define CHECKOK(ok, var) ok &= var ? true : false; ^ layer1/Extrude.c:1708:47: note: 'TN' was declared here float *sv, *sn, *tv, *tn, *tv1, *tn1, *TV, *TN; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUTHel12.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel12.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Setting.c -o build/temp.linux-armv7l-2.7/layer1/Setting.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/ButMode.c -o build/temp.linux-armv7l-2.7/layer1/ButMode.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer0/ShaderMgr.c -o build/temp.linux-armv7l-2.7/layer0/ShaderMgr.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Pop.c -o build/temp.linux-armv7l-2.7/layer1/Pop.o -ffast-math -funroll-loops -O3 -fcommon layer0/ShaderMgr.c: In function 'CShaderPrg_ReplaceStringsInPlace': layer0/ShaderMgr.c:161:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] while(rstr=strstr(dest_line, replaceStrings[i])){ ^ layer0/ShaderMgr.c: In function 'CShaderMgr_Reload_Shader_Variables': layer0/ShaderMgr.c:401:7: warning: variable 'bg_image_mode_solid' set but not used [-Wunused-but-set-variable] int bg_image_mode_solid; ^ layer0/ShaderMgr.c: In function 'CShaderPrg_BindAttribLocations': layer0/ShaderMgr.c:509:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:513:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:517:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c: In function 'CShaderPrg_BindLabelAttribLocations': layer0/ShaderMgr.c:528:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:535:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c: In function 'CShaderPrg_BindCylinderAttribLocations': layer0/ShaderMgr.c:549:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:553:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:557:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:561:5: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c: In function 'CShaderPrg_Reload': layer0/ShaderMgr.c:700:24: warning: unused variable 'needAttach' [-Wunused-variable] int status, howLong, needAttach = 0; ^ layer0/ShaderMgr.c: In function 'ShaderMgrConfig': layer0/ShaderMgr.c:836:14: warning: unused variable 'err' [-Wunused-variable] GLenum err ; ^ layer0/ShaderMgr.c:885:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c:889:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] if (err = glGetError()){ ^ layer0/ShaderMgr.c: In function 'CShaderMgr_ReadShaderFromDisk': layer0/ShaderMgr.c:1225:7: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'size_t {aka unsigned int}' [-Wformat=] " PyMOLShader_NewFromFile-Error: size(%ld)!=res(%ld)\n", size,res ENDFB(G); ^ layer0/ShaderMgr.c: In function 'CShaderPrg_Enable_CylinderShader': layer0/ShaderMgr.c:1882:10: warning: variable 'm' set but not used [-Wunused-but-set-variable] float *m; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Rep.c -o build/temp.linux-armv7l-2.7/layer1/Rep.o -ffast-math -funroll-loops -O3 -fcommon layer1/CGO.c: In function 'CGOCombineBeginEnd': layer1/CGO.c:1998:73: warning: 'normalVals' may be used uninitialized in this function [-Wmaybe-uninitialized] normalVals[pl] = tmp_ptr[0]; normalVals[pl+1] = tmp_ptr[1]; normalVals[pl+2] = tmp_ptr[2]; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUT9x15.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUT9x15.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/ScrollBar.c -o build/temp.linux-armv7l-2.7/layer1/ScrollBar.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUT8x13.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUT8x13.o -ffast-math -funroll-loops -O3 -fcommon layer1/CGO.c: In function 'OptimizePointsToVBO': layer1/CGO.c:2607:8: warning: 'pickColorValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized] SetVertexValuesForVBO(I->G, cgo, arrays, pl, plc, cnt, incr++, ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDistDash.c -o build/temp.linux-armv7l-2.7/layer2/RepDistDash.o -ffast-math -funroll-loops -O3 -fcommon layer1/CGO.c: In function 'CGOProcessCGOtoArrays': layer1/CGO.c:2907:8: warning: 'pickColorValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized] SetVertexValuesForVBO(G, cgo, arrays, pl, plc, cnt, incr++, ^ layer1/CGO.c:2927:8: warning: 'accessibilityValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized] SetVertexValuesForVBO(G, cgo, arrays, pl, plc, cnt, incr++, ^ layer1/CGO.c:2907:8: warning: 'normalValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized] SetVertexValuesForVBO(G, cgo, arrays, pl, plc, cnt, incr++, ^ layer2/RepDistDash.c: In function 'RepDistDashNew': layer2/RepDistDash.c:351:29: warning: variable 'd1' set but not used [-Wunused-but-set-variable] float *v, *v1, *v2, d[3], d1[3]; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectVolume.c -o build/temp.linux-armv7l-2.7/layer2/ObjectVolume.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/CoordSet.c -o build/temp.linux-armv7l-2.7/layer2/CoordSet.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectVolume.c: In function 'ObjectVolumeNewFromPyList': layer2/ObjectVolume.c:269:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/ObjectVolume.c: In function 'ObjectVolumeFree': layer2/ObjectVolume.c:341:9: warning: unused variable 'i' [-Wunused-variable] int a,i; ^ layer2/ObjectVolume.c: In function 'ObjectVolumeUpdate': layer2/ObjectVolume.c:451:50: warning: statement with no effect [-Wunused-value] a, vs->RefreshFlag, vs->ResurfaceFlag ENDFD(G); ^ layer2/ObjectVolume.c:474:9: warning: suggest parentheses around '&&' within '||' [-Wparentheses] && vs->Ramp[5 * (vs->RampSize - 1)] == 359.f) { ^ layer2/ObjectVolume.c:515:26: warning: variable 'max_ext' set but not used [-Wunused-but-set-variable] float *min_ext, *max_ext; ^ layer2/ObjectVolume.c:515:16: warning: variable 'min_ext' set but not used [-Wunused-but-set-variable] float *min_ext, *max_ext; ^ layer2/ObjectVolume.c:569:39: warning: pointer targets in passing argument 2 of 'FieldNew' differ in signedness [-Wpointer-sign] vs->carvemask = FieldNew(G, vs->dim, 3, sizeof(GLubyte), cFieldOther); ^ In file included from layer0/Isosurf.h:24:0, from layer2/ObjectMap.h:24, from layer2/ObjectVolume.h:19, from layer2/ObjectVolume.c:26: layer0/Field.h:65:9: note: expected 'int *' but argument is of type 'unsigned int *' CField *FieldNew(PyMOLGlobals * G, int *dim, int n_dim, unsigned int base_size, int type); ^ layer2/ObjectVolume.c: At top level: layer2/ObjectVolume.c:714:15: warning: function declaration isn't a prototype [-Wstrict-prototypes] static GLuint tex3dGenBind() ^ layer2/ObjectVolume.c: In function 'ObjectVolumeRender': layer2/ObjectVolume.c:924:89: warning: suggest parentheses around '&&' within '||' [-Wparentheses] CShaderPrg_Set1f(shaderPrg, "fogIsSolidColor", bg_gradient || bg_image_filename && bg_image_filename[0] ? 0.f : 1.f); ^ layer1/CGO.c: In function 'CGOOptimizeToVBONotIndexedWithReturnedData': layer1/CGO.c:3457:8: warning: 'pickColorValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized] SetVertexValuesForVBO(I->G, cgo, arrays, pl, plc, cnt, incr++, ^ layer1/CGO.c:3457:8: warning: 'normalValsDA' may be used uninitialized in this function [-Wmaybe-uninitialized] arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Wizard.c -o build/temp.linux-armv7l-2.7/layer1/Wizard.o -ffast-math -funroll-loops -O3 -fcommon layer2/CoordSet.c: In function 'CoordSetAtomToChemPyAtom': layer2/CoordSet.c:1021:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Font.c -o build/temp.linux-armv7l-2.7/layer1/Font.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/TypeFace.c -o build/temp.linux-armv7l-2.7/layer1/TypeFace.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/AtomInfo.c -o build/temp.linux-armv7l-2.7/layer2/AtomInfo.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Character.c -o build/temp.linux-armv7l-2.7/layer1/Character.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMolecule.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule.o -ffast-math -funroll-loops -O3 -fcommon layer1/Character.c: In function 'CharacterRenderOpenGL': layer1/Character.c:273:18: warning: unused variable 'texVals' [-Wunused-variable] const GLfloat texVals [] = { ^ layer1/Character.c:267:18: warning: unused variable 'vertexVals' [-Wunused-variable] const GLfloat vertexVals [] = { ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeFixSeleHydrogens': layer2/ObjectMolecule.c:731:13: warning: variable 'cs' set but not used [-Wunused-but-set-variable] CoordSet *cs; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadTRJFile': layer2/ObjectMolecule.c:886:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadPMOFile': layer2/ObjectMolecule.c:2855:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeRenderSele': layer2/ObjectMolecule.c:3290:51: warning: variable 'ai' set but not used [-Wunused-but-set-variable] register AtomInfoType *atInfo = I->AtomInfo, *ai; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadXYZFile': layer2/ObjectMolecule.c:3881:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeAttach': layer2/ObjectMolecule.c:4477:10: warning: variable 'nn' set but not used [-Wunused-but-set-variable] int n, nn; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeFindOpenValenceVector': layer2/ObjectMolecule.c:4700:22: warning: variable 'ai1' set but not used [-Wunused-but-set-variable] AtomInfoType *ai, *ai1; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeCreateSpheroid': layer2/ObjectMolecule.c:4881:10: warning: variable 'spl' set but not used [-Wunused-but-set-variable] float *spl; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeGuessValences': layer2/ObjectMolecule.c:6350:29: warning: variable 'bnd2' set but not used [-Wunused-but-set-variable] int bnd2[5]; ^ layer2/ObjectMolecule.c:6124:38: warning: variable 'c2_len' set but not used [-Wunused-but-set-variable] float c1_len = 0.0F, c2_len = 0.0F; ^ layer2/ObjectMolecule.c:6124:23: warning: variable 'c1_len' set but not used [-Wunused-but-set-variable] float c1_len = 0.0F, c2_len = 0.0F; ^ layer2/ObjectMolecule.c:6123:56: warning: variable 'c2_bd' set but not used [-Wunused-but-set-variable] int c1_at = -1, c2_at = -1, c1_bd = 0, c2_bd = 0; ^ layer2/ObjectMolecule.c:6123:45: warning: variable 'c1_bd' set but not used [-Wunused-but-set-variable] int c1_at = -1, c2_at = -1, c1_bd = 0, c2_bd = 0; ^ layer2/ObjectMolecule.c:6118:68: warning: variable 'o4_len' set but not used [-Wunused-but-set-variable] float o1_len = 0.0F, o2_len = 0.0F, o3_len = 0.0F, o4_len = 0.0F; ^ layer2/ObjectMolecule.c:6118:53: warning: variable 'o3_len' set but not used [-Wunused-but-set-variable] float o1_len = 0.0F, o2_len = 0.0F, o3_len = 0.0F, o4_len = 0.0F; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUTHel18.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel18.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectMolecule.c: In function 'ObjectMoleculeMOL2SetFormalCharges': layer2/ObjectMolecule.c:8969:46: warning: variable 'n' set but not used [-Wunused-but-set-variable] int at, fcharge = 0, isProtein = 0, k, n; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeMOL2Str2CoordSet': layer2/ObjectMolecule.c:9368:38: warning: variable 'resv_flag' set but not used [-Wunused-but-set-variable] int chain_flag, resn_flag, resv_flag; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeInvalidateAtomType': layer2/ObjectMolecule.c:12194:16: warning: variable 'a' set but not used [-Wunused-but-set-variable] int ai, atm, a; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Ortho.c -o build/temp.linux-armv7l-2.7/layer1/Ortho.o -ffast-math -funroll-loops -O3 -fcommon layer1/Ortho.c: In function 'OrthoDoDraw': layer1/Ortho.c:1520:10: warning: variable 'v' set but not used [-Wunused-but-set-variable] float *v; ^ layer1/CGO.c: In function 'CGOSimplify': layer1/CGO.c:5213:73: warning: 'normalVals' may be used uninitialized in this function [-Wmaybe-uninitialized] normalVals[pl] = tmp_ptr[0]; normalVals[pl+1] = tmp_ptr[1]; normalVals[pl+2] = tmp_ptr[2]; ^ layer1/Ortho.c: In function 'bg_grad': layer1/Ortho.c:1430:7: warning: 'cgo2' may be used uninitialized in this function [-Wmaybe-uninitialized] CGOFree(cgo2); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepSurface.c -o build/temp.linux-armv7l-2.7/layer2/RepSurface.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepSurface.c: In function 'RepSurfaceRender': layer2/RepSurface.c:1960:11: warning: variable 'col' set but not used [-Wunused-but-set-variable] float *col; ^ layer2/RepSurface.c:2221:28: warning: variable 'col' set but not used [-Wunused-but-set-variable] float *col; ^ layer2/RepSurface.c: In function 'RepSurfaceColor': layer2/RepSurface.c:3714:22: warning: variable 'planew' set but not used [-Wunused-but-set-variable] float d[3], *vn0, planew, v0mod[3]; ^ layer2/RepSurface.c:3793:29: warning: variable 'planew' set but not used [-Wunused-but-set-variable] float d[3], *vn0, pt[3], planew, v0mod[3]; ^ layer2/RepSurface.c:3793:22: warning: variable 'pt' set but not used [-Wunused-but-set-variable] float d[3], *vn0, pt[3], planew, v0mod[3]; ^ layer2/RepSurface.c:3949:36: warning: variable 'pai2' set but not used [-Wunused-but-set-variable] AtomInfoType *pai = NULL, *pai2 = NULL; /* variables for color smoothing */ ^ layer2/RepSurface.c: In function 'SolventDotNew': layer2/RepSurface.c:5687:7: warning: variable 'maxDot' set but not used [-Wunused-but-set-variable] int maxDot = 0; ^ layer1/CGO.c: In function 'CGORenderRay': layer1/CGO.c:6244:9: warning: 'vertexVals' may be used uninitialized in this function [-Wmaybe-uninitialized] v0 = &vertexVals[pl]; ^ layer1/CGO.c: In function 'CGORenderGLPicking': layer1/CGO.c:7753:13: warning: 'pca' may be used uninitialized in this function [-Wmaybe-uninitialized] float *pca; ^ layer1/CGO.c:7775:26: warning: 'nverts' may be used uninitialized in this function [-Wmaybe-uninitialized] pickColorVals = pca + nverts; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectGadgetRamp.c -o build/temp.linux-armv7l-2.7/layer2/ObjectGadgetRamp.o -ffast-math -funroll-loops -O3 -fcommon layer1/CGO.c: In function 'CGORenderGL': layer1/CGO.c:8085:12: warning: 'normalVals_tmp' may be used uninitialized in this function [-Wmaybe-uninitialized] n2 = normalVals_tmp + 3; ^ layer2/ObjectGadgetRamp.c: In function 'ObjectGadgetRampUpdateCGO': layer2/ObjectGadgetRamp.c:651:10: warning: variable 'p' set but not used [-Wunused-but-set-variable] float *p; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepRibbon.c -o build/temp.linux-armv7l-2.7/layer2/RepRibbon.o -ffast-math -funroll-loops -O3 -fcommon In file included from layer0/OOMac.h:22:0, from layer1/CGO.c:26: layer1/CGO.c: In function 'CGOOptimizeGLSLCylindersToVBOIndexedImpl': layer0/MemoryDebug.h:182:15: warning: 'org_colorVals' may be used uninitialized in this function [-Wmaybe-uninitialized] #define mfree free ^ layer1/CGO.c:4373:12: note: 'org_colorVals' was declared here float *org_colorVals; ^ layer2/RepSurface.c: In function 'SurfaceJobRun': layer2/RepSurface.c:4648:11: warning: 'solv_map' may be used uninitialized in this function [-Wmaybe-uninitialized] MapFree(solv_map); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontGLUT.c -o build/temp.linux-armv7l-2.7/layer1/FontGLUT.o -ffast-math -funroll-loops -O3 -fcommon In file included from layer0/OOMac.h:22:0, from layer2/ObjectMolecule.c:25: layer2/ObjectMolecule.c: In function 'ObjectMoleculeLoadRSTFile': layer0/MemoryDebug.h:182:15: warning: 'buffer' may be used uninitialized in this function [-Wmaybe-uninitialized] #define mfree free ^ layer2/ObjectMolecule.c:1280:9: note: 'buffer' was declared here char *buffer, *p; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Color.c -o build/temp.linux-armv7l-2.7/layer1/Color.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepCartoon.c -o build/temp.linux-armv7l-2.7/layer2/RepCartoon.o -ffast-math -funroll-loops -O3 -fcommon layer1/Color.c: In function 'ColorExtFromPyList': layer1/Color.c:406:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer1/Color.c: In function 'ColorDef': layer1/Color.c:576:7: warning: variable 'best' set but not used [-Wunused-but-set-variable] int best; ^ layer1/Color.c: In function 'Color3fToInt': layer1/Color.c:3069:16: warning: unused variable 'result' [-Wunused-variable] unsigned int result; ^ layer2/RepSurface.c: In function 'RepSurfaceRender': layer2/RepSurface.c:3324:6: warning: 'simple' may be used uninitialized in this function [-Wmaybe-uninitialized] CGOFree(simple); ^ layer2/RepCartoon.c: In function 'do_ring': layer2/RepCartoon.c:282:7: warning: variable 'cartoon_color' set but not used [-Wunused-but-set-variable] int cartoon_color; ^ layer2/RepCartoon.c: In function 'nuc_acid': layer2/RepCartoon.c:1497:22: warning: variable 'v_n' set but not used [-Wunused-but-set-variable] float *v_o, *v_c, *v_n, t0[3]; ^ layer2/RepCartoon.c: In function 'GenerateRepCartoonCGO': layer2/RepCartoon.c:1662:31: warning: variable 'ring_finder_eff' set but not used [-Wunused-but-set-variable] int ring_mode, ring_finder, ring_finder_eff; ^ layer2/RepCartoon.c: In function 'RepCartoonNew': layer2/RepCartoon.c:2889:9: warning: variable 'alpha' set but not used [-Wunused-but-set-variable] float alpha; ^ layer2/RepCartoon.c:2876:7: warning: variable 'skip_to' set but not used [-Wunused-but-set-variable] int skip_to; ^ layer2/RepCartoon.c:2865:7: warning: variable 'highlight_color' set but not used [-Wunused-but-set-variable] int highlight_color; ^ layer2/RepCartoon.c:2861:7: warning: variable 'cartoon_debug' set but not used [-Wunused-but-set-variable] int cartoon_debug; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Scene.c -o build/temp.linux-armv7l-2.7/layer1/Scene.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/VFont.c -o build/temp.linux-armv7l-2.7/layer2/VFont.o -ffast-math -funroll-loops -O3 -fcommon layer1/Scene.c: In function 'SceneDrawImageOverlay': layer1/Scene.c:3348:20: warning: variable 'color_word' set but not used [-Wunused-but-set-variable] unsigned int color_word; ^ layer1/Scene.c: In function 'SceneReadTriplets': layer1/Scene.c:3571:7: warning: variable 'dim' set but not used [-Wunused-but-set-variable] int dim[3]; ^ layer1/Scene.c: In function 'SceneDrag': layer1/Scene.c:5957:8: warning: variable 'result' set but not used [-Wunused-but-set-variable] int result, which_light; ^ layer1/Scene.c:6005:8: warning: variable 'result' set but not used [-Wunused-but-set-variable] int result, which_light; ^ layer1/Scene.c: In function 'SceneReshape': layer1/Scene.c:6381:7: warning: variable 'y' set but not used [-Wunused-but-set-variable] int y = height; ^ layer1/Scene.c: In function 'SceneApplyImageGamma': layer1/Scene.c:6538:7: warning: variable 'big_endian' set but not used [-Wunused-but-set-variable] int big_endian; ^ layer1/Scene.c: In function 'SceneRay': layer1/Scene.c:6766:7: warning: variable 'curState' set but not used [-Wunused-but-set-variable] int curState; ^ layer2/VFont.c: In function 'VFontIndent': layer2/VFont.c:145:10: warning: variable 'pc' set but not used [-Wunused-but-set-variable] float *pc; ^ layer2/VFont.c:144:9: warning: variable 'base' set but not used [-Wunused-but-set-variable] float base[3], pen[3]; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMolecule2.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule2.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectGadget.c -o build/temp.linux-armv7l-2.7/layer2/ObjectGadget.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectMolecule2.c:1639:17: warning: function declaration isn't a prototype [-Wstrict-prototypes] static SSHash * sshash_new() { ^ layer2/ObjectMolecule2.c: In function 'ObjectMoleculePDBStr2CoordSet': layer2/ObjectMolecule2.c:1793:7: warning: variable 'have_conect' set but not used [-Wunused-but-set-variable] int have_conect = false; ^ layer2/ObjectMolecule2.c:1792:7: warning: variable 'seen_conect' set but not used [-Wunused-but-set-variable] int seen_conect = false; ^ layer2/ObjectMolecule2.c:1758:10: warning: unused variable 'b' [-Wunused-variable] int a, b, c; ^ layer2/ObjectMolecule2.c: In function 'ObjectMoleculeNewFromPyList': layer2/ObjectMolecule2.c:3702:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/ObjectGadget.c: In function 'ObjectGadgetInitFromPyList': layer2/ObjectGadget.c:305:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepLabel.c -o build/temp.linux-armv7l-2.7/layer2/RepLabel.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/SculptCache.c -o build/temp.linux-armv7l-2.7/layer2/SculptCache.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepNonbonded.c -o build/temp.linux-armv7l-2.7/layer2/RepNonbonded.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMap.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMap.o -ffast-math -funroll-loops -O3 -fcommon In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1781:0, from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:18, from layer2/ObjectMap.c:45: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ layer2/ObjectMap.c: In function 'ObjectMapStateTrim': layer2/ObjectMap.c:480:7: warning: variable 'max' set but not used [-Wunused-but-set-variable] int max[3]; ^ layer2/ObjectMap.c: In function 'ObjectMapStateInterpolate': layer2/ObjectMap.c:1110:10: warning: variable 'out' set but not used [-Wunused-but-set-variable] float *out; ^ layer2/ObjectMap.c: In function 'ObjectMapNewFromPyList': layer2/ObjectMap.c:1589:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/ObjectMap.c: In function 'ObjectMapCCP4StrToMap': layer2/ObjectMap.c:2727:41: warning: passing argument 2 of 'UtilNCopy' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] UtilNCopy(ms->Symmetry->SpaceGroup, space_group_numbers[ispg], WordLength); ^ In file included from layer2/ObjectMap.c:41:0: layer0/Util.h:34:6: note: expected 'char *' but argument is of type 'const char *' void UtilNCopy(char *dst, char *src, ov_size n); /* up to N-1 chars */ ^ layer2/ObjectMap.c:2470:14: warning: variable 'xref' set but not used [-Wunused-but-set-variable] int cc[3], xref[3]; ^ layer2/ObjectMap.c: In function 'ObjectMapLoadCCP4': layer2/ObjectMap.c:4593:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMap.c: In function 'ObjectMapLoadPHI': layer2/ObjectMap.c:4764:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMap.c: In function 'ObjectMapLoadDXFile': layer2/ObjectMap.c:5119:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMap.c: In function 'ObjectMapLoadACNTFile': layer2/ObjectMap.c:5367:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMap.c: In function 'ObjectMapLoadFLDFile': layer2/ObjectMap.c:5420:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ In file included from /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ndarrayobject.h:27:0, from layer2/ObjectMap.c:45: layer2/ObjectMap.c: At top level: /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1634:1: warning: '_import_array' defined but not used [-Wunused-function] _import_array(void) ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeMerge': layer2/ObjectMolecule.c:9993:16: warning: 'i2a' may be used uninitialized in this function [-Wmaybe-uninitialized] cs->IdxToAtm = i2a; ^ layer2/ObjectMolecule.c:9818:7: warning: 'nAt' may be used uninitialized in this function [-Wmaybe-uninitialized] int nAt, nBd, nBond; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/FontType.c -o build/temp.linux-armv7l-2.7/layer1/FontType.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectMolecule.c: In function 'ObjectMoleculeAddSeleHydrogens': layer2/ObjectMolecule.c:4091:16: warning: 'cs' may be used uninitialized in this function [-Wmaybe-uninitialized] if(cs->fFree) ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Text.c -o build/temp.linux-armv7l-2.7/layer1/Text.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectMesh.c -o build/temp.linux-armv7l-2.7/layer2/ObjectMesh.o -ffast-math -funroll-loops -O3 -fcommon In file included from layer0/OOMac.h:22:0, from layer2/ObjectMolecule2.c:26: layer2/ObjectMolecule2.c: In function 'ObjectMoleculeSort': layer0/MemoryDebug.h:137:33: warning: 'dAtmToIdx' may be used uninitialized in this function [-Wmaybe-uninitialized] #define VLAFreeP(ptr) {if(ptr) {VLAFree(ptr);ptr=NULL;}} ^ layer2/ObjectMolecule2.c:4328:8: note: 'dAtmToIdx' was declared here int *dAtmToIdx; ^ layer2/ObjectMesh.c: In function 'ObjectMeshNewFromPyList': layer2/ObjectMesh.c:231:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/ObjectMesh.c: In function 'ObjectMeshUpdate': layer2/ObjectMesh.c:604:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/ObjectMolecule.c: In function 'ObjectMoleculeFillOpenValences': layer2/ObjectMolecule.c:4620:9: warning: 'cs' may be used uninitialized in this function [-Wmaybe-uninitialized] cs->fFree(cs); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepMesh.c -o build/temp.linux-armv7l-2.7/layer2/RepMesh.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepMesh.c: In function 'RepMeshRender': layer2/RepMesh.c:315:27: warning: 'origin' may be used uninitialized in this function [-Wmaybe-uninitialized] axis[2] = v[2] - origin[2]; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepCylBond.c -o build/temp.linux-armv7l-2.7/layer2/RepCylBond.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepCylBond.c: In function 'RepCylBondPopulateAdjacentAtoms': layer2/RepCylBond.c:1383:25: warning: variable 'h_scale' set but not used [-Wunused-but-set-variable] float radius, transp, h_scale; ^ layer2/RepCylBond.c:1383:17: warning: variable 'transp' set but not used [-Wunused-but-set-variable] float radius, transp, h_scale; ^ layer2/RepCylBond.c:1383:9: warning: variable 'radius' set but not used [-Wunused-but-set-variable] float radius, transp, h_scale; ^ layer2/RepCylBond.c:1380:10: warning: variable 'ord' set but not used [-Wunused-but-set-variable] int a, ord, a1, a2, stick_color, c1, c2, s1, s2, half_bonds, hide_long = false; ^ layer2/RepCylBond.c: In function 'RepCylBondNew': layer2/RepCylBond.c:1543:16: warning: variable 'v_size' set but not used [-Wunused-but-set-variable] unsigned int v_size, vr_size; ^ layer2/RepCylBond.c:1536:7: warning: variable 'stick_round_nub' set but not used [-Wunused-but-set-variable] int stick_round_nub; ^ layer2/RepCylBond.c: At top level: layer2/RepCylBond.c:2363:13: warning: 'subdivide' defined but not used [-Wunused-function] static void subdivide(int n, float *x, float *y) ^ layer2/RepMesh.c: In function 'RepMeshNew': layer2/RepMesh.c:1175:8: warning: 'field' may be used uninitialized in this function [-Wmaybe-uninitialized] if (field) ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectDist.c -o build/temp.linux-armv7l-2.7/layer2/ObjectDist.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectDist.c: In function 'ObjectDistGetDistSetFromM4XBond': layer2/ObjectDist.c:187:25: warning: variable 'dist' set but not used [-Wunused-but-set-variable] float *vv0, *vv1, dist; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/Sculpt.c -o build/temp.linux-armv7l-2.7/layer2/Sculpt.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDistLabel.c -o build/temp.linux-armv7l-2.7/layer2/RepDistLabel.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepDistLabel.c: In function 'RepDistLabelNew': layer2/RepDistLabel.c:404:24: warning: variable 'v6' set but not used [-Wunused-but-set-variable] float *v4, *v5, *v6; ^ layer2/RepDistLabel.c:404:19: warning: variable 'v5' set but not used [-Wunused-but-set-variable] float *v4, *v5, *v6; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepEllipsoid.c -o build/temp.linux-armv7l-2.7/layer2/RepEllipsoid.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Executive.c -o build/temp.linux-armv7l-2.7/layer3/Executive.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepNonbondedSphere.c -o build/temp.linux-armv7l-2.7/layer2/RepNonbondedSphere.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepNonbondedSphere.c: In function 'RepNonbondedSphereRender': layer2/RepNonbondedSphere.c:197:25: warning: variable 'use_default_shader' set but not used [-Wunused-but-set-variable] short use_shader, use_default_shader, use_sphere_shader, generate_shader_cgo = 0, use_display_lists = 0; ^ layer3/Executive.c: In function 'ExecutiveGetHistogram': layer3/Executive.c:4512:7: warning: too many arguments for format [-Wformat-extra-args] " GetHistogram-Error: wrong object type.", objName ENDFB(G); ^ In file included from layer0/OOMac.h:21:0, from layer3/Executive.c:24: layer3/Executive.c: In function 'ExecutiveSetSymmetry': layer3/Executive.c:5899:19: warning: assignment makes integer from pointer without a cast [-Wint-conversion] ok_assert(1, ok = symmetry); ^ layer0/Err.h:32:31: note: in definition of macro 'ok_assert' #define ok_assert(x, c) {if(!(c)) ok_raise(x);} ^ layer3/Executive.c: In function 'ExecutiveMapSet': layer3/Executive.c:6547:21: warning: variable 'tmp' set but not used [-Wunused-but-set-variable] float tmp[3]; ^ layer3/Executive.c: In function 'ExecutiveSculptIterate': layer3/Executive.c:7022:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer3/Executive.c: In function 'ExecutiveRemoveAtoms': layer3/Executive.c:9382:7: warning: variable 'flag' set but not used [-Wunused-but-set-variable] int flag = false; ^ layer3/Executive.c: In function 'ExecutiveIterateList': layer3/Executive.c:10699:14: warning: variable 'cs' set but not used [-Wunused-but-set-variable] CoordSet *cs = NULL; ^ layer3/Executive.c: In function 'ExecutiveCenter': layer3/Executive.c:13688:23: warning: variable 'df' set but not used [-Wunused-but-set-variable] float mn[3], mx[3], df[3]; ^ layer3/Executive.c: In function 'ExecutiveRelease': layer3/Executive.c:15726:7: warning: variable 'n' set but not used [-Wunused-but-set-variable] int n; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/DistSet.c -o build/temp.linux-armv7l-2.7/layer2/DistSet.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepWireBond.c -o build/temp.linux-armv7l-2.7/layer2/RepWireBond.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDihedral.c -o build/temp.linux-armv7l-2.7/layer2/RepDihedral.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepDihedral.c: In function 'RepDihedralNew': layer2/RepDihedral.c:527:15: warning: variable 'mod_pos' set but not used [-Wunused-but-set-variable] float mod_pos; ^ layer2/RepDihedral.c:383:37: warning: variable 'v6' set but not used [-Wunused-but-set-variable] float *v1, *v2, *v3, *v4, *v5, *v6; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/GadgetSet.c -o build/temp.linux-armv7l-2.7/layer2/GadgetSet.o -ffast-math -funroll-loops -O3 -fcommon layer2/GadgetSet.c: In function 'GadgetSetFromPyList': layer2/GadgetSet.c:93:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/GadgetSet.c: In function 'GadgetSetRender': layer2/GadgetSet.c:303:13: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer2/GadgetSet.c:290:9: warning: variable 'use_shader' set but not used [-Wunused-but-set-variable] short use_shader; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Seeker.c -o build/temp.linux-armv7l-2.7/layer3/Seeker.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectGroup.c -o build/temp.linux-armv7l-2.7/layer2/ObjectGroup.o -ffast-math -funroll-loops -O3 -fcommon layer3/Seeker.c: In function 'SeekerRefresh': layer3/Seeker.c:505:22: warning: variable 'not_selected' set but not used [-Wunused-but-set-variable] register int not_selected; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepDot.c -o build/temp.linux-armv7l-2.7/layer2/RepDot.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepDot.c: In function 'RepDotRender': layer2/RepDot.c:195:33: warning: "/*" within comment [-Wcomment] /* if(normals) /* NORMALS do not get set for points ^ layer2/RepDot.c:220:6: warning: 'tmpCGO' may be used uninitialized in this function [-Wmaybe-uninitialized] CGOFreeWithoutVBOs(tmpCGO); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepAngle.c -o build/temp.linux-armv7l-2.7/layer2/RepAngle.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepAngle.c: In function 'RepAngleNew': layer2/RepAngle.c:453:15: warning: variable 'mod_pos' set but not used [-Wunused-but-set-variable] float mod_pos; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectAlignment.c -o build/temp.linux-armv7l-2.7/layer2/ObjectAlignment.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Editor.c -o build/temp.linux-armv7l-2.7/layer3/Editor.o -ffast-math -funroll-loops -O3 -fcommon layer3/Editor.c: In function 'EditorDrawDihedral': layer3/Editor.c:113:22: warning: variable 'sele3' set but not used [-Wunused-but-set-variable] int sele0, sele3; ^ layer3/Editor.c:113:15: warning: variable 'sele0' set but not used [-Wunused-but-set-variable] int sele0, sele3; ^ layer3/Editor.c: In function 'EditorAttach': layer3/Editor.c:934:7: warning: variable 'state' set but not used [-Wunused-but-set-variable] int state; ^ layer3/Editor.c: In function 'EditorReplace': layer3/Editor.c:1115:7: warning: variable 'state' set but not used [-Wunused-but-set-variable] int state; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectSurface.c -o build/temp.linux-armv7l-2.7/layer2/ObjectSurface.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectSurface.c: In function 'ObjectSurfaceUpdate': layer2/ObjectSurface.c:498:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/Control.c -o build/temp.linux-armv7l-2.7/layer1/Control.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/PlugIOManager.c -o build/temp.linux-armv7l-2.7/layer3/PlugIOManager.o -ffast-math -funroll-loops -O3 -fcommon layer1/Control.c: In function 'ControlDrag': layer1/Control.c:252:7: warning: variable 'width' set but not used [-Wunused-but-set-variable] int width; ^ layer3/PlugIOManager.c: In function 'PlugIOManagerLoadTraj': layer3/PlugIOManager.c:232:31: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if(stop > 0 && cnt >= stop || max > 0 && ncnt >= max) { ^ layer3/PlugIOManager.c: In function 'PlugIOManagerLoadVol': layer3/PlugIOManager.c:349:17: warning: variable 'isNew' set but not used [-Wunused-but-set-variable] int isNew = false; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/RepSphere.c -o build/temp.linux-armv7l-2.7/layer2/RepSphere.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/Cmd.c -o build/temp.linux-armv7l-2.7/layer4/Cmd.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer1/P.c -o build/temp.linux-armv7l-2.7/layer1/P.o -ffast-math -funroll-loops -O3 -fcommon layer2/RepSphere.c: In function 'RenderSphereMode_Direct': layer2/RepSphere.c:855:13: warning: variable 'last_vdw' set but not used [-Wunused-but-set-variable] float last_vdw = -1.0F; ^ layer2/RepSphere.c: In function 'RepSphereComputeSphereNormals': layer2/RepSphere.c:2176:15: warning: variable 'nbr_flag' set but not used [-Wunused-but-set-variable] register int nbr_flag; ^ layer2/RepSphere.c: In function 'RepSphereNew': layer2/RepSphere.c:2529:17: warning: variable 'ai2' set but not used [-Wunused-but-set-variable] AtomInfoType *ai2; ^ layer4/Cmd.c: In function 'APIEnter': layer4/Cmd.c:131:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " APIEnter-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident() ^ layer4/Cmd.c: In function 'APIEnterBlocked': layer4/Cmd.c:166:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " APIEnterBlocked-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident() ^ layer4/Cmd.c: In function 'APIExit': layer4/Cmd.c:202:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " APIExit-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident() ^ layer4/Cmd.c: In function 'APIExitBlocked': layer4/Cmd.c:212:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " APIExitBlocked-DEBUG: as thread 0x%x.\n", PyThread_get_thread_ident() ^ layer1/P.c: In function 'PLabelExprUsesVariable': layer1/P.c:191:17: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] OrthoLineType buffer; ^ layer4/Cmd.c: In function 'CmdAlign': layer4/Cmd.c:2182:9: warning: variable 'result' set but not used [-Wunused-but-set-variable] float result = -1.0; ^ layer1/P.c: In function 'PLabelAtomAlt': layer1/P.c:343:8: warning: the address of 'tok' will always evaluate as 'true' [-Waddress] if (tok && tok[0]){ ^ layer1/P.c: In function 'PAlterAtomState': layer1/P.c:824:59: warning: variable 'z_id1' set but not used [-Wunused-but-set-variable] PyObject *x_id1, *x_id2 = NULL, *y_id1, *y_id2 = NULL, *z_id1, *z_id2 = NULL; ^ layer1/P.c:824:36: warning: variable 'y_id1' set but not used [-Wunused-but-set-variable] PyObject *x_id1, *x_id2 = NULL, *y_id1, *y_id2 = NULL, *z_id1, *z_id2 = NULL; ^ layer1/P.c:824:13: warning: variable 'x_id1' set but not used [-Wunused-but-set-variable] PyObject *x_id1, *x_id2 = NULL, *y_id1, *y_id2 = NULL, *z_id1, *z_id2 = NULL; ^ layer4/Cmd.c: In function 'Cmd_New': layer4/Cmd.c:4172:11: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ layer1/P.c: In function 'PUnlockAPIAsGlut': layer1/P.c:1467:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident() ^ layer1/P.c: In function 'PUnlockAPIAsGlutNoFlush': layer1/P.c:1481:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " PUnlockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident() ^ layer1/P.c: In function 'PLockAPIAsGlut': layer1/P.c:1532:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] "*PLockAPIAsGlut-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident() ^ layer1/P.c:1544:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] "#PLockAPIAsGlut-DEBUG: acquiring lock as thread 0x%x\n", PyThread_get_thread_ident() ^ layer1/P.c:1562:7: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] "-PLockAPIAsGlut-DEBUG: glut_thread_keep_out 0x%x\n", PyThread_get_thread_ident() ^ layer1/P.c: In function 'PFlush': layer1/P.c:2635:7: warning: suggest parentheses around assignment used as truth value [-Wparentheses] while(size = OrthoCommandOutSize(G)){ ^ layer1/P.c: In function 'PFlushFast': layer1/P.c:2679:3: warning: suggest parentheses around assignment used as truth value [-Wparentheses] while(size = OrthoCommandOutSize(G)){ ^ layer1/P.c:2691:7: warning: format '%x' expects argument of type 'unsigned int', but argument 4 has type 'long int' [-Wformat=] " PFlushFast-DEBUG: executing '%s' as thread 0x%x\n", buffer, ^ layer1/P.c: In function 'PAutoBlock': layer1/P.c:2787:9: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " PAutoBlock-DEBUG: blocked 0x%x (0x%x, 0x%x, 0x%x)\n", ^ layer1/P.c:2796:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " PAutoBlock-DEBUG: 0x%x not found, thus already blocked.\n", ^ layer1/P.c: In function 'PUnblock': layer1/P.c:2817:5: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'long int' [-Wformat=] " PUnblock-DEBUG: entered as thread 0x%x\n", PyThread_get_thread_ident() ^ layer4/Cmd.c: In function 'CmdPNG': layer4/Cmd.c:5964:29: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if(ray || !G->HaveGUI && (!SceneGetCopyType(G) || width || height)) { ^ layer4/Cmd.c: In function 'CmdLoadObject': layer4/Cmd.c:6916:9: warning: variable 'isTmp' set but not used [-Wunused-but-set-variable] int isTmp; ^ layer4/Cmd.c: In function 'CmdLoadCoords': layer4/Cmd.c:7070:33: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] if(!origObj || !origObj->type == cObjectMolecule) { ^ layer4/Cmd.c: In function 'CmdSetObjectColor': layer4/Cmd.c:7870:7: warning: variable 'result' set but not used [-Wunused-but-set-variable] int result = -1; ^ layer2/RepSphere.c: In function 'RepSphereRender': layer2/RepSphere.c:2003:6: warning: 'radius' may be used uninitialized in this function [-Wmaybe-uninitialized] RenderSphereMode_Points(G, I, info, radius, c); ^ layer2/RepSphere.c:2009:6: warning: 'n_quad_verts' may be used uninitialized in this function [-Wmaybe-uninitialized] RenderSphereMode_9(G, I, info, n_quad_verts, &v, radius, c); ^ layer2/RepSphere.c: In function 'RepSphereGenerateGeometryCullForSphere': layer2/RepSphere.c:2356:13: warning: 'v1[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] float v1[3]; ^ layer2/RepSphere.c: In function 'RepSphereNew': layer2/RepSphere.c:2654:7: warning: 'mf' may be used uninitialized in this function [-Wmaybe-uninitialized] RepSphereAddAtomVisInfoToStoredVC(I, obj, cs, state, v, a1, ati1, a, mf, sphere_scale, sphere_color, transp, &variable_alpha, sphere_add); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function 'vtf_parse_atom': contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:234:21: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[16]' [-Wformat=] if (sscanf(s, "%16s %n", &atom.name, &n) < 1) { ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:243:21: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[16]' [-Wformat=] if (sscanf(s, "%16s %n", &atom.type, &n) < 1) { ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:269:16: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[8]' [-Wformat=] if (sscanf(s, "%8s %n", &atom.resname, &n) < 1) { ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:284:21: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[8]' [-Wformat=] if (sscanf(s, "%8s %n", &atom.segid, &n) < 1) { ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:293:21: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[2]' [-Wformat=] if (sscanf(s, "%2s %n", &atom.insertion, &n) < 1) { ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:305:16: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[2]' [-Wformat=] if (sscanf(s, "%2s %n", &atom.chain, &n) < 1) { ^ contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:339:16: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'char (*)[2]' [-Wformat=] if (sscanf(s, "%2s %n", &atom.altloc, &n) < 1) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectSlice.c -o build/temp.linux-armv7l-2.7/layer2/ObjectSlice.o -ffast-math -funroll-loops -O3 -fcommon layer2/ObjectSlice.c: In function 'ObjectSliceStateFromPyList': layer2/ObjectSlice.c:103:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/ObjectSlice.c: In function 'ObjectSliceNewFromPyList': layer2/ObjectSlice.c:172:7: warning: variable 'll' set but not used [-Wunused-but-set-variable] int ll; ^ layer2/ObjectSlice.c: In function 'ObjectSliceUpdate': layer2/ObjectSlice.c:709:7: warning: variable 'ok' set but not used [-Wunused-but-set-variable] int ok = true; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:42:0: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes] static vasp_plugindata_t *vasp_plugindata_malloc() ^ contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_data': contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:238:60: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:283:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_metadata': contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:151:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'open_vaspchgcar_read': contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:72:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:76:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:82:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:93:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:104:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:132:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer3/Selector.c -o build/temp.linux-armv7l-2.7/layer3/Selector.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:42:0: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes] static vasp_plugindata_t *vasp_plugindata_malloc() ^ contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_data': contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:239:60: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_metadata': contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:151:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'open_vaspparchg_read': contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:72:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:76:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:82:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:93:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:104:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:132:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^ layer3/Selector.c: In function 'SelectorGetSpacialMapFromSeleCoord': layer3/Selector.c:1491:23: warning: variable 'ai' set but not used [-Wunused-but-set-variable] AtomInfoType *ai; ^ layer3/Selector.c: In function 'SelectorAssignSS': layer3/Selector.c:2089:11: warning: variable 'c' set but not used [-Wunused-but-set-variable] int c, i, h, k, l; ^ layer2/ObjectSlice.c: In function 'GenerateOutlineOfSlice': layer2/ObjectSlice.c:1120:5: warning: 'origin' may be used uninitialized in this function [-Wmaybe-uninitialized] CGOSphere(cgo, origin, 1.f); ^ layer3/Selector.c: In function 'SelectorGetPairIndices': layer3/Selector.c:3563:23: warning: variable 'ai2' set but not used [-Wunused-but-set-variable] AtomInfoType *ai1, *ai2; ^ layer3/Selector.c:3563:17: warning: variable 'ai1' set but not used [-Wunused-but-set-variable] AtomInfoType *ai1, *ai2; ^ layer3/Selector.c: In function 'SelectorMapMaskVDW': layer3/Selector.c:5356:11: warning: variable 'n2' set but not used [-Wunused-but-set-variable] int n1, n2; ^ layer3/Selector.c: In function 'SelectorSelect0': layer3/Selector.c:8623:15: warning: variable 's' set but not used [-Wunused-but-set-variable] int at, s; ^ layer3/Selector.c:8669:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] b > 2 && b < 5 || ^ layer3/Selector.c:8671:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] b > 18 && b < 32 || ^ layer3/Selector.c:8672:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] b > 36 && b < 51 || ^ layer3/Selector.c:8673:18: warning: suggest parentheses around '&&' within '||' [-Wparentheses] b > 54 && b < 85 || ^ layer3/Selector.c: In function 'SelectorSelect1': layer3/Selector.c:9091:11: warning: variable 'prevmodel' set but not used [-Wunused-but-set-variable] int prevmodel; ^ layer3/Selector.c:9153:11: warning: variable 'prevmodel' set but not used [-Wunused-but-set-variable] int prevmodel; ^ layer3/Selector.c: In function 'SelectorLogic1': layer3/Selector.c:10326:21: warning: variable 'ai' set but not used [-Wunused-but-set-variable] AtomInfoType *ai; ^ layer3/Selector.c: In function 'SelectorEvaluate': layer3/Selector.c:10858:19: warning: variable 'cc2' set but not used [-Wunused-but-set-variable] char *q, *cc1, *cc2; ^ layer3/Selector.c:10857:15: warning: variable 'opFlag2' set but not used [-Wunused-but-set-variable] int opFlag, opFlag2, maxLevel; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40:0: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes] static vasp_plugindata_t *vasp_plugindata_malloc() ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:41:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_timestep': contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_structure': contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'open_vaspposcar_read': contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:70:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:74:27: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectCallback.c -o build/temp.linux-armv7l-2.7/layer2/ObjectCallback.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer2/ObjectCGO.c -o build/temp.linux-armv7l-2.7/layer2/ObjectCGO.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'read_molden_rundata': contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:585:25: warning: variable 'hessian_data' set but not used [-Wunused-but-set-variable] molfile_qm_hessian_t *hessian_data; ^ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'get_basis': contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:828:36: warning: unused variable 's_coeff2' [-Wunused-variable] char s_expon[128], s_coeff1[128], s_coeff2[128]; ^ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:828:21: warning: unused variable 's_coeff1' [-Wunused-variable] char s_expon[128], s_coeff1[128], s_coeff2[128]; ^ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:828:7: warning: unused variable 's_expon' [-Wunused-variable] char s_expon[128], s_coeff1[128], s_coeff2[128]; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:37:0: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'get_pte_mass' defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'get_pte_vdw_radius' defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:38:0: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:706:12: warning: 'symmetry_expand' defined but not used [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1001:12: warning: 'have_keyline' defined but not used [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1072:13: warning: 'thisline' defined but not used [-Wunused-function] static void thisline(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1092:13: warning: 'whereami' defined but not used [-Wunused-function] static void whereami(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:485:13: warning: 'replace_wavefunction' defined but not used [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:502:13: warning: 'del_wavefunction' defined but not used [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:580:13: warning: 'print_matrix4' defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'eatline': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'open_molden_read': contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:213:11: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, "%d", &natm); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function 'open_namdbin_read': contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:70:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&filen, sizeof(namdbin_int32), 1, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40:0: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes] static vasp_plugindata_t *vasp_plugindata_malloc() ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:41:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_timestep': contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:240:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:243:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_structure': contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:205:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'open_vaspoutcar_read': contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:88:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function 'open_binpos_read': contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(magicchar,sizeof(char),4,fd); ^ contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&igarb,sizeof(int),1,fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'have_gamess': contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1101:8: warning: variable 'word' set but not used [-Wunused-but-set-variable] char word[3][BUFSIZ]; ^ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_basis_stats': contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2258:8: warning: variable 'word' set but not used [-Wunused-but-set-variable] char word[7][BUFSIZ]; ^ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_wavefunction': contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:3561:8: warning: variable 'word' set but not used [-Wunused-but-set-variable] char word[6][BUFSIZ]; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160:0: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: At top level: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:890:12: warning: 'iswhiteline' defined but not used [-Wunused-function] static int iswhiteline(char *s) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:896:14: warning: 'strtoupper' defined but not used [-Wunused-function] static char *strtoupper(char *s) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1072:13: warning: 'thisline' defined but not used [-Wunused-function] static void thisline(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1092:13: warning: 'whereami' defined but not used [-Wunused-function] static void whereami(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:580:13: warning: 'print_matrix4' defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1023:12: warning: 'fpexpftoc' defined but not used [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'get_pte_mass' defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'get_pte_vdw_radius' defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:997:13: warning: 'print_input_data' defined but not used [-Wunused-function] static void print_input_data(qmdata_t *data) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160:0: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'eatline': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_timestep': contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:420:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(fbuffer, 1024, data->file); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: In function 'write_psf_structure': contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:652:19: warning: variable 'atomname' set but not used [-Wunused-but-set-variable] const char *atomname; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28:0, from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:29: contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: At top level: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'swap8_aligned' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:29:0: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'fort_eat_recmark' defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'fort_get_endian_reclen' defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: 'fortread_4' defined but not used [-Wunused-function] static int fortread_4(void *dest, int n, int swap, FILE *fd) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/PopUp.c -o build/temp.linux-armv7l-2.7/layer4/PopUp.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function 'get_atom_radius': contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable 'type' set but not used [-Wunused-but-set-variable] char *name, *type; ^ contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable 'name' set but not used [-Wunused-but-set-variable] char *name, *type; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/Menu.c -o build/temp.linux-armv7l-2.7/layer4/Menu.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40:0: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes] static vasp_plugindata_t *vasp_plugindata_malloc() ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:41:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'read_vaspxdatcar_timestep': contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:284:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'read_vaspxdatcar_structure': contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:229:27: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 4; ++i) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:234:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:238:32: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:253:44: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 10 - data->version; ++i) fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'open_vaspxdatcar_read': contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:90:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:93:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:98:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:112:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:122:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer4/Export.c -o build/temp.linux-armv7l-2.7/layer4/Export.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer5/main.c -o build/temp.linux-armv7l-2.7/layer5/main.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c: In function 'read_js_structure': contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:403:16: warning: unused variable 'bszmask' [-Wunused-variable] fio_size_t bszmask; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/hash.h:37:0, from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:87: contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c: At top level: contrib/uiuc/plugins/molfile_plugin/src/hash.c:183:21: warning: 'hash_delete' defined but not used [-Wunused-function] VMDEXTERNSTATIC int hash_delete(hash_t *tptr, const char *key) { ^ contrib/uiuc/plugins/molfile_plugin/src/hash.c:270:24: warning: 'hash_stats' defined but not used [-Wunused-function] VMDEXTERNSTATIC char * hash_stats(hash_t *tptr) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:88:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer5/TestPyMOL.c -o build/temp.linux-armv7l-2.7/layer5/TestPyMOL.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -ffast-math -funroll-loops -O3 -fcommon layer5/TestPyMOL.c: In function 'get_st': layer5/TestPyMOL.c:76:25: warning: variable 'p' set but not used [-Wunused-but-set-variable] char *result = NULL, *p; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51:0: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:468:12: warning: 'fio_read_int32' defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:472:12: warning: 'fio_write_str' defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c layer5/PyMOL.c -o build/temp.linux-armv7l-2.7/layer5/PyMOL.o -ffast-math -funroll-loops -O3 -fcommon layer5/PyMOL.c: In function 'PyMOL_CmdGetNames': layer5/PyMOL.c:4588:15: warning: variable 'arg' set but not used [-Wunused-but-set-variable] char *res, *arg; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:43:0: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:706:12: warning: 'symmetry_expand' defined but not used [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:830:13: warning: 'eatline' defined but not used [-Wunused-function] static void eatline(FILE * fd, int n) ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:841:13: warning: 'eatwhitelines' defined but not used [-Wunused-function] static void eatwhitelines(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:890:12: warning: 'iswhiteline' defined but not used [-Wunused-function] static int iswhiteline(char *s) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:896:14: warning: 'strtoupper' defined but not used [-Wunused-function] static char *strtoupper(char *s) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:957:12: warning: 'goto_keyline' defined but not used [-Wunused-function] static int goto_keyline(FILE *file, ...) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1001:12: warning: 'have_keyline' defined but not used [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1072:13: warning: 'thisline' defined but not used [-Wunused-function] static void thisline(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1092:13: warning: 'whereami' defined but not used [-Wunused-function] static void whereami(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:433:18: warning: 'init_qmdata' defined but not used [-Wunused-function] static qmdata_t* init_qmdata(qmdata_t *data) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:466:27: warning: 'add_wavefunction' defined but not used [-Wunused-function] static qm_wavefunction_t* add_wavefunction(qm_timestep_t *ts) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:485:13: warning: 'replace_wavefunction' defined but not used [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:502:13: warning: 'del_wavefunction' defined but not used [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:535:13: warning: 'angular_momentum_expon' defined but not used [-Wunused-function] static void angular_momentum_expon(int *ang_mom_expon, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:580:13: warning: 'print_matrix4' defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1023:12: warning: 'fpexpftoc' defined but not used [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'int read_dsn6_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(brick, sizeof(char), 512, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'void* open_dsn6_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:43: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(fileHeader, sizeof(short), 19, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:63:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: 'void swap4_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:33:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function 'void* open_fs4_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:47:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:48:0: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: 'void strnwscpy(char*, const char*, int)' defined but not used [-Wunused-function] static void strnwscpy(char *target, const char *source, const int len) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function 'void eatline(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:234:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function 'void* open_xsf_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:405:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:439:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:441:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:443:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:445:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:447:43: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:467:45: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:504:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -ffast-math -funroll-loops -O3 -fcommon In file included from contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:37:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'int get_pte_idx_from_string(const char*)' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47:0: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:44:27: warning: function declaration isn't a prototype [-Wstrict-prototypes] static vasp_plugindata_t *vasp_plugindata_malloc() ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:48:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function 'read_vaspxml_structure': contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:140:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:145:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function 'open_vaspxml_read': contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:87:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:93:8: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function 'void* open_grid_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:40: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:59:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:60:0: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'int fort_eat_recmark(FILE*, int)' defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'int fort_get_endian_reclen(int, int, int, int*, int*)' defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: 'void strnwscpy(char*, const char*, int)' defined but not used [-Wunused-function] static void strnwscpy(char *target, const char *source, const int len) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/hash.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function 'open_rst_read': contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:43:11: warning: variable 'timesteprst' set but not used [-Wunused-but-set-variable] double timesteprst; ^ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:57:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(title, 82, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:60:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 82, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In member function 'bool desres::molfile::Timekeys::init(const string&)': contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:486:71: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] fprintf(stderr, "non-constant framesize at frame %ld\n", i); ^ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:488:48: warning: format '%d' expects argument of type 'int', but argument 2 has type 'uint64_t {aka long long unsigned int}' [-Wformat=] keys[i].size(), m_framesize); ^ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:488:48: warning: format '%d' expects argument of type 'int', but argument 3 has type 'uint64_t {aka long long unsigned int}' [-Wformat=] contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:494:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] "non-constant time interval at frame %ld\n", i); ^ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:499:67: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t {aka unsigned int}' [-Wformat=] fprintf(stderr, "unexpected offset for frame %ld\n", i); ^ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'int handle_wrapped_v2({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1302:28: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t {aka long long unsigned int}' [-Wformat=] 3*natoms, pos.count); ^ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1311:30: warning: format '%ld' expects argument of type 'long int', but argument 4 has type 'uint64_t {aka long long unsigned int}' [-Wformat=] 3*natoms, vel.count); ^ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'int handle_wrapped_v1({anonymous}::BlobMap&, uint32_t, bool, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1573:34: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'uint64_t {aka long long unsigned int}' [-Wformat=] velblob.count, 3*natoms); ^ contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c: In function 'write_crd_timestep': contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c:167:6: warning: 'lfdone' may be used uninitialized in this function [-Wmaybe-uninitialized] if (!lfdone) ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -ffast-math -funroll-loops -O3 -fcommon contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_timestep': contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_structure': contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'open_car_read': contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function 'void line3(FILE*, GRASSP*)': contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(line3, 1, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)': contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:29: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:50: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(vertex, 3 * sizeof(float), nvert, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:50: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(access, 3 * sizeof(float), nvert, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:50: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(normal, 3 * sizeof(float), nvert, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:57: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(triangle, 3 * sizeof(int), ntriangles, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:56: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(properties, 3 * sizeof(float), nvert, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:60: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(striangle, sizeof(short), 3 * ntriangles, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] TRASH; ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:56: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(properties, sizeof(float), 3 * nvert, infile); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_bonds_aux(void*, int*, int**, int**, float**)': contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_structure(void*, int*, molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'void* open_bgf_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mmcif.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp: In function 'int read_mmcif_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp:85:14: warning: unused variable 'data' [-Wunused-variable] mmcifdata *data = (mmcifdata *)mydata; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp:64:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'const char* get_pte_label(int)' defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'float get_pte_mass(int)' defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'float get_pte_vdw_radius(int)' defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'int get_pte_idx(const char*)' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'int get_pte_idx_from_string(const char*)' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ contrib/uiuc/plugins/molfile_plugin/src/mmcif.cpp:98:14: warning: 'void* open_mmcif_write(const char*, const char*, int)' defined but not used [-Wunused-function] static void *open_mmcif_write(const char *filename, const char *filetype, ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_bonds_aux(void*, int*, int**, int**, float**)': contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:35: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:41: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_structure(void*, int*, molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'void* open_xbgf_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:22: warning: variable 'o' set but not used [-Wunused-but-set-variable] float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:28: warning: variable 's' set but not used [-Wunused-but-set-variable] float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'int read_uhbd_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:254:66: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (fread(datablock + z*xysize, sizeof(float), xysize, fd) != xysize) { ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:41: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&headersize, sizeof(int), 1, fd); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp: In function 'int read_pbeq_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:262:55: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] printf("pbeqplugin) offset: %d\n", ftell(fd)); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:53:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)': contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24:0: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h: In member function 'int {anonymous}::ReadPARM::readparm(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:53: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Charges[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:444:45: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Masses[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:510:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Rk[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:517:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Req[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:524:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Tk[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:531:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Teq[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:538:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pk[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:545:48: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pn[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:552:51: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Phase[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:559:51: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Solty[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:567:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn1[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:575:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn2[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:756:50: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB12[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:763:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB6[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:771:42: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &H[i]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:854:46: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] &prm->Box[0], &prm->Box[1], &prm->Box[2]); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:869:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] &prm->Xcap, &prm->Ycap, &prm->Zcap); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-armv7l-2.7/modules/cealign/src/ccealignmodule.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:70:0: contrib/uiuc/plugins/molfile_plugin/src/vmddir.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/vmddir.h:137:12: warning: 'int vmd_file_is_executable(const char*)' defined but not used [-Wunused-function] static int vmd_file_is_executable(const char * filename) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: 'void swap4_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function 'int read_ccp4_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:370:57: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( fread(rowdata, sizeof(float), extent[0], fd) != extent[0] ) { ^ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function 'void* open_ccp4_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:183:29: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(symData, 81, fd); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:44:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int count_mdf_bonds(const char*)': contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:135:7: warning: unused variable 'retval' [-Wunused-variable] int retval; ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_bonds(void*, int*, int**, int**, float**, int**, int*, char***)': contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:280:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:299:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:321:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:359:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_structure(void*, int*, molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:225:37: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:243:39: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'void* open_mdf_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:166:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:178:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:185:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function 'int read_edm_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:207:10: warning: unused variable 'l' [-Wunused-variable] int z, l, sentinel, convcnt; ^ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:220:7: warning: unused variable 'leftover' [-Wunused-variable] int leftover = (nperslice - (nlines - 1) * 6); ^ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:270:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 13, edm->fd); ^ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function 'void eatline(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:44:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/hash.h:37:0, from contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:45: contrib/uiuc/plugins/molfile_plugin/src/hash.c: At global scope: contrib/uiuc/plugins/molfile_plugin/src/hash.c:183:21: warning: 'int hash_delete(hash_t*, const char*)' defined but not used [-Wunused-function] VMDEXTERNSTATIC int hash_delete(hash_t *tptr, const char *key) { ^ contrib/uiuc/plugins/molfile_plugin/src/hash.c:270:24: warning: 'char* hash_stats(hash_t*)' defined but not used [-Wunused-function] VMDEXTERNSTATIC char * hash_stats(hash_t *tptr) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:289:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2_bonds_aux(void*, int*, int**, int**, float**)': contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:199:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:209:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2(void*, int*, molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:127:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:138:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'void* open_mol2_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:74:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:81:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_name ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:82:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read the molecule info ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:91:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_type ^ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:28: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read the charge_type ^ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function 'int {anonymous}::write_structure(void*, int, const molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1883:9: warning: unused variable 'last_ctnumber' [-Wunused-variable] int last_ctnumber = -1; ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c build/generated/ShaderText.c -o build/temp.linux-armv7l-2.7/build/generated/ShaderText.o -ffast-math -funroll-loops -O3 -fcommon arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp:51:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function 'void* open_cube_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:32: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, cube->fd); // go on to next line ^ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:351:41: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(cube->fd, "%d", &cube->nsets); ^ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:356:35: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(cube->fd, "%d", &orb); ^ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function 'void eatline(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:141:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:42:0: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'int get_pte_idx(const char*)' defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'int get_pte_idx_from_string(const char*)' defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function 'int read_spider_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:277:7: warning: unused variable 'x' [-Wunused-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^ contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:277:10: warning: unused variable 'y' [-Wunused-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^ contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:277:13: warning: unused variable 'z' [-Wunused-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^ contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:49: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(datablock, total * sizeof(float), 1, fd); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:36:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp: In function 'int read_parm7_structure(void*, int*, molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:76:30: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); // format ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:25:0: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_atoms(const char*, int, molfile_atom_t*, FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:202:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_atype(const char*, int, molfile_atom_t*, FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:254:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_resnames(const char*, int, char*, FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:272:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int parse_parm7_respointers(const char*, int, molfile_atom_t*, int, const char*, FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:286:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " %d", &cur); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'parmstruct* read_parm7_header(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:365:25: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sdum, 512, file); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:379:46: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(prm->title, sizeof(prm->title), file); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:407:36: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(sdum, sizeof(sdum), file); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:422:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] &prm->Jparm, &prm->Nparm); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:426:34: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] &prm->Natyp, &prm->Nphb); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:429:49: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] &prm->IfBox, &prm->Nmxrs, &prm->IfCap); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:431:36: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file,"%8d",&prm->Numextra); //BB ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function 'int read_parm7_flag(FILE*, const char*, const char*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:78:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:86:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ^ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:96:28: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'int read_plt_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:143:51: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if ( fread(datablock, sizeof(float), ndata, fd) != ndata ) { ^ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'void* open_plt_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:39: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(intHeader, sizeof(int), 5, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:43: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(floatHeader, sizeof(float), 6, fd); ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42:0: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'void swap8_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ In file included from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30:0: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function 'int mdio_readline(md_file*, char*, int, int)': contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:22: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets(buf, n, mf->f); ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function 'int xtc_3dfcoord(md_file*, float*, int*, float*)': contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1831:32: warning: 'smallidx' may be used uninitialized in this function [-Wmaybe-uninitialized] small = xtc_magicints[smallidx] / 2; ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1816:36: warning: '*((void*)& maxint +4)' may be used uninitialized in this function [-Wmaybe-uninitialized] sizeint[1] = maxint[1] - minint[1]+1; ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1815:36: warning: 'maxint' may be used uninitialized in this function [-Wmaybe-uninitialized] sizeint[0] = maxint[0] - minint[0]+1; ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1861:28: warning: '*((void*)& minint +8)' may be used uninitialized in this function [-Wmaybe-uninitialized] thiscoord[2] += minint[2]; ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1860:28: warning: '*((void*)& minint +4)' may be used uninitialized in this function [-Wmaybe-uninitialized] thiscoord[1] += minint[1]; ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1859:28: warning: 'minint' may be used uninitialized in this function [-Wmaybe-uninitialized] thiscoord[0] += minint[0]; ^ contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:1817:36: warning: '*((void*)& maxint +8)' may be used uninitialized in this function [-Wmaybe-uninitialized] sizeint[2] = maxint[2] - minint[2]+1; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:48:0, from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'void swap2_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'void swap4_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'void swap8_unaligned(void*, long int)' defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'void swap2_aligned(void*, long int)' defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -D_PYMOL_LIBPNG -D_PYMOL_INLINE -D_PYMOL_OPENGL_SHADERS -D_PYMOL_CGO_DRAWARRAYS -D_PYMOL_CGO_DRAWBUFFERS -D_PYMOL_GL_CALLLISTS -D_PYMOL_VMD_PLUGINS -D_PYMOL_FREETYPE -DNO_MMLIBS -D_CGO_DRAWARRAYS -DOPENGL_ES_2 -D_PYMOL_NUMPY -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Imodules/cealign/src/tnt -Ibuild/generated -Icontrib/uiuc/plugins/include -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/python2.7 -c contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -ffast-math -funroll-loops -O3 -fcommon cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'int read_brix_data(void*, int, float*, float*)': contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:44: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(brick, sizeof(char), 512, fd); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'void* open_brix_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:29: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%3s", keyWord); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:62: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:62: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:65: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:110:74: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:39: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &prod); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:39: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &plus); ^ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:40: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &sigma); ^ c++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/ov/src/OVContext.o build/temp.linux-armv7l-2.7/ov/src/OVLexicon.o build/temp.linux-armv7l-2.7/ov/src/OVHeap.o build/temp.linux-armv7l-2.7/ov/src/ov_utility.o build/temp.linux-armv7l-2.7/ov/src/OVOneToAny.o build/temp.linux-armv7l-2.7/ov/src/OVHeapArray.o build/temp.linux-armv7l-2.7/ov/src/OVRandom.o build/temp.linux-armv7l-2.7/ov/src/OVOneToOne.o build/temp.linux-armv7l-2.7/layer0/Map.o build/temp.linux-armv7l-2.7/layer0/MyPNG.o build/temp.linux-armv7l-2.7/layer0/Word.o build/temp.linux-armv7l-2.7/layer0/Raw.o build/temp.linux-armv7l-2.7/layer0/Match.o build/temp.linux-armv7l-2.7/layer0/Debug.o build/temp.linux-armv7l-2.7/layer0/Pixmap.o build/temp.linux-armv7l-2.7/layer0/os_gl.o build/temp.linux-armv7l-2.7/layer0/Triangle.o build/temp.linux-armv7l-2.7/layer0/MemoryCache.o build/temp.linux-armv7l-2.7/layer0/Tracker.o build/temp.linux-armv7l-2.7/layer0/Tetsurf.o build/temp.linux-armv7l-2.7/layer0/Crystal.o build/temp.linux-armv7l-2.7/layer0/MemoryDebug.o build/temp.linux-armv7l-2.7/layer0/Err.o build/temp.linux-armv7l-2.7/layer0/Queue.o build/temp.linux-armv7l-2.7/layer0/Parse.o build/temp.linux-armv7l-2.7/layer0/Sphere.o build/temp.linux-armv7l-2.7/layer0/Isosurf.o build/temp.linux-armv7l-2.7/layer0/Deferred.o build/temp.linux-armv7l-2.7/layer0/Block.o build/temp.linux-armv7l-2.7/layer0/Util.o build/temp.linux-armv7l-2.7/layer0/Feedback.o build/temp.linux-armv7l-2.7/layer0/Vector.o build/temp.linux-armv7l-2.7/layer0/Texture.o build/temp.linux-armv7l-2.7/layer0/Field.o build/temp.linux-armv7l-2.7/layer0/Matrix.o build/temp.linux-armv7l-2.7/layer0/ShaderMgr.o build/temp.linux-armv7l-2.7/layer1/PConv.o build/temp.linux-armv7l-2.7/layer1/Basis.o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel10.o build/temp.linux-armv7l-2.7/layer1/Ray.o build/temp.linux-armv7l-2.7/layer1/Symmetry.o build/temp.linux-armv7l-2.7/layer1/Setting.o build/temp.linux-armv7l-2.7/layer1/Wizard.o build/temp.linux-armv7l-2.7/layer1/Font.o build/temp.linux-armv7l-2.7/layer1/TypeFace.o build/temp.linux-armv7l-2.7/layer1/Character.o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel18.o build/temp.linux-armv7l-2.7/layer1/Ortho.o build/temp.linux-armv7l-2.7/layer1/Seq.o build/temp.linux-armv7l-2.7/layer1/PyMOLObject.o build/temp.linux-armv7l-2.7/layer1/Movie.o build/temp.linux-armv7l-2.7/layer1/View.o build/temp.linux-armv7l-2.7/layer1/Extrude.o build/temp.linux-armv7l-2.7/layer1/FontGLUTHel12.o build/temp.linux-armv7l-2.7/layer1/ButMode.o build/temp.linux-armv7l-2.7/layer1/Pop.o build/temp.linux-armv7l-2.7/layer1/Rep.o build/temp.linux-armv7l-2.7/layer1/FontGLUT9x15.o build/temp.linux-armv7l-2.7/layer1/ScrollBar.o build/temp.linux-armv7l-2.7/layer1/FontGLUT8x13.o build/temp.linux-armv7l-2.7/layer1/Shaker.o build/temp.linux-armv7l-2.7/layer1/CGO.o build/temp.linux-armv7l-2.7/layer1/FontGLUT.o build/temp.linux-armv7l-2.7/layer1/Color.o build/temp.linux-armv7l-2.7/layer1/Scene.o build/temp.linux-armv7l-2.7/layer1/FontType.o build/temp.linux-armv7l-2.7/layer1/Text.o build/temp.linux-armv7l-2.7/layer1/Control.o build/temp.linux-armv7l-2.7/layer1/P.o build/temp.linux-armv7l-2.7/layer2/ObjectSlice.o build/temp.linux-armv7l-2.7/layer2/ObjectCallback.o build/temp.linux-armv7l-2.7/layer2/ObjectCGO.o build/temp.linux-armv7l-2.7/layer2/RepDistDash.o build/temp.linux-armv7l-2.7/layer2/CoordSet.o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule.o build/temp.linux-armv7l-2.7/layer2/Sculpt.o build/temp.linux-armv7l-2.7/layer2/RepDihedral.o build/temp.linux-armv7l-2.7/layer2/GadgetSet.o build/temp.linux-armv7l-2.7/layer2/ObjectGroup.o build/temp.linux-armv7l-2.7/layer2/RepDot.o build/temp.linux-armv7l-2.7/layer2/RepAngle.o build/temp.linux-armv7l-2.7/layer2/ObjectAlignment.o build/temp.linux-armv7l-2.7/layer2/ObjectSurface.o build/temp.linux-armv7l-2.7/layer2/RepSphere.o build/temp.linux-armv7l-2.7/layer2/ObjectVolume.o build/temp.linux-armv7l-2.7/layer2/AtomInfo.o build/temp.linux-armv7l-2.7/layer2/RepSurface.o build/temp.linux-armv7l-2.7/layer2/VFont.o build/temp.linux-armv7l-2.7/layer2/ObjectMolecule2.o build/temp.linux-armv7l-2.7/layer2/RepMesh.o build/temp.linux-armv7l-2.7/layer2/ObjectDist.o build/temp.linux-armv7l-2.7/layer2/RepDistLabel.o build/temp.linux-armv7l-2.7/layer2/RepEllipsoid.o build/temp.linux-armv7l-2.7/layer2/RepNonbondedSphere.o build/temp.linux-armv7l-2.7/layer2/DistSet.o build/temp.linux-armv7l-2.7/layer2/RepWireBond.o build/temp.linux-armv7l-2.7/layer2/ObjectGadgetRamp.o build/temp.linux-armv7l-2.7/layer2/RepRibbon.o build/temp.linux-armv7l-2.7/layer2/RepCartoon.o build/temp.linux-armv7l-2.7/layer2/ObjectGadget.o build/temp.linux-armv7l-2.7/layer2/RepLabel.o build/temp.linux-armv7l-2.7/layer2/SculptCache.o build/temp.linux-armv7l-2.7/layer2/RepNonbonded.o build/temp.linux-armv7l-2.7/layer2/ObjectMap.o build/temp.linux-armv7l-2.7/layer2/ObjectMesh.o build/temp.linux-armv7l-2.7/layer2/RepCylBond.o build/temp.linux-armv7l-2.7/layer3/Executive.o build/temp.linux-armv7l-2.7/layer3/Selector.o build/temp.linux-armv7l-2.7/layer3/Seeker.o build/temp.linux-armv7l-2.7/layer3/Editor.o build/temp.linux-armv7l-2.7/layer3/PlugIOManager.o build/temp.linux-armv7l-2.7/layer4/Cmd.o build/temp.linux-armv7l-2.7/layer4/PopUp.o build/temp.linux-armv7l-2.7/layer4/Menu.o build/temp.linux-armv7l-2.7/layer4/Export.o build/temp.linux-armv7l-2.7/layer5/main.o build/temp.linux-armv7l-2.7/layer5/TestPyMOL.o build/temp.linux-armv7l-2.7/layer5/PyMOL.o build/temp.linux-armv7l-2.7/modules/cealign/src/ccealignmodule.o build/temp.linux-armv7l-2.7/build/generated/ShaderText.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/hash.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mmcif.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o build/temp.linux-armv7l-2.7/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -lpng -lfreetype -lGLEW -lGL -lGLU -lglut -o build/lib.linux-armv7l-2.7/pymol/_cmd.so building 'chempy.champ._champ' extension creating build/temp.linux-armv7l-2.7/contrib/champ arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/strblock.c -o build/temp.linux-armv7l-2.7/contrib/champ/strblock.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/err2.c -o build/temp.linux-armv7l-2.7/contrib/champ/err2.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/feedback2.c -o build/temp.linux-armv7l-2.7/contrib/champ/feedback2.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/os_memory.c -o build/temp.linux-armv7l-2.7/contrib/champ/os_memory.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/list.c -o build/temp.linux-armv7l-2.7/contrib/champ/list.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/chiral.c -o build/temp.linux-armv7l-2.7/contrib/champ/chiral.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/champ.c -o build/temp.linux-armv7l-2.7/contrib/champ/champ.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/sort.c -o build/temp.linux-armv7l-2.7/contrib/champ/sort.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/vla.c -o build/temp.linux-armv7l-2.7/contrib/champ/vla.o arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -fPIC -Icontrib/champ -I/usr/include/python2.7 -c contrib/champ/champ_module.c -o build/temp.linux-armv7l-2.7/contrib/champ/champ_module.o contrib/champ/champ.c: In function 'ChampSmiToPat': contrib/champ/champ.c:5004:9: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'int' [-Wformat=] " champ: error parsing smiles string at '%c' (char %ld) in\n champ: '%s'\n",*c,c-orig_c,orig_c ^ arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wdate-time -D_FORTIFY_SOURCE=2 -g -fstack-protector-strong -Wformat -Werror=format-security build/temp.linux-armv7l-2.7/contrib/champ/strblock.o build/temp.linux-armv7l-2.7/contrib/champ/err2.o build/temp.linux-armv7l-2.7/contrib/champ/feedback2.o build/temp.linux-armv7l-2.7/contrib/champ/os_memory.o build/temp.linux-armv7l-2.7/contrib/champ/list.o build/temp.linux-armv7l-2.7/contrib/champ/chiral.o build/temp.linux-armv7l-2.7/contrib/champ/champ.o build/temp.linux-armv7l-2.7/contrib/champ/sort.o build/temp.linux-armv7l-2.7/contrib/champ/vla.o build/temp.linux-armv7l-2.7/contrib/champ/champ_module.o -o build/lib.linux-armv7l-2.7/chempy/champ/_champ.so make[1]: Leaving directory '/«PKGBUILDDIR»' debian/rules override_dh_auto_test make[1]: Entering directory '/«PKGBUILDDIR»' #dh_auto_test chmod +x test/pymol-test (cd test && python run) run_tests: C0001quit... run_tests: C0001quit.log DIFFERS over about 4 lines: ['1,8d0\n', '< PyMOL>quit\n', '< ================================= HEAP =================================\n', '< OVHeap: Summary: Blocks expected 0, found 0, peaked at 79.\n', '< OVHeap: Summary: Total bytes allocated 0x0 (0.000 MB).\n', '< ========================================================================\n', '< Memory: 0 blocks expected, 0 found, 118 maximum allocated.\n', '< Memory: current memory allocated 0 bytes (0.0 MB).\n', '< PyMOL: normal program termination.\n'] run_tests: C0010hello... run_tests: C0010hello.log DIFFERS over about 1 lines: ['1,2d0\n', '< PyMOL>print "hello"\n', '< hello\n'] run_tests: C0020pdb... run_tests: C0020pdb.log DIFFERS over about 4 lines: ['1,8d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>print cmd.select("(all)")\n', '< 107\n', '< PyMOL>save cmp/C0020pdb.pdb\n', '< Save: wrote "cmp/C0020pdb.pdb".\n'] run_tests: C0020pdb.pdb is missing. run_tests: C0021pdbstr... run_tests: C0021pdbstr.log DIFFERS over about 3 lines: ['1,6d0\n', '< PyMOL>f=open("dat/pept.pdb","rb")\n', '< PyMOL>l=f.read()\n', '< PyMOL>f.close()\n', '< PyMOL>cmd.read_pdbstr(l,"test")\n', '< PyMOL>print cmd.count_atoms()\n', '< 107\n'] run_tests: C0025mol... run_tests: C0025mol.log DIFFERS over about 3 lines: ['1,6d0\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>print cmd.get_names()\n', "< ['small01']\n", '< PyMOL>print cmd.select("(all)")\n', '< 36\n'] run_tests: C0026sdf... run_tests: C0026sdf.log DIFFERS over about 17 lines: ['1,34d0\n', '< PyMOL>load dat/ligs3d.sdf\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>print cmd.get_names()\n', "< ['ligs3d']\n", '< PyMOL>print cmd.select("(all)")\n', '< 337\n', '< PyMOL>set ray_default_renderer=2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>frame 1\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 91 graphics primitives.\n', '< PyMOL>frame 10\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 70 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>show sticks\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 70 graphics primitives.\n', '< PyMOL>unset valence\n', '< Setting: valence set to off.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 42 graphics primitives.\n'] run_tests: C0027mol2... run_tests: C0027mol2.log DIFFERS over about 36 lines: ['1,71d0\n', '< PyMOL>load dat/small03.mol2\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/small03.mol2" loaded as "small03", through state 16.\n', '< PyMOL>print cmd.get_names()\n', "< ['small03']\n", '< PyMOL>print cmd.count_states()\n', '< 16\n', '< PyMOL>print cmd.select("(all)")\n', '< 389\n', '< PyMOL>set ray_default_renderer=2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>frame 1\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 19 graphics primitives.\n', '< PyMOL>frame 10\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 41 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>show sticks\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 41 graphics primitives.\n', '< PyMOL>unset valence\n', '< Setting: valence set to off.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 37 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small03.mol2, discrete=0\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/small03.mol2" loaded as "small03", through state 16.\n', '< PyMOL>count_atoms\n', '< count_atoms: 369 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small03.mol2, multiplex=1\n', '< ExecutiveLoad: loaded 16 objects from "dat/small03.mol2".\n', '< PyMOL>print cmd.get_names()\n', "< ['AGLYSL01', 'AMHTAR01', 'AMPTRB10', 'ARGIND11', 'BAOXLM01', 'BBSPRT10', 'BEVJER10', 'BEWCUB', 'BEWKUJ04', 'BIHKEI01', 'BIPDEJ02', 'BIPJUF10', 'BIPYCL01', 'BITNAT10', 'BIYBIU10', 'BODKOU']\n", '< PyMOL>print cmd.count_states()\n', '< 1\n', '< PyMOL>print cmd.select("(all)")\n', '< 389\n', '< PyMOL>dele all\n', '< PyMOL>set multiplex, 1\n', '< Setting: multiplex set to 1.\n', '< PyMOL>load dat/small03.mol2\n', '< ExecutiveLoad: loaded 16 objects from "dat/small03.mol2".\n', '< PyMOL>print cmd.get_names()\n', "< ['AGLYSL01', 'AMHTAR01', 'AMPTRB10', 'ARGIND11', 'BAOXLM01', 'BBSPRT10', 'BEVJER10', 'BEWCUB', 'BEWKUJ04', 'BIHKEI01', 'BIPDEJ02', 'BIPJUF10', 'BIPYCL01', 'BITNAT10', 'BIYBIU10', 'BODKOU']\n", '< PyMOL>print cmd.count_states()\n', '< 1\n', '< PyMOL>print cmd.select("(all)")\n', '< 389\n'] run_tests: C0030pkl... run_tests: C0030pkl.pdb is missing. run_tests: C0030pkl.log DIFFERS over about 4 lines: ['1,8d0\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>print cmd.select("(all)")\n', '< 198\n', '< PyMOL>save cmp/C0030pkl.pdb\n', '< Save: wrote "cmp/C0030pkl.pdb".\n'] run_tests: C0050multi... run_tests: C0050multi.log DIFFERS over about 4 lines: ['1,8d0\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/tiny.pdb\n', '< CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>load dat/water.pdb\n', '< CmdLoad: "dat/water.pdb" loaded as "water".\n'] run_tests: C0060delete... run_tests: C0060delete.log DIFFERS over about 19 lines: ['1,37d0\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>delete pept\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>delete pept\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>delete pept\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept']\n", '< PyMOL>delete il2\n', '< PyMOL>delete pept\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>delete il2\n', '< PyMOL>delete pept\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>delete il2\n', '< PyMOL>delete pept\n', '< PyMOL>print cmd.get_names()\n', '< []\n'] run_tests: C0070rep... run_tests: C0070rep.log DIFFERS over about 9 lines: ['1,17d0\n', '< PyMOL>load dat/tiny.pdb\n', '< CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>print cmd.get_names()\n', "< ['tiny']\n", '< PyMOL>show sticks\n', '< PyMOL>refresh\n', '< PyMOL>show spheres\n', '< PyMOL>refresh\n', '< PyMOL>show dots\n', '< PyMOL>refresh\n', '< PyMOL>show surface\n', '< PyMOL>refresh\n', '< RepSurface: 318 surface points.\n', '< RepSurface: 632 triangles.\n', '< PyMOL>show mesh\n', '< PyMOL>refresh\n', '< IsosurfVolume: Surface generated using 1747 lines.\n'] run_tests: C0080create... run_tests: C0080create.1.pdb is missing. run_tests: C0080create.2.pdb is missing. run_tests: C0080create.log DIFFERS over about 61 lines: ['1,121d0\n', '< PyMOL>load dat/pept.pkl\n', '< Executive: object "pept" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>create cpy=(pept)\n', '< Selector: found 198 atoms.\n', '< Executive: object "cpy" created.\n', '< PyMOL>create pc1=(resi 1 and pept)\n', '< Selector: found 12 atoms.\n', '< Executive: object "pc1" created.\n', '< PyMOL>create pc2=(resi 2 and pept)\n', '< Selector: found 10 atoms.\n', '< Executive: object "pc2" created.\n', '< PyMOL>create pc3=(resi 3 and pept)\n', '< Selector: found 10 atoms.\n', '< Executive: object "pc3" created.\n', '< PyMOL>create pc4=(resi 4 and pept)\n', '< Selector: found 24 atoms.\n', '< Executive: object "pc4" created.\n', '< PyMOL>create pc5=(resi 5 and pept)\n', '< Selector: found 17 atoms.\n', '< Executive: object "pc5" created.\n', '< PyMOL>create pc6=(resi 6 and pept)\n', '< Selector: found 19 atoms.\n', '< Executive: object "pc6" created.\n', '< PyMOL>create pc7=(resi 7 and pept)\n', '< Selector: found 7 atoms.\n', '< Executive: object "pc7" created.\n', '< PyMOL>create pc8=(resi 8 and pept)\n', '< Selector: found 15 atoms.\n', '< Executive: object "pc8" created.\n', '< PyMOL>create pc9=(resi 9 and pept)\n', '< Selector: found 19 atoms.\n', '< Executive: object "pc9" created.\n', '< PyMOL>create pc10=(resi 10 and pept)\n', '< Selector: found 16 atoms.\n', '< Executive: object "pc10" created.\n', '< PyMOL>create pc11=(resi 11 and pept)\n', '< Selector: found 24 atoms.\n', '< Executive: object "pc11" created.\n', '< PyMOL>create pc12=(resi 12 and pept)\n', '< Selector: found 10 atoms.\n', '< Executive: object "pc12" created.\n', '< PyMOL>create pc13=(resi 13 and pept)\n', '< Selector: found 15 atoms.\n', '< Executive: object "pc13" created.\n', '< PyMOL>create chk = (pc1 | pc2 | pc3 | pc4 | pc5 | pc6 | pc7 | pc8 | pc9 | pc10 | pc11 | pc12 | pc13 )\n', '< Selector: found 198 atoms.\n', '< Executive: object "chk" created.\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'cpy', 'pc1', 'pc2', 'pc3', 'pc4', 'pc5', 'pc6', 'pc7', 'pc8', 'pc9', 'pc10', 'pc11', 'pc12', 'pc13', 'chk']\n", '< PyMOL>delete pc*\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'cpy', 'chk']\n", '< PyMOL>save cmp/C0080create.1.pdb,(cpy and resi 4:6)\n', '< Save: wrote "cmp/C0080create.1.pdb".\n', '< PyMOL>save cmp/C0080create.2.pdb,(chk and resi 4:6)\n', '< Save: wrote "cmp/C0080create.2.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load dat/ligs3d.sdf\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>create cpy,il2\n', '< Selector: found 2084 atoms.\n', '< Executive: object "cpy" created.\n', '< PyMOL>print cmd.count_states("il2")\n', '< 1\n', '< PyMOL>print cmd.count_states("ligs3d")\n', '< 10\n', '< PyMOL>print cmd.count_states("cpy")\n', '< 1\n', '< PyMOL>create tst2,ligs3d, 5, 3\n', '< Selector: found 32 atoms.\n', '< Executive: object "tst2" created.\n', '< PyMOL>print cmd.count_states("tst2")\n', '< 3\n', '< PyMOL>print cmd.count_atoms("tst2 and state 1")\n', '< 0\n', '< PyMOL>print cmd.count_atoms("tst2 and state 2")\n', '< 0\n', '< PyMOL>print cmd.count_atoms("tst2 and state 3")\n', '< 32\n', '< PyMOL>print cmd.count_atoms("ligs3d and state 3")\n', '< 33\n', '< PyMOL>print cmd.count_atoms("ligs3d and state 5")\n', '< 32\n', '< PyMOL>print cmd.count_atoms("tst2 and state 5")\n', '< 0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/ligs3d.sdf\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>create tmp, ligs3d, 0, 4\n', '< Selector: found 337 atoms.\n', '< Executive: object "tmp" created.\n', '< PyMOL>count_states\n', '< cmd.count_states: 13 states.\n', '< PyMOL>disable\n', '< PyMOL>enable tmp\n', '< PyMOL>count_states\n', '< cmd.count_states: 13 states.\n'] run_tests: C0100select... run_tests: C0100select.log DIFFERS over about 90 lines: ['1,180d0\n', '< PyMOL>load dat/tiny.pdb\n', '< CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>print cmd.get_names()\n', "< ['tiny', 'il2']\n", '< PyMOL>select tst = (all)\n', '< Selector: selection "tst" defined with 2121 atoms.\n', '< PyMOL>select tst = (none)\n', '< Selector: selection "tst" defined with 0 atoms.\n', '< PyMOL>select tst = (name c)\n', '< Selector: selection "tst" defined with 129 atoms.\n', '< PyMOL>dele tst\n', '< PyMOL>select tst = (segi e)\n', '< Selector: selection "tst" defined with 9 atoms.\n', '< PyMOL>select tst = (all)\n', '< Selector: selection "tst" defined with 2121 atoms.\n', "< PyMOL>select (segi '')\n", '< Selector: selection "sel01" defined with 2112 atoms.\n', '< PyMOL>select (name ca,c,n,o)\n', '< Selector: selection "sel02" defined with 515 atoms.\n', '< PyMOL>select (n;ca,c)\n', '< Selector: selection "sel03" defined with 257 atoms.\n', '< PyMOL>select (resn pro)\n', '< Selector: selection "sel04" defined with 56 atoms.\n', '< PyMOL>select (r;pro)\n', '< Selector: selection "sel05" defined with 56 atoms.\n', '< PyMOL>select (chain c,e)\n', '< Selector: selection "sel06" defined with 36 atoms.\n', '< PyMOL>select (c;c,e)\n', '< Selector: selection "sel07" defined with 36 atoms.\n', '< PyMOL>select (resi 100)\n', '< Selector: selection "sel08" defined with 15 atoms.\n', '< PyMOL>select (i;100)\n', '< Selector: selection "sel09" defined with 15 atoms.\n', '< PyMOL>select (id 50)\n', '< Selector: selection "sel10" defined with 1 atoms.\n', '< PyMOL>select (byres id 50)\n', '< Selector: selection "sel11" defined with 22 atoms.\n', "< PyMOL>select (alt '')\n", '< Selector: selection "sel12" defined with 2121 atoms.\n', '< PyMOL>select (tiny)\n', '< Selector: selection "sel13" defined with 37 atoms.\n', '< PyMOL>select (tiny or il2)\n', '< Selector: selection "sel14" defined with 2121 atoms.\n', '< PyMOL>select (tiny | il2)\n', '< Selector: selection "sel15" defined with 2121 atoms.\n', '< PyMOL>select (vis)\n', '< Selector: selection "sel16" defined with 2121 atoms.\n', '< PyMOL>hide (tiny)\n', '< PyMOL>select (vis)\n', '< Selector: selection "sel17" defined with 2084 atoms.\n', "< PyMOL>print cmd.get_names('all')\n", "< ['tiny', 'il2', 'tst', 'sel01', 'sel02', 'sel03', 'sel04', 'sel05', 'sel06', 'sel07', 'sel08', 'sel09', 'sel10', 'sel11', 'sel12', 'sel13', 'sel14', 'sel15', 'sel16', 'sel17']\n", '< PyMOL>delete sel*\n', "< PyMOL>print cmd.get_names('all')\n", "< ['tiny', 'il2', 'tst']\n", '< PyMOL>select foo = (name c)\n', '< Selector: selection "foo" defined with 129 atoms.\n', '< PyMOL>select fie = (name n,c)\n', '< Selector: selection "fie" defined with 257 atoms.\n', '< PyMOL>select (foo and not fie)\n', '< Selector: selection "sel18" defined with 0 atoms.\n', '< PyMOL>select (fie &! foo)\n', '< Selector: selection "sel19" defined with 128 atoms.\n', '< PyMOL>select foe = (tiny a; 30)\n', '< Selector: selection "foe" defined with 105 atoms.\n', '< PyMOL>select fum = (il2 and not foe)\n', '< Selector: selection "fum" defined with 1979 atoms.\n', '< PyMOL>select (hydro)\n', '< Selector: selection "sel20" defined with 1075 atoms.\n', '< PyMOL>select (b<30 and b>0.1)\n', '< Selector: selection "sel21" defined with 362 atoms.\n', '< PyMOL>select (q=0.0)\n', '< Selector: selection "sel22" defined with 9 atoms.\n', '< PyMOL>select (q=1.0)\n', '< Selector: selection "sel23" defined with 2112 atoms.\n', '< PyMOL>select (b=0.0)\n', '< Selector: selection "sel24" defined with 1080 atoms.\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>select tst,pept within 5 of tiny\n', '< Selector: selection "tst" defined with 0 atoms.\n', '< PyMOL>select tst,pept within 50 of tiny\n', '< Selector: selection "tst" defined with 67 atoms.\n', '< PyMOL>select tst, pept w. 1 of pept\n', '< Selector: selection "tst" defined with 107 atoms.\n', '< PyMOL>print cmd.select("(none)")\n', '< 0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb,mult\n', '< CmdLoad: "dat/pept.pdb" loaded as "mult".\n', '< PyMOL>load dat/il2.pdb,mult\n', '< CmdLoad: "dat/il2.pdb" appended into object "mult", state 2.\n', '< PyMOL>frame 1\n', '< PyMOL>select tst,mult and present\n', '< Selector: selection "tst" defined with 107 atoms.\n', '< PyMOL>frame 2\n', '< PyMOL>select tst,mult and present\n', '< Selector: selection "tst" defined with 2084 atoms.\n', '< PyMOL>select tst,state 1\n', '< Selector: selection "tst" defined with 107 atoms.\n', '< PyMOL>select tst,state 2\n', '< Selector: selection "tst" defined with 2084 atoms.\n', '< PyMOL>hide\n', '< PyMOL>show sph,name c\n', '< PyMOL>select tst,present and vis\n', '< Selector: selection "tst" defined with 126 atoms.\n', '< PyMOL>frame 1\n', '< PyMOL>select tst,present and vis\n', '< Selector: selection "tst" defined with 13 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>indicate name ca\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 13 atoms\n', '< PyMOL>indicate name *c*\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 69 atoms\n', '< PyMOL>indicate (name *c*,*n*)\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 86 atoms\n', '< PyMOL>indicate (name *c*+*n*)\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 86 atoms\n', '< PyMOL>indicate name *G\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 9 atoms\n', '< PyMOL>indicate */*G\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 9 atoms\n', '< PyMOL>indicate rank -3+5+10-23+7+40-\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 87 atoms\n', '< PyMOL>indicate id -3+5+10-23+7+40-\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 87 atoms\n', '< PyMOL>indicate index -3+5+10-23+7+40-\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 87 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER ENTEROTOXIN 20-MAR-96 1TII\n', '< TITLE ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND 3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND 4 SYNONYM: LT-IIB;\n', '< COMPND 5 ENGINEERED: YES;\n', '< COMPND 6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>indicate A:C+F/10+90+100-/ca+c+n*\n', '< PyMOL>count_atoms indicate\n', '< count_atoms: 435 atoms\n', '< PyMOL>count_atoms 1TII\n', '< count_atoms: 5684 atoms\n', '< PyMOL>count_atoms 1tii\n', '< count_atoms: 5684 atoms\n', '< PyMOL>count_atoms HOH`307/ expand 5\n', '< count_atoms: 12 atoms\n', '< PyMOL>count_atoms a// c//\n', '< count_atoms: 1769 atoms\n', '< PyMOL>count_atoms a// c// d//\n', '< count_atoms: 2509 atoms\n', '< PyMOL>count_atoms (a// c//) d//\n', '< count_atoms: 2509 atoms\n', '< PyMOL>count_atoms a// c//&none\n', '< count_atoms: 1479 atoms\n', '< PyMOL>count_atoms c//&none a//\n', '< count_atoms: 1479 atoms\n', '< PyMOL>count_atoms c//&none (a//&none a//)\n', '< count_atoms: 1479 atoms\n', '< PyMOL>count_atoms (c//&none) a// (a//&none)\n', '< count_atoms: 1479 atoms\n', '< PyMOL>count_atoms (a// (d// c//)) & (e// (b// a//))\n', '< count_atoms: 1479 atoms\n'] run_tests: C0105names... run_tests: C0105names.log DIFFERS over about 27 lines: ['1,54d0\n', '< PyMOL>load dat/names.pdb\n', '< CmdLoad: "dat/names.pdb" loaded as "names".\n', "< PyMOL>select test,name O4'\n", '< Selector: selection "test" defined with 2 atoms.\n', "< PyMOL>select test,*/O4'\n", '< Selector: selection "test" defined with 2 atoms.\n', "< PyMOL>select test,*/O4'+O3'\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,(*/O4',O3')\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name O4'+O3'\n", '< Selector: selection "test" defined with 4 atoms.\n', '< PyMOL>select test,name "O4\'+O3\'"\n', '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name O4'+Na\\+\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,(name Na\\+,O4')\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name Na\\++O4'\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,*/Na\\++O4'\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,*/O4'+O4\n", '< Selector: selection "test" defined with 3 atoms.\n', '< PyMOL>select test,*/O2\\*+O2\n', '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,*/O2\\*+O2'\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name 'O4''\n", '< Selector: selection "test" defined with 2 atoms.\n', '< PyMOL>select test,name "O4\'"+O2\'\n', '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name 'O4''+O2'\n", '< Selector: selection "test" defined with 4 atoms.\n', "< PyMOL>select test,name O4'+C2+C4+Na\\++Cl\\-\n", '< Selector: selection "test" defined with 13 atoms.\n', "< PyMOL>select test,*/O4'+C2+C4+Na\\++Cl\\-\n", '< Selector: selection "test" defined with 13 atoms.\n', "< PyMOL>select test,names////O4'\n", '< Selector: selection "test" defined with 2 atoms.\n', "< PyMOL>select test,names and */O4'+'Na\\+'+'C2'+'C4'\n", '< Selector: selection "test" defined with 12 atoms.\n', "< PyMOL>select test,chain ''\n", '< Selector: selection "test" defined with 0 atoms.\n', "< PyMOL>select test,segi ''\n", '< Selector: selection "test" defined with 86 atoms.\n', "< PyMOL>select test,chain R+''\n", '< Selector: selection "test" defined with 82 atoms.\n', "< PyMOL>select test,chain ''+R\n", '< Selector: selection "test" defined with 82 atoms.\n', '< PyMOL>select test,name Na\\+\n', '< Selector: selection "test" defined with 2 atoms.\n', '< PyMOL>select test,name "Na\\+"\n', '< Selector: selection "test" defined with 2 atoms.\n'] run_tests: C0106order... run_tests: C0106order.log DIFFERS over about 49 lines: ['1,98d0\n', '< PyMOL>order does_not_exist\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *,location=top\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *,location=bottom\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>order *,location=current\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>order pept\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *,location=bottom\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>order *,location=current\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order il2,location=current\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order il2,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept']\n", '< PyMOL>order il2,location=bottom\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'il2']\n", '< PyMOL>order il2 pept\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept']\n", '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'pept', 'small01']\n", '< PyMOL>order small01 pept\n', '< PyMOL>print cmd.get_names()\n', "< ['il2', 'small01', 'pept']\n", '< PyMOL>order small01 pept il2\n', '< PyMOL>print cmd.get_names()\n', "< ['small01', 'pept', 'il2']\n", '< PyMOL>order *\n', '< PyMOL>print cmd.get_names()\n', "< ['small01', 'pept', 'il2']\n", '< PyMOL>create aaa,pept\n', '< Selector: found 107 atoms.\n', '< Executive: object "aaa" created.\n', '< PyMOL>order *,sort=1\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'small01']\n", '< PyMOL>create zzz,pept\n', '< Selector: found 107 atoms.\n', '< Executive: object "zzz" created.\n', '< PyMOL>order *,sort=1\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'small01', 'zzz']\n", '< PyMOL>create pept2, pept\n', '< Selector: found 107 atoms.\n', '< Executive: object "pept2" created.\n', '< PyMOL>create pept1, pept\n', '< Selector: found 107 atoms.\n', '< Executive: object "pept1" created.\n', '< PyMOL>order pept*\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'pept2', 'pept1', 'small01', 'zzz']\n", '< PyMOL>order pept*,sort=1\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'pept', 'pept1', 'pept2', 'small01', 'zzz']\n", '< PyMOL>order pept*,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'pept1', 'pept2', 'aaa', 'il2', 'small01', 'zzz']\n", '< PyMOL>order pept*,location=bottom\n', '< PyMOL>print cmd.get_names()\n', "< ['aaa', 'il2', 'small01', 'zzz', 'pept', 'pept1', 'pept2']\n", '< PyMOL>order aaa,location=bottom\n', '< PyMOL>order zzz,location=top\n', '< PyMOL>print cmd.get_names()\n', "< ['zzz', 'il2', 'small01', 'pept', 'pept1', 'pept2', 'aaa']\n"] run_tests: C0140iterate... run_tests: C0140iterate.log DIFFERS over about 23 lines: ['1,45d0\n', '< PyMOL>load dat/tiny.pdb\n', '< CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>names = []\n', '< PyMOL>iterate (all),names.append(name)\n', '< Iterate: iterated over 37 atoms.\n', '< PyMOL>print names\n', "< ['C', 'O', 'N', 'CA', 'C', 'O', 'CB', 'CG', 'CD', 'HA', '2HB', '3HB', '2HG', '3HG', '2HD', '3HD', 'N', 'CA', 'C', 'O', 'CB', 'OG', 'H', 'HA', '2HB', '3HB', 'HG', 'O', 'O01', 'C02', 'C03', 'C04', 'C05', 'H01', 'H04', 'H05', 'H06']\n", '< PyMOL>bfct = []\n', '< PyMOL>iterate (resn pro),bfct.append(b)\n', '< Iterate: iterated over 14 atoms.\n', '< 50.7800\n', '< 48.1600\n', '< 43.9800\n', '< 44.4900\n', '< 38.5700\n', '< 54.5800\n', '< 46.5900\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', "< PyMOL>iterate (all),resn = 'NON'\n", '< Iterate: iterated over 37 atoms.\n', '< PyMOL>iterate (all),b = b + 10\n', '< Iterate: iterated over 37 atoms.\n', '< PyMOL>bfct = []\n', '< PyMOL>iterate (resn pro),bfct.append(b)\n', '< Iterate: iterated over 14 atoms.\n', '< 50.7800\n', '< 48.1600\n', '< 43.9800\n', '< 44.4900\n', '< 38.5700\n', '< 54.5800\n', '< 46.5900\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n', '< 0.0000\n'] run_tests: C0150alter... run_tests: C0150alter.1.pdb is missing. run_tests: C0150alter.log DIFFERS over about 11 lines: ['1,22d0\n', '< PyMOL>load dat/tiny.pdb\n', '< CmdLoad: "dat/tiny.pdb" loaded as "tiny".\n', '< PyMOL>alter (all),resn = name\n', '< Alter: modified 37 atoms.\n', '< PyMOL>alter (all),b = b + 10\n', '< Alter: modified 37 atoms.\n', '< PyMOL>alter (all),q = 0.95\n', '< Alter: modified 37 atoms.\n', '< PyMOL>alter (all),name = name[0:2]\n', '< Alter: modified 37 atoms.\n', "< PyMOL>alter (het),type = 'ATOM'\n", '< Alter: modified 10 atoms.\n', "< PyMOL>alter (resi 9),type ='HETATM'\n", '< Alter: modified 11 atoms.\n', "< PyMOL>alter (e;c),elem = 'X'\n", '< Alter: modified 13 atoms.\n', '< PyMOL>alter (resi 8),resi=str(int(resi)+10)\n', '< Alter: modified 14 atoms.\n', "< PyMOL>alter (resi 7),alt='B'\n", '< Alter: modified 2 atoms.\n', '< PyMOL>save cmp/C0150alter.1.pdb\n', '< Save: wrote "cmp/C0150alter.1.pdb".\n'] run_tests: C0160get... run_tests: C0160get.log DIFFERS over about 42 lines: ['1,84d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" appended into object "pept", state 2.\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" appended into object "pept", state 3.\n', '< PyMOL>get line_width\n', '< get: line_width = 1.49000\n', '< PyMOL>get line_width,doesnotexist\n', '< SettingGet-Error: object "doesnotexist" not found.\n', '< PyMOL>get line_width,doesnotexist,5\n', '< SettingGet-Error: object "doesnotexist" not found.\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,0\n', '< get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 1.49000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 1.49000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 1.49000 in object pept state 3\n', '< PyMOL>get line_width,pept,4\n', '< SettingGet-Error: object "pept" lacks state 4.\n', '< PyMOL>set line_width,2.0,pept\n', '< Setting: line_width set to 2.00000 in object "pept".\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 2.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 2.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>set line_width,4.0,pept,1\n', '< Setting: line_width set to 4.00000 in object "pept", state 1.\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 2.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>set line_width,6.0,pept,2\n', '< Setting: line_width set to 6.00000 in object "pept", state 2.\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 6.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>unset line_width,pept,2\n', '< Setting: line_width unset in object "pept", state 2.\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 2.00000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 2.00000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 2.00000 in object pept state 3\n', '< PyMOL>unset line_width,pept\n', '< Setting: line_width unset in object "pept".\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 4.00000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 1.49000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 1.49000 in object pept state 3\n', '< PyMOL>unset line_width,pept,1\n', '< Setting: line_width unset in object "pept", state 1.\n', '< PyMOL>get line_width,pept\n', '< get: line_width = 1.49000 in object pept\n', '< PyMOL>get line_width,pept,1\n', '< get: line_width = 1.49000 in object pept state 1\n', '< PyMOL>get line_width,pept,2\n', '< get: line_width = 1.49000 in object pept state 2\n', '< PyMOL>get line_width,pept,3\n', '< get: line_width = 1.49000 in object pept state 3\n'] run_tests: C0170scene... run_tests: C0170scene.log DIFFERS over about 125 lines: ['1,250d0\n', '< PyMOL>scene -10\n', "< Error: unknown scene: '-10'. Choices:\n", '< PyMOL>scene 9999\n', "< Error: unknown scene: '9999'. Choices:\n", '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>scene 1,store\n', '< scene: scene stored as "1".\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>scene 2,store\n', '< scene: scene stored as "2".\n', '< PyMOL>scene 1,recall\n', '< Scene: view updated.\n', '< scene: "1" recalled.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>scene 2\n', '< Scene: view updated.\n', '< scene: "2" recalled.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>dist tst,5/ca,8/ca\n', '< Executive: object "tst" created.\n', '< PyMOL>turn x,5\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.996 0.087 0.000 -0.087 0.996\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>scene 3,store\n', '< scene: scene stored as "3".\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 180 graphics primitives.\n', '< PyMOL>hide dashes,tst\n', '< PyMOL>turn y,5\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 0.996 0.000 -0.087 0.008 0.996 0.087 0.087 -0.087 0.992\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>scene 4,store\n', '< scene: scene stored as "4".\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 172 graphics primitives.\n', '< PyMOL>scene 3\n', '< Scene: view updated.\n', '< scene: "3" recalled.\n', '< PyMOL>disable tst\n', '< PyMOL>turn z,20\n', '< PyMOL>scene 5,store\n', '< scene: scene stored as "5".\n', '< PyMOL>scene 1\n', '< Scene: view updated.\n', '< scene: "1" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>scene 2\n', '< Scene: view updated.\n', '< scene: "2" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>scene 3\n', '< Scene: view updated.\n', '< scene: "3" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.996 0.087 0.000 -0.087 0.996\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 180 graphics primitives.\n', '< PyMOL>scene 4\n', '< Scene: view updated.\n', '< scene: "4" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 0.996 0.000 -0.087 0.008 0.996 0.087 0.087 -0.087 0.992\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 172 graphics primitives.\n', '< PyMOL>scene 5\n', '< Scene: view updated.\n', '< scene: "5" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 0.940 0.342 0.000 -0.341 0.936 0.087 0.030 -0.082 0.996\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>scene 0\n', "< Error: unknown scene: '0'. Choices:\n", '< 1 2 3 4 5\n', '< PyMOL>scene 6\n', "< Error: unknown scene: '6'. Choices:\n", '< 1 2 3 4 5\n', '< PyMOL>scene 1000\n', "< Error: unknown scene: '1000'. Choices:\n", '< 1 2 3 4 5\n', '< PyMOL>scene 4,clear\n', "< scene: '4' deleted.\n", '< PyMOL>scene 4\n', "< Error: unknown scene: '4'. Choices:\n", '< 1 2 3 5\n', '< PyMOL>scene *\n', '< scene: current order:\n', '< 1 2 3 5\n', '< PyMOL>scene *,clear\n', '< PyMOL>scene *\n', '< scene: current order:\n', '< PyMOL>scene 1\n', "< Error: unknown scene: '1'. Choices:\n", '< PyMOL>hide\n', '< PyMOL>show lines\n', '< PyMOL>color red\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>scene 1, store\n', '< scene: scene stored as "1".\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 0 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>show sticks\n', '< PyMOL>color blue\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>scene 2, store\n', '< scene: scene stored as "2".\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 107 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 1\n', '< Scene: view updated.\n', '< scene: "1" recalled.\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 0 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 2\n', '< Scene: view updated.\n', '< scene: "2" recalled.\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 107 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 2,rename,new_key=3\n', "< scene: '2' renamed to '3'.\n", '< PyMOL>scene 1\n', '< Scene: view updated.\n', '< scene: "1" recalled.\n', '< PyMOL>count_atoms rep lines\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep sticks\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 0 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 3\n', '< Scene: view updated.\n', '< scene: "3" recalled.\n', '< PyMOL>count_atoms rep lines\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 107 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 2\n', "< Error: unknown scene: '2'. Choices:\n", '< 1 3\n', '< PyMOL>count_atoms rep lines\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 107 atoms\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 112 graphics primitives.\n', '< PyMOL>scene 3\n', '< Scene: view updated.\n', '< scene: "3" recalled.\n', '< PyMOL>hide\n', '< PyMOL>color green\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>show spheres\n', '< PyMOL>scene auto, update\n', '< scene: scene updated as "3".\n', '< PyMOL>count_atoms rep spheres\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color green\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep lines\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 0 atoms\n', '< PyMOL>scene 1\n', '< Scene: view updated.\n', '< scene: "1" recalled.\n', '< PyMOL>count_atoms rep spheres\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color green\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep lines\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep sticks\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 0 atoms\n', '< PyMOL>scene 3\n', '< Scene: view updated.\n', '< scene: "3" recalled.\n', '< PyMOL>count_atoms rep spheres\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms color green\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms rep lines\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color red\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms rep sticks\n', '< count_atoms: 0 atoms\n', '< PyMOL>count_atoms color blue\n', '< count_atoms: 0 atoms\n'] run_tests: C0180embed... run_tests: C0180embed.log DIFFERS over about 45 lines: ['1,90d0\n', '< PyMOL>load dat/embed01.p1m\n', '< PyMOL>embed peptide\n', '< Embed: read 108 lines.\n', '< PyMOL>load_embedded peptide\n', '< CmdLoad: PDB-string loaded into object "peptide", state 1.\n', '< PyMOL>count_atoms\n', '< count_atoms: 107 atoms\n', '< PyMOL>hide everything, peptide\n', '< PyMOL>show sticks, peptide\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>set ray_default_renderer,2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 207 graphics primitives.\n', '< PyMOL>load dat/embed02.p1m\n', '< PyMOL>embed sm, mol\n', '< Embed: read 78 lines.\n', '< PyMOL>load_embedded sm\n', '< ExecutiveLoad: content loaded into object "sm", through state 1.\n', '< PyMOL>hide everything, sm\n', '< PyMOL>show sticks, sm\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 269 graphics primitives.\n', '< PyMOL>load dat/embed03.p1m\n', '< PyMOL>embed ligands,sdf\n', '< Embed: read 923 lines.\n', '< PyMOL>load_embedded ligands\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: content loaded into object "ligands", through state 10.\n', '< PyMOL>hide everything, ligands\n', '< PyMOL>show sticks, ligands\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>frame 5\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 343 graphics primitives.\n', '< PyMOL>load dat/embed04.p1m\n', '< PyMOL>embed m2, mol2\n', '< Embed: read 963 lines.\n', '< PyMOL>load_embedded m2\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: content loaded into object "m2", through state 16.\n', '< PyMOL>hide everything, m2\n', '< PyMOL>show sticks, m2\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 356 graphics primitives.\n', '< PyMOL>load dat/embed05.p1m\n', '< PyMOL>embed ligand, mol\n', '< Embed: read 77 lines.\n', '< PyMOL>embed protein\n', '< Embed: read 227 lines.\n', '< PyMOL>load_embedded ligand\n', '< ExecutiveLoad: content loaded into object "ligand", through state 1.\n', '< PyMOL>load_embedded protein\n', '< CmdLoad: PDB-string loaded into object "protein", state 1.\n', '< PyMOL>hide lines, ligand\n', '< PyMOL>show sticks, ligand\n', '< PyMOL>set valence\n', '< Setting: valence set to on.\n', '< PyMOL>dist hbond, protein, ligand, mode=2\n', '< Executive: object "hbond" created.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 868 graphics primitives.\n', '< PyMOL>print cmd.get_state()\n', '< 5\n', '< PyMOL>print cmd.get_names()\n', "< ['peptide', 'sm', 'ligands', 'm2', 'ligand', 'protein', 'hbond']\n"] run_tests: C0181embed... run_tests: C0181embed.log DIFFERS over about 10 lines: ['1,20d0\n', '< PyMOL>load dat/embed06.p1m\n', '< PyMOL>embed\n', '< Embed: read 108 lines.\n', '< PyMOL>load_embedded\n', '< CmdLoad: PDB-string loaded into object "embed06", state 1.\n', '< PyMOL>hide\n', '< PyMOL>show surface\n', '< PyMOL>set transparency, 0.5\n', '< Setting: transparency set to 0.50000.\n', '< PyMOL>set surface_color, white\n', '< Setting: surface_color set to white.\n', '< PyMOL>show sticks\n', '< PyMOL>set ray_default_renderer,2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '< RepSurface: 1319 surface points.\n', '< RepSurface: 2634 triangles.\n', '< RayRenderTest: obtained 2800 graphics primitives.\n', '< PyMOL>print cmd.get_names()\n', "< ['embed06']\n"] run_tests: C0200feedback... run_tests: C0200feedback.log DIFFERS over about 127 lines: ['1,253d0\n', '< PyMOL>feedback\n', '< feedback: possible actions: \n', '< set, enable, disable\n', '< feedback: Please specify module names:\n', '< all\n', '< api\n', '< ccmd\n', '< cgo\n', '< cmd\n', '< color\n', '< coordset\n', '< distset\n', '< editor\n', '< executive\n', '< export\n', '< extrude\n', '< feedback\n', '< gadgetset\n', '< isomesh\n', '< isosurface\n', '< main\n', '< map\n', '< match\n', '< matrix\n', '< movie\n', '< mypng\n', '< nag\n', '< object\n', '< objectcallback\n', '< objectcgo\n', '< objectdist\n', '< objectgadget\n', '< objectmap\n', '< objectmesh\n', '< objectmolecule\n', '< objectslice\n', '< objectsurface\n', '< opengl\n', '< ortho\n', '< parser\n', '< python\n', '< raw\n', '< ray\n', '< rep\n', '< repangle\n', '< repcartoon\n', '< repcylbond\n', '< repdihederal\n', '< repdistdash\n', '< repdistlabel\n', '< repdot\n', '< replabel\n', '< repmesh\n', '< repnonbonded\n', '< repnonbondedsphere\n', '< repribbon\n', '< repsphere\n', '< repsurface\n', '< repwirebond\n', '< scene\n', '< sculpt\n', '< selector\n', '< setting\n', '< shaker\n', '< symmetry\n', '< threads\n', '< triangle\n', '< vfont\n', '< feedback: Please specify masks:\n', '< actions\n', '< blather\n', '< debugging\n', '< details\n', '< errors\n', '< everything\n', '< output\n', '< results\n', '< warnings\n', '< PyMOL>feedback ?\n', '< Usage: feedback [ action [, module [, mask ]]]\n', '< PyMOL>feedback enable\n', '< feedback: Please specify module names:\n', '< all\n', '< api\n', '< ccmd\n', '< cgo\n', '< cmd\n', '< color\n', '< coordset\n', '< distset\n', '< editor\n', '< executive\n', '< export\n', '< extrude\n', '< feedback\n', '< gadgetset\n', '< isomesh\n', '< isosurface\n', '< main\n', '< map\n', '< match\n', '< matrix\n', '< movie\n', '< mypng\n', '< nag\n', '< object\n', '< objectcallback\n', '< objectcgo\n', '< objectdist\n', '< objectgadget\n', '< objectmap\n', '< objectmesh\n', '< objectmolecule\n', '< objectslice\n', '< objectsurface\n', '< opengl\n', '< ortho\n', '< parser\n', '< python\n', '< raw\n', '< ray\n', '< rep\n', '< repangle\n', '< repcartoon\n', '< repcylbond\n', '< repdihederal\n', '< repdistdash\n', '< repdistlabel\n', '< repdot\n', '< replabel\n', '< repmesh\n', '< repnonbonded\n', '< repnonbondedsphere\n', '< repribbon\n', '< repsphere\n', '< repsurface\n', '< repwirebond\n', '< scene\n', '< sculpt\n', '< selector\n', '< setting\n', '< shaker\n', '< symmetry\n', '< threads\n', '< triangle\n', '< vfont\n', '< feedback: Please specify masks:\n', '< actions\n', '< blather\n', '< debugging\n', '< details\n', '< errors\n', '< everything\n', '< output\n', '< results\n', '< warnings\n', '< PyMOL>feedback enable, selector\n', '< feedback: Please specify masks:\n', '< actions\n', '< blather\n', '< debugging\n', '< details\n', '< errors\n', '< everything\n', '< output\n', '< results\n', '< warnings\n', '< PyMOL>feedback enable, selector, everything\n', '< PyMOL>feedback enable, repcartoon extrude, everything\n', '< PyMOL>load dat/pept.pdb\n', '< SelectorCreate-Debug: entered...\n', '< SelectorUpdateTableSingleObject-Debug: entered for pept...\n', '< SelectorUpdateTableSingleObject-Debug: leaving...\n', '< Selector: Embedded pept, 107 atoms.\n', '< SelectorCreate: "pept" created with 107 atoms.\n', '< SelectorUpdateTableSingleObject-Debug: entered for pept...\n', '< SelectorUpdateTableSingleObject-Debug: leaving...\n', '< SelectorUpdateTableSingleObject-Debug: entered for pept...\n', '< SelectorUpdateTableSingleObject-Debug: leaving...\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>show cartoon\n', '< SelectorGetTmp-Debug: entered with "all".\n', '< SelectorGetTmp-Debug: leaving with "all".\n', '< PyMOL>refresh\n', '< RepCartoonNew-Debug: entered.\n', '< RepCartoon: found CA in 1; a2 -1\n', '< RepCartoon: found CA in 1; a2 -1\n', '< RepCartoon: found CA in 2; a2 1\n', '< RepCartoon: found CA in 2; a2 1\n', '< RepCartoon: found CA in 3; a2 9\n', '< RepCartoon: found CA in 3; a2 9\n', '< RepCartoon: found CA in 4; a2 15\n', '< RepCartoon: found CA in 4; a2 15\n', '< RepCartoon: found CA in 5; a2 20\n', '< RepCartoon: found CA in 5; a2 20\n', '< RepCartoon: found CA in 6; a2 34\n', '< RepCartoon: found CA in 6; a2 34\n', '< RepCartoon: found CA in 7; a2 44\n', '< RepCartoon: found CA in 7; a2 44\n', '< RepCartoon: found CA in 8; a2 52\n', '< RepCartoon: found CA in 8; a2 52\n', '< RepCartoon: found CA in 9; a2 56\n', '< RepCartoon: found CA in 9; a2 56\n', '< RepCartoon: found CA in 10; a2 65\n', '< RepCartoon: found CA in 10; a2 65\n', '< RepCartoon: found CA in 11; a2 73\n', '< RepCartoon: found CA in 11; a2 73\n', '< RepCartoon: found CA in 12; a2 80\n', '< RepCartoon: found CA in 12; a2 80\n', '< RepCartoon: found CA in 13; a2 94\n', '< RepCartoon: found CA in 13; a2 94\n', '< RepCartoon-Debug: path outlined, interpolating...\n', '< RepCartoon: seg 0 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 1 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 2 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 3 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 4 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 5 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 6 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 7 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 8 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 9 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 10 *s 1 , *(s+1) 1\n', '< RepCartoon: seg 11 *s 1 , *(s+1) 1\n', '< RepCartoon-Debug: generating coordinate systems...\n', '< RepCartoon-Debug: creating 3D scaffold...\n', '< ExtrudeComputeTangents-DEBUG: entered.\n', '< ExtrudeComputeTangents-DEBUG: exiting...\n', '< ExtrudeRectangle-DEBUG: entered...\n', '< ExtrudeRectangle-DEBUG: exiting...\n', '< ExtrudeBuildNormals2f-DEBUG: entered.\n', '< ExtrudeBuildNormals2f-DEBUG: entering...\n', '< ExtrudeCGOSurfaceStrand-DEBUG: entered.\n', '< ExtrudeCGOSurfaceStrand-DEBUG: exiting...\n', '< ExtrudeComputeTangents-DEBUG: entered.\n', '< ExtrudeComputeTangents-DEBUG: exiting...\n', '< ExtrudeCircle-DEBUG: entered.\n', '< ExtrudeCircle-DEBUG: exiting...\n', '< ExtrudeBuildNormals1f-DEBUG: entered.\n', '< ExtrudeBuildNormals1f-DEBUG: exiting...\n', '< ExtrudeCGOSurfaceTube-DEBUG: entered.\n', '< ExtrudeCGOSurfaceTube-DEBUG: exiting...\n', '< ExtrudeComputeTangents-DEBUG: entered.\n', '< ExtrudeComputeTangents-DEBUG: exiting...\n', '< ExtrudeRectangle-DEBUG: entered...\n', '< ExtrudeRectangle-DEBUG: exiting...\n', '< ExtrudeBuildNormals2f-DEBUG: entered.\n', '< ExtrudeBuildNormals2f-DEBUG: entering...\n', '< ExtrudeCGOSurfaceStrand-DEBUG: entered.\n', '< ExtrudeCGOSurfaceStrand-DEBUG: exiting...\n', '< PyMOL>feedback disable, repcartoon extrude, everything\n', '< PyMOL>rebuild\n', '< PyMOL>refresh\n'] run_tests: C0201extend... run_tests: C0201extend.log DIFFERS over about 11 lines: ['1,22d0\n', '< PyMOL>def foo(moo=2): print moo\n', "< PyMOL>cmd.extend('foo',foo)\n", '< PyMOL>foo\n', '< 2\n', '< PyMOL>foo 3\n', '< 3\n', '< PyMOL>foo moo=5\n', '< 5\n', '< PyMOL>foo ?\n', '< Usage: foo [ moo ]\n', '< PyMOL>def fie(moo=3):\\\n', '< PyMOL>"help for fie" \\\n', '< PyMOL>print moo\n', '< PyMOL>print fie.__doc__\n', '< help for fie\n', '< PyMOL>help fie\n', "< Error: unknown topic: 'fie'.\n", "< PyMOL>cmd.extend('fie',fie)\n", '< PyMOL>help fie\n', '< \n', '< help for fie \n', '< \n'] run_tests: C0202help_python... run_tests: C0202help_python.log DIFFERS over about 50 lines: ['1,99d0\n', '< PyMOL>help def\n', '< \n', '< DESCRIPTION\n', '< \n', '< You have asked for help on a Python keyword which is available\n', '< from within the PyMOL command language. Please consult the\n', '< official Python documentation at http://www.python.org for\n', '< detailed information on Python keywords.\n', '< \n', '< You may include Python blocks in your PyMOL command scripts, but do\n', '< note that multi-line blocks of Python in PyMOL command files will\n', '< require explicit continuation syntax in order to execute properly\n', '< (see below).\n', '< \n', '< Generally, if you want to write Python block which span multiple\n', '< lines, you will want to use ".py" file, and then use "extend" in\n', '< order to expose your new code to the PyMOL command language. This\n', '< will give you better error checking and more predictable results.\n', '< \n', '< EXAMPLES\n', '< \n', '< a=1\n', '< while a<10: \\\n', '< print a \\\n', '< a=a+1\n', '< \n', '< SEE ALSO\n', '< \n', '< extend, run, @ \n', '< \n', "< PyMOL>cmd.python_help.__doc__='python help'\n", '< PyMOL>help for\n', '< \n', '< python help \n', '< \n', '< PyMOL>help pass\n', '< \n', '< python help \n', '< \n', '< PyMOL>help raise\n', '< \n', '< python help \n', '< \n', '< PyMOL>help return\n', '< \n', '< python help \n', '< \n', '< PyMOL>help try\n', '< \n', '< python help \n', '< \n', '< PyMOL>help except\n', '< \n', '< python help \n', '< \n', '< PyMOL>help finally\n', '< \n', '< python help \n', '< \n', '< PyMOL>help while\n', '< \n', '< python help \n', '< \n', '< PyMOL>help assert\n', '< \n', '< python help \n', '< \n', '< PyMOL>help class\n', '< \n', '< python help \n', '< \n', '< PyMOL>help continue\n', '< \n', '< python help \n', '< \n', '< PyMOL>help del\n', '< \n', '< python help \n', '< \n', '< PyMOL>help elif\n', '< \n', '< python help \n', '< \n', '< PyMOL>help else\n', '< \n', '< python help \n', '< \n', '< PyMOL>help global\n', '< \n', '< python help \n', '< \n', '< PyMOL>help if\n', '< \n', '< python help \n', '< \n', '< PyMOL>help import\n', '< \n', '< python help \n', '< \n'] run_tests: C0300session... run_tests: C0300session.log DIFFERS over about 13 lines: ['1,26d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>select cas,name ca\n', '< Selector: selection "cas" defined with 13 atoms.\n', '< PyMOL>set line_width,5\n', '< Setting: line_width set to 5.00000.\n', '< PyMOL>show spheres,name n\n', '< PyMOL>save tmp/session.pse\n', '< Save: wrote "tmp/session.pse".\n', '< PyMOL>reinitialize\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>get line_width\n', '< get: line_width = 1.49000\n', '< PyMOL>count_atoms rep spheres\n', '< count_atoms: 0 atoms\n', '< PyMOL>load tmp/session.pse\n', '< Executive: Loading version 1.20 session...\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>get line_width\n', '< get: line_width = 5.00000\n', '< PyMOL>count_atoms rep spheres\n', '< count_atoms: 13 atoms\n', '< PyMOL>count_atoms cas\n', '< count_atoms: 13 atoms\n'] run_tests: C0500misc... run_tests: C0500misc.log DIFFERS over about 129 lines: ['1,258d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>cls\n', '< \n', '< PyMOL>print cmd.count_states()\n', '< 1\n', '< PyMOL>print cmd.count_states("pept")\n', '< 1\n', '< PyMOL>cmd.do("print \'it be done\'")\n', "< PyMOL>print 'it be done'\n", '< it be done\n', '< PyMOL>viewport 200,150\n', '< PyMOL>stereo on\n', '< PyMOL>turn x,90\n', '< PyMOL>origin\n', '< PyMOL>origin (i;11)\n', '< PyMOL>origin pept\n', '< PyMOL>zoom (i;11)\n', '< PyMOL>zoom pept\n', '< PyMOL>zoom\n', '< PyMOL>frame 1\n', '< PyMOL>frame 2\n', '< PyMOL>move x,2\n', '< PyMOL>clip near,2\n', '< PyMOL>clip far,2\n', '< PyMOL>refresh\n', '< PyMOL>reset\n', '< PyMOL>meter_reset\n', '< PyMOL>mclear\n', '< PyMOL>mset 1 x10\n', '< PyMOL>mdo 1:turn x,5\n', '< PyMOL>mdo 2:turn y,10\n', '< PyMOL>rock\n', '< PyMOL>rock\n', '< PyMOL>forward\n', '< PyMOL>backward\n', '< PyMOL>rewind\n', '< PyMOL>ending\n', '< PyMOL>middle\n', '< PyMOL>mplay\n', '< PyMOL>mstop\n', '< PyMOL>color red\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>color blue,(name n)\n', '< Executive: Colored 13 atoms.\n', '< PyMOL>flag 3=(resn his)\n', '< Flag: flag 3 is set in 10 of 107 atoms.\n', '< PyMOL>set_color dude = [ 1.0,0.6,0.3]\n', '< Color: "dude" defined as [ 1.000, 0.600, 0.300 ].\n', '< PyMOL>color dude,(name o)\n', '< Executive: Colored 13 atoms.\n', '< PyMOL>show sticks,(all)\n', '< PyMOL>hide\n', '< PyMOL>show lines\n', '< PyMOL>mmatrix store\n', '< PyMOL>turn x,45\n', '< PyMOL>mmatrix recall\n', '< PyMOL>disable\n', '< PyMOL>enable\n', '< PyMOL>mmatrix clear\n', '< PyMOL>refresh\n', '< PyMOL>rebuild\n', '< PyMOL>refresh\n', '< PyMOL>set line_smooth=1\n', '< Setting: line_smooth set to on.\n', '< PyMOL>label (all),chain\n', '< Label: labelled 107 atoms.\n', "< PyMOL>label (all),''\n", '< Label: labelled 107 atoms.\n', '< PyMOL>stored.cnt = 0\n', '< PyMOL>iterate (all),stored.cnt=stored.cnt+1\n', '< Iterate: iterated over 107 atoms.\n', '< PyMOL>print stored.cnt\n', '< 107\n', '< PyMOL>stored.x = 0\n', '< PyMOL>iterate_state 1,(all),stored.x=stored.x+x\n', '< IterateState: iterated over 107 atom coordinate states.\n', '< PyMOL>print "%8.4f"%stored.x\n', '< 130.9720\n', "< PyMOL>alter (all),segi='PEPT'\n", '< Alter: modified 107 atoms.\n', '< PyMOL>alter_state 1,(all),x = x + 1.0\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>print "%8.4f"%cmd.get_dihedral("(i;11&n;n)","(i;11&n;ca)","(i;11&n;cb)","(i;11&n;cg)")\n', '< -160.7909\n', '< PyMOL>edit (i;11&n;n), (i;11&n;c), pkbond=0\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>dist\n', '< Executive: object "dist01" created.\n', '< PyMOL>dist (pk1),(pk2)\n', '< Executive: object "dist02" created.\n', '< PyMOL>dist tst\n', '< Executive: object "tst" created.\n', '< PyMOL>dist tst2 = (pk1),(pk2)\n', '< Executive: object "tst2" created.\n', '< PyMOL>bond\n', '< Bond: 1 bonds added to model "pept".\n', '< PyMOL>unbond\n', '< Unbond: 1 bonds removed from model "pept".\n', '< PyMOL>bond (pk1),(pk2),2\n', '< Bond: 1 bonds added to model "pept".\n', '< PyMOL>unbond (pk1),(pk2)\n', '< Unbond: 1 bonds removed from model "pept".\n', '< PyMOL>copy cpy=pept\n', '< Executive: object "cpy" created.\n', '< Executive: object cpy created.\n', '< PyMOL>select cpy_sel = (cpy)\n', '< Selector: selection "cpy_sel" defined with 107 atoms.\n', '< PyMOL>alter_state 1,(cpy),x=x+math.cos(y+z)\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>rms cpy,pept\n', '< Executive: RMS = 0.695 (107 to 107 atoms)\n', '< PyMOL>rms (cpy and name ca),pept\n', '< Executive: RMS = 0.639 (13 to 13 atoms)\n', '< PyMOL>rms (cpy and name ca),(pept &n;ca)\n', '< Executive: RMS = 0.639 (13 to 13 atoms)\n', '< PyMOL>rms_cur cpy,pept\n', '< Executive: RMS = 0.700 (107 to 107 atoms)\n', '< PyMOL>rms_cur (cpy and name ca),pept\n', '< Executive: RMS = 0.722 (13 to 13 atoms)\n', '< PyMOL>rms_cur (cpy and name ca),(pept &n;ca)\n', '< Executive: RMS = 0.722 (13 to 13 atoms)\n', '< PyMOL>fit cpy,pept\n', '< Executive: RMS = 0.695 (107 to 107 atoms)\n', '< PyMOL>fit (cpy),(pept)\n', '< Executive: RMS = 0.695 (107 to 107 atoms)\n', '< PyMOL>fit (cpy and name ca),(pept &n;ca)\n', '< Executive: RMS = 0.639 (13 to 13 atoms)\n', '< PyMOL>pair_fit (cpy&i;11&n;ca),(pept&i;11&n;ca),\\\n', '< PyMOL>(cpy&i;5&n;ca),(pept&i;5&n;ca),\\\n', '< PyMOL>(cpy&i;1&n;ca),(pept&i;1&n;ca),\\\n', '< PyMOL>(cpy&i;8&n;ca),(pept&i;8&n;ca)\n', '< ExecutiveRMS: RMS = 0.478 (4 to 4 atoms)\n', '< PyMOL>update (cpy),(pept)\n', '< Update: coordinates updated for 107 atoms.\n', '< PyMOL>remove (cpy and name c)\n', '< Remove: eliminated 13 atoms in model "cpy".\n', '< PyMOL>edit (cpy and i;11 & n;ca)\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>remove_picked\n', '< Remove: eliminated 1 atoms in model "cpy".\n', '< PyMOL>edit (cpy and i;5 & n;ca),(cpy and i;5 and n;cb)\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', "< PyMOL>alter (cpy),name=''\n", '< Alter: modified 93 atoms.\n', '< PyMOL>rename cpy\n', '< Rename: renamed 93 atoms.\n', '< PyMOL>rename cpy,1\n', '< Rename: renamed 93 atoms.\n', '< PyMOL>cycle_valence\n', '< PyMOL>cycle_valence\n', '< Remove: eliminated 1 atoms in model "cpy".\n', '< Remove: eliminated 1 atoms in model "cpy".\n', '< PyMOL>cycle_valence\n', '< PyMOL>remove_picked\n', '< PyMOL>edit (cpy and i;11 &n;n)\n', '< Editor-Error: Invalid input selection(s).\n', '< PyMOL>cmd.attach("H",1,1)\n', '< PyMOL>create tmp = (cpy&i;5)\n', '< Selector: found 13 atoms.\n', '< Executive: object "tmp" created.\n', '< PyMOL>fuse (cpy&i;11&n;cb),(tmp&n;cb)\n', '< PyMOL>edit (cpy and i;10 & n;n)\n', '< Editor-Error: Invalid input selection(s).\n', '< PyMOL>h_fill\n', '< PyMOL>h_fill\n', '< PyMOL>h_add (cpy)\n', '< PyMOL>edit (cpy and i;8 &n;o)\n', '< Editor-Error: Invalid input selection(s).\n', '< PyMOL>cmd.replace("S",3,1)\n', '< Error: you must first pick an atom to replace.\n', '< PyMOL>delete tmp\n', '< PyMOL>delete cpy\n', '< PyMOL>delete cpy_sel\n', '< PyMOL>edit (i;11&n;ca)\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>unpick\n', '< PyMOL>protect (pept and n;ca)\n', '< Protect: 13 atoms protected from movement.\n', '< PyMOL>protect pept\n', '< Protect: 107 atoms protected from movement.\n', '< PyMOL>protect\n', '< Protect: 107 atoms protected from movement.\n', '< PyMOL>deprotect (pept and n;ca)\n', '< Protect: 13 atoms deprotected.\n', '< PyMOL>deprotect\n', '< Protect: 107 atoms deprotected.\n', '< PyMOL>mask (pept and n;ca)\n', '< Mask: 13 atoms masked (cannot be picked or selected).\n', '< PyMOL>mask pept\n', '< Mask: 107 atoms masked (cannot be picked or selected).\n', '< PyMOL>mask\n', '< Mask: 107 atoms masked (cannot be picked or selected).\n', '< PyMOL>unmask (pept and n;ca)\n', '< Mask: 13 atoms unmasked.\n', '< PyMOL>unmask\n', '< Mask: 107 atoms unmasked.\n', '< PyMOL>edit (i;11&n;ca),(i;11&n;n),(i;11&n;c)\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< Selector: selection "pk3" defined with 1 atoms.\n', '< PyMOL>invert\n', '< Editor: Inverted atom.\n', '< PyMOL>invert\n', '< Editor: Inverted atom.\n', '< PyMOL>edit (i;11&n;ca),(i;11&n;cb)\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>torsion 10\n', '< PyMOL>torsion -10\n', '< PyMOL>torsion 180\n', '< PyMOL>torsion 180\n', '< PyMOL>print cmd.get_model().__class__\n', '< chempy.models.Indexed\n', '< PyMOL>print "%8.3f"%cmd.get_area()\n', '< 1381.186\n', '< PyMOL>print "%8.3f"%cmd.get_area("(name ca)")\n', '< 112.133\n', '< PyMOL>print cmd.get_names()\n', "< ['pept', 'dist01', 'dist02', 'tst', 'tst2']\n", "< PyMOL>print cmd.get_type('pept')\n", '< object:molecule\n', '< PyMOL>print cmd.identify("(i;7)")\n', '< [52, 53, 54, 55]\n', '< PyMOL>print "%8.4f %8.4f %8.4f %8.4f %8.4f %8.4f"%(ext[0][0],ext[0][1],ext[0][2],ext[1][0],ext[1][1],ext[1][2])\n', '< -4.1880 -20.3310 13.1570 9.9190 0.8630 27.0580\n', '< PyMOL>sort\n', '< PyMOL>sort pept\n', '< PyMOL>spheroid\n', "< Warning: 'spheroid' is experimental, incomplete, and unstable.\n", '< ObjectMolecule: computing spheroid from states 1 to 1.\n', '< PyMOL>spheroid pept\n', "< Warning: 'spheroid' is experimental, incomplete, and unstable.\n", '< ObjectMolecule: computing spheroid from states 1 to 1.\n', '< PyMOL>cmd.config_mouse(quiet=0)\n', '< config_mouse: three_button\n', '< PyMOL>rewind\n', '< PyMOL>dele all\n', '< PyMOL>load dat/ligs3d.sdf\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/ligs3d.sdf" loaded as "ligs3d", through state 10.\n', '< PyMOL>split_states ligs3d\n', '< PyMOL>print cmd.get_names()\n', "< ['ligs3d', 'MFCD02681585', 'MFCD01567969', 'MFCD00023789', 'MFCD02579443', 'MFCD02579410', 'MFCD02579135', 'MFCD02681468', 'MFCD00141070', 'MFCD02983625', 'MFCD00115818']\n", '< PyMOL>rewind\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 564 graphics primitives.\n'] run_tests: C0550pseudo... run_tests: C0550pseudo.log DIFFERS over about 36 lines: ['1,72d0\n', '< PyMOL>pseudoatom test\n', '< ObjMol: created test/PSDO/P/PSD`1/PS1\n', '< PyMOL>move x,10\n', '< PyMOL>pseudoatom test\n', '< ObjMol: created test/PSDO/P/PSD`1/PS2\n', '< PyMOL>count_atoms\n', '< count_atoms: 2 atoms\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 6 graphics primitives.\n', '< PyMOL>iterate all,print name+ " %0.2f"%vdw\n', '< PS1 1.00\n', '< PS2 1.00\n', '< Iterate: iterated over 2 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>pseudoatom test, pept and resi 1\n', '< ObjMol: created test/PSDO/P/PSD`1/PS1\n', '< PyMOL>pseudoatom test, pept and resi 2\n', '< ObjMol: created test/PSDO/P/PSD`1/PS2\n', '< PyMOL>pseudoatom test, pept and resi 10\n', '< ObjMol: created test/PSDO/P/PSD`1/PS3\n', '< PyMOL>iterate name PS*, print name+ " %0.2f"%vdw\n', '< PS1 1.81\n', '< PS2 1.79\n', '< PS3 1.81\n', '< Iterate: iterated over 3 atoms.\n', '< PyMOL>hide\n', '< PyMOL>as spheres, test\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 3 graphics primitives.\n', '< PyMOL>bond name PS2, name PS3\n', '< Bond: 1 bonds added to model "test".\n', '< PyMOL>show sticks, test\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 4 graphics primitives.\n', '< PyMOL>pseudoatom test, vdw=5.0\n', '< ObjMol: created test/PSDO/P/PSD`1/PS4\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 7 graphics primitives.\n', '< PyMOL>pseudoatom test, color=blue\n', '< ObjMol: created test/PSDO/P/PSD`1/PS5\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 10 graphics primitives.\n', '< PyMOL>pseudoatom test, label=Hello world\n', '< ObjMol: created test/PSDO/P/PSD`1/PS6\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 32 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>pseudoatom pept, pept and resi 1\n', '< ObjMol: created pept/PSDO/P/PSD`1/PS1\n', '< PyMOL>pseudoatom pept, pept and resi 2\n', '< ObjMol: created pept/PSDO/P/PSD`1/PS2\n', '< PyMOL>pseudoatom pept, pept and resi 10\n', '< ObjMol: created pept/PSDO/P/PSD`1/PS3\n', '< PyMOL>count_atoms pept\n', '< count_atoms: 110 atoms\n', '< PyMOL>bond name PS2, name PS3\n', '< Bond: 1 bonds added to model "pept".\n', '< PyMOL>hide nonbonded\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 167 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', "< PyMOL>pseudoatom test, all, b=1.5, q=1.6, resn=abc, resi=10, name=ilk, elem=s, vdw=5, segi=asdf, chain=''\n", '< ObjMol: created test/asdf//abc`10/ilk\n', '< PyMOL>iterate name ilk,print "%8.3f %8.3f %8.3f"%(b,q,vdw)\n', '< 1.500 1.600 5.000\n', '< Iterate: iterated over 1 atoms.\n'] run_tests: C0600util... run_tests: C0600util.log DIFFERS over about 27 lines: ['1,54d0\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1\n', '< TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND 3 CHAIN: A, B;\n', '< COMPND 4 ENGINEERED: YES;\n', '< COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 2 symmetry operators.\n', '< CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>util.ss\n', '< util.ss: WARNING: This is not a "correct" secondary structure\n', '< util.ss: assignment algorithm! Please use only as a last resort.\n', '< util.ss: initiating secondary structure assignment on 163 residues.\n', '< util.ss: extracting sequence and relationships...\n', '< util.ss: analyzing phi/psi angles (slow)...\n', '< util.ss: finding hydrogen bonds...\n', '< util.ss: verifying beta sheets...\n', '< util.ss: assignment complete.\n', '< PyMOL>util.cbac\n', '< Executive: Colored 1948 atoms.\n', '< Executive: Colored 922 atoms.\n', '< PyMOL>util.cbay\n', '< Executive: Colored 1948 atoms.\n', '< Executive: Colored 922 atoms.\n', '< PyMOL>util.cbaw\n', '< Executive: Colored 1948 atoms.\n', '< Executive: Colored 922 atoms.\n', '< PyMOL>util.cbas\n', '< Executive: Colored 1948 atoms.\n', '< Executive: Colored 922 atoms.\n', '< PyMOL>util.cbc\n', '< util.cbc: color 26,(chain A)\n', '< Executive: Colored 279 atoms.\n', '< util.cbc: color 5,(chain B)\n', '< Executive: Colored 310 atoms.\n', '< util.cbc: color 154,(chain E)\n', '< Executive: Colored 107 atoms.\n', "< util.cbc: color 6,(chain '')\n", '< Executive: Colored 2174 atoms.\n', '< PyMOL>hide\n', '< PyMOL>show car\n', '< PyMOL>zoom\n', '< PyMOL>set ray_default_renderer=2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 19492 graphics primitives.\n', '< PyMOL>util.rainbow("pept")\n'] run_tests: C0700odd... run_tests: C0700odd.B.pdb is missing. run_tests: C0700odd.3.pdb is missing. run_tests: C0700odd.1.pdb is missing. run_tests: C0700odd.F.pdb is missing. run_tests: C0700odd.8.pdb is missing. run_tests: C0700odd.E.pdb is missing. run_tests: C0700odd.log DIFFERS over about 204 lines: ['1,408d0\n', '< PyMOL>unset pdb_hetatm_guess_valences\n', '< Setting: pdb_hetatm_guess_valences set to off.\n', '< PyMOL>reinitialize store_defaults\n', '< PyMOL>load dat/odd01.pdb\n', '< CmdLoad: "dat/odd01.pdb" loaded as "odd01".\n', '< PyMOL>iterate all, print name\n', '< CZ\n', '< NH1\n', '< NH2\n', '< HE\n', '< HH11\n', '< HH12\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< LMN\n', '< XYZ\n', '< PE\n', '< O1B\n', '< AC5\n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>save cmp/C0700odd.1.pdb\n', '< Save: wrote "cmp/C0700odd.1.pdb".\n', '< PyMOL>set retain_order\n', '< Setting: retain_order set to 1.\n', '< PyMOL>iterate all, print name\n', '< HE\n', '< CZ\n', '< NH1\n', '< HH11\n', '< HH12\n', '< NH2\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< XYZ\n', '< LMN\n', '< PE\n', '< O1B\n', '< AC5\n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>save cmp/C0700odd.2.pdb\n', '< Save: wrote "cmp/C0700odd.2.pdb".\n', '< PyMOL>set pdb_no_end_record\n', '< Setting: pdb_no_end_record set to on.\n', '< PyMOL>save cmp/C0700odd.3.pdb\n', '< Save: wrote "cmp/C0700odd.3.pdb".\n', '< PyMOL>set pdb_retain_ids\n', '< Setting: pdb_retain_ids set to on.\n', '< PyMOL>save cmp/C0700odd.4.pdb\n', '< Save: wrote "cmp/C0700odd.4.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>set retain_order\n', '< Setting: retain_order set to 1.\n', '< PyMOL>load dat/odd01.pdb\n', '< CmdLoad: "dat/odd01.pdb" loaded as "odd01".\n', '< PyMOL>iterate all,print name\n', '< HE\n', '< CZ\n', '< NH1\n', '< HH11\n', '< HH12\n', '< NH2\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< XYZ\n', '< LMN\n', '< PE\n', '< O1B\n', '< AC5\n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>set pdb_reformat_names_mode, 1\n', '< Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>save cmp/C0700odd.5.pdb\n', '< Save: wrote "cmp/C0700odd.5.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.3.pdb\n', '< CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".\n', '< PyMOL>set pdb_reformat_names_mode, 0\n', '< Setting: pdb_reformat_names_mode set to 0.\n', '< PyMOL>save cmp/C0700odd.6.pdb\n', '< Save: wrote "cmp/C0700odd.6.pdb".\n', '< PyMOL>iterate all,print name\n', '< HE\n', '< CZ\n', '< NH1\n', '< 1HH1\n', '< 2HH1\n', '< NH2\n', '< 1HH2\n', '< 2HH2\n', '< CA\n', '< CA\n', '< 2OA2\n', '< 3OA2\n', '< ABCD\n', '< XYZ\n', '< LMN\n', '< PE\n', '< O1B\n', '< AC5\n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>reinit\n', '< PyMOL>set pdb_reformat_names_mode, 1\n', '< Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>load cmp/C0700odd.3.pdb\n', '< CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".\n', '< PyMOL>iterate all,print name\n', '< CZ\n', '< NH1\n', '< NH2\n', '< HE\n', '< 1HH1\n', '< 2HH1\n', '< 1HH2\n', '< 2HH2\n', '< CA\n', '< CA\n', '< 2OA2\n', '< 3OA2\n', '< ABCD\n', '< LMN\n', '< XYZ\n', '< PE\n', '< O1B\n', '< AC5\n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>save cmp/C0700odd.7.pdb\n', '< Save: wrote "cmp/C0700odd.7.pdb".\n', '< PyMOL>set pdb_reformat_names_mode,2\n', '< Setting: pdb_reformat_names_mode set to 2.\n', '< PyMOL>save cmp/C0700odd.8.pdb\n', '< Save: wrote "cmp/C0700odd.8.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.5.pdb\n', '< CmdLoad: "cmp/C0700odd.5.pdb" loaded as "C0700odd.5".\n', '< PyMOL>iterate all,print name\n', '< CZ\n', '< NH1\n', '< NH2\n', '< HE\n', '< HH11\n', '< HH12\n', '< HH21\n', '< HH22\n', '< CA\n', '< CA\n', '< OA22\n', '< OA23\n', '< ABCD\n', '< LMN\n', '< XYZ\n', '< PE\n', '< O1B\n', '< AC5\n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>set pdb_reformat_names_mode,0\n', '< Setting: pdb_reformat_names_mode set to 0.\n', '< PyMOL>save cmp/C0700odd.9.pdb\n', '< Save: wrote "cmp/C0700odd.9.pdb".\n', '< PyMOL>set pdb_reformat_names_mode,1\n', '< Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>save cmp/C0700odd.A.pdb\n', '< Save: wrote "cmp/C0700odd.A.pdb".\n', '< PyMOL>set pdb_literal_names, 1\n', '< Setting: pdb_literal_names set to on.\n', '< PyMOL>save cmp/C0700odd.B.pdb\n', '< Save: wrote "cmp/C0700odd.B.pdb".\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.3.pdb\n', '< CmdLoad: "cmp/C0700odd.3.pdb" loaded as "C0700odd.3".\n', '< PyMOL>iterate all,print name\n', '< CZ \n', '< HE \n', '< NH1\n', '< NH2\n', '< HH11\n', '< HH12\n', '< HH21\n', '< HH22\n', '< CA \n', '< CA \n', '< OA22\n', '< OA23\n', '< LMN\n', '< XYZ\n', '< ABCD\n', '< O1B\n', '< PE \n', '< AC5 \n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load cmp/C0700odd.5.pdb\n', '< CmdLoad: "cmp/C0700odd.5.pdb" loaded as "C0700odd.5".\n', '< PyMOL>iterate all,print name\n', '< CZ \n', '< HE \n', '< NH1\n', '< NH2\n', '< 1HH1\n', '< 2HH1\n', '< 1HH2\n', '< 2HH2\n', '< CA \n', '< CA \n', '< 2OA2\n', '< 3OA2\n', '< LMN\n', '< XYZ\n', '< ABCD\n', '< O1B\n', '< PE \n', '< AC5 \n', '< Iterate: iterated over 18 atoms.\n', '< PyMOL>reinit\n', '< PyMOL>load dat/small02.pdb\n', '< CmdLoad: "dat/small02.pdb" loaded as "small02".\n', '< PyMOL>save cmp/C0700odd.C.pdb\n', '< Save: wrote "cmp/C0700odd.C.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>set pdb_reformat_names_mode, 1\n', '< Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>load dat/small02.pdb\n', '< CmdLoad: "dat/small02.pdb" loaded as "small02".\n', '< PyMOL>iterate all, print name\n', '< CL16\n', '< C1\n', '< C4\n', '< C6\n', '< C9\n', '< N12\n', '< C13\n', '< C17\n', '< C19\n', '< C20\n', '< C22\n', '< C25\n', '< C28\n', '< C29\n', '< C30\n', '< N32\n', '< C33\n', '< C35\n', '< C39\n', '< C40\n', '< C41\n', '< C42\n', '< C43\n', '< C46\n', '< C49\n', '< C51\n', '< N54\n', '< C55\n', '< N56\n', '< O57\n', '< C58\n', '< C61\n', '< O64\n', '< C65\n', '< BR37\n', '< BR38\n', '< Iterate: iterated over 36 atoms.\n', '< PyMOL>save cmp/C0700odd.D.pdb\n', '< Save: wrote "cmp/C0700odd.D.pdb".\n', '< PyMOL>set pdb_reformat_names_mode, 2\n', '< Setting: pdb_reformat_names_mode set to 2.\n', '< PyMOL>load dat/small02.pdb\n', '< CmdLoad: "dat/small02.pdb" appended into object "small02", state 2.\n', '< PyMOL>iterate all, print name\n', '< CL16\n', '< C1\n', '< C4\n', '< C6\n', '< C9\n', '< N12\n', '< C13\n', '< C17\n', '< C19\n', '< C20\n', '< C22\n', '< C25\n', '< C28\n', '< C29\n', '< C30\n', '< N32\n', '< C33\n', '< C35\n', '< C39\n', '< C40\n', '< C41\n', '< C42\n', '< C43\n', '< C46\n', '< C49\n', '< C51\n', '< N54\n', '< C55\n', '< N56\n', '< O57\n', '< C58\n', '< C61\n', '< O64\n', '< C65\n', '< BR37\n', '< BR38\n', '< Iterate: iterated over 36 atoms.\n', '< PyMOL>save cmp/C0700odd.E.pdb\n', '< Save: wrote "cmp/C0700odd.E.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>set pdb_literal_names\n', '< Setting: pdb_literal_names set to on.\n', '< PyMOL>set retain_order\n', '< Setting: retain_order set to 1.\n', '< PyMOL>set pdb_retain_ids\n', '< Setting: pdb_retain_ids set to on.\n', '< PyMOL>set pdb_no_end_record\n', '< Setting: pdb_no_end_record set to on.\n', '< PyMOL>unset pdb_use_ter_records\n', '< Setting: pdb_use_ter_records set to 0.\n', '< PyMOL>load dat/odd01.pdb\n', '< CmdLoad: "dat/odd01.pdb" loaded as "odd01".\n', '< PyMOL>save cmp/C0700odd.F.pdb\n', '< Save: wrote "cmp/C0700odd.F.pdb".\n', '< PyMOL>reinit\n', '< PyMOL>load dat/helix_amber.pdb\n', '< CmdLoad: "dat/helix_amber.pdb" loaded as "helix_amber".\n', '< PyMOL>iterate resi 2, print name, elem\n', '< N N\n', '< CA C\n', '< C C\n', '< O O\n', '< CB C\n', '< SG S\n', '< H H\n', '< HA H\n', '< HB2 H\n', '< HB3 H\n', '< N N\n', '< CA C\n', '< C C\n', '< O O\n', '< CB C\n', '< H H\n', '< HA H\n', '< HB1 H\n', '< HB2 H\n', '< HB3 H\n', '< Iterate: iterated over 20 atoms.\n', '< PyMOL>reinit\n', '< PyMOL>load dat/odd02.pdb\n', '< CmdLoad: "dat/odd02.pdb" loaded as "odd02".\n', '< PyMOL>iterate all, print name, elem\n', '< C C\n', '< O O\n', '< CG C\n', '< CD C\n', '< NE N\n', '< CZ C\n', '< NH1 N\n', '< NH2 N\n', '< HG1 H\n', '< HG2 H\n', '< HD1 H\n', '< HD2 H\n', '< HE H\n', '< HH11 H\n', '< HH12 H\n', '< HH21 H\n', '< Hh22 Hh\n', '< N N\n', '< CA C\n', '< C C\n', '< O O\n', '< CB C\n', '< CG1 C\n', '< CG2 C\n', '< HN H\n', '< HA H\n', '< HB H\n', '< HG11 H\n', '< HG12 H\n', '< HG21 H\n', '< HG22 H\n', '< HG23 H\n', '< Hg13 Hg\n', '< N N\n', '< CA C\n', '< HN H\n', '< Iterate: iterated over 36 atoms.\n', '< PyMOL>save cmp/C0700.odd.G.pdb\n', '< Save: wrote "cmp/C0700.odd.G.pdb".\n', '< PyMOL>set pdb_reformat_names_mode,1\n', '< Setting: pdb_reformat_names_mode set to 1.\n', '< PyMOL>save cmp/C0700.odd.H.pdb\n', '< Save: wrote "cmp/C0700.odd.H.pdb".\n'] run_tests: C0700odd.A.pdb is missing. run_tests: C0700odd.2.pdb is missing. run_tests: C0700odd.C.pdb is missing. run_tests: C0700odd.6.pdb is missing. run_tests: C0700odd.D.pdb is missing. run_tests: C0700odd.4.pdb is missing. run_tests: C0700odd.5.pdb is missing. run_tests: C0700odd.7.pdb is missing. run_tests: C0700odd.9.pdb is missing. run_tests: C0740multipdb... run_tests: C0740multipdb.log DIFFERS over about 45 lines: ['1,89d0\n', '< PyMOL>ATOM 1 N GLY A 252 39.368 46.327 27.875 1.00 46.28 N \\\n', '< PyMOL>ATOM 2 CA GLY A 252 39.565 46.477 29.344 1.00 46.89 C \\\n', '< PyMOL>ATOM 3 C GLY A 252 40.602 45.521 29.907 1.00 48.55 C \\\n', '< PyMOL>ATOM 4 O GLY A 252 40.907 44.497 29.293 1.00 46.16 O \\\n', '< PyMOL>ATOM 5 N SER A 253 41.144 45.862 31.078 1.00 45.72 N \\\n', '< PyMOL>ATOM 6 CA SER A 253 42.152 45.043 31.757 1.00 46.42 C \\\n', '< PyMOL>ATOM 7 C SER A 253 41.824 44.945 33.254 1.00 47.72 C \\\n', '< PyMOL>ATOM 8 O SER A 253 41.053 45.756 33.778 1.00 46.62 O \\\n', '< PyMOL>ATOM 9 CB SER A 253 43.543 45.667 31.587 1.00 45.55 C \\\n', '< PyMOL>HEADER STEP\\\n', '< PyMOL>ATOM 1 N SER E 258 55.863 54.272 24.437 1.00 37.51 N \\\n', '< PyMOL>ATOM 2 CA SER E 258 56.590 54.677 23.240 1.00 36.33 C \\\n', '< PyMOL>ATOM 3 C SER E 258 58.022 54.180 23.260 1.00 35.14 C \\\n', '< PyMOL>ATOM 4 O SER E 258 58.647 54.090 24.306 1.00 34.89 O \\\n', '< PyMOL>ATOM 5 CB SER E 258 56.566 56.199 23.083 1.00 35.95 C \\\n', '< PyMOL>ATOM 6 OG SER E 258 57.340 56.607 21.975 1.00 36.25 O \\\n', '< PyMOL>ATOM 7 N ARG E 259 58.546 53.842 22.088 1.00 34.24 N """\n', '< PyMOL>cmd.read_pdbstr(pdbstr,"test")\n', '< PyMOL>print cmd.get_names()\n', "< ['PTPBR7', 'STEP']\n", '< PyMOL>count_atoms\n', '< count_atoms: 16 atoms\n', '< PyMOL>reinit\n', '< PyMOL>cmd.read_pdbstr("""\\\n', '< PyMOL>HEADER OXIDOREDUCTASE 13-JUL-94 3MDD 3MDD 2\\\n', '< PyMOL>ATOM 1 N GLY A 11 22.422 32.842 -15.744 1.00 24.74 3MDD 172\\\n', '< PyMOL>ATOM 2 CA GLY A 11 21.837 32.022 -14.672 1.00 24.52 3MDD 173\\\n', '< PyMOL>ATOM 3 C GLY A 11 21.575 30.609 -15.194 1.00 24.62 3MDD 174\\\n', '< PyMOL>ATOM 4 O GLY A 11 22.036 30.238 -16.285 1.00 24.99 3MDD 175\\\n', '< PyMOL>ATOM 5 N PHE A 12 20.843 29.864 -14.390 1.00 24.29 3MDD 176\\\n', '< PyMOL>ATOM 6 CA PHE A 12 20.481 28.469 -14.679 1.00 24.00 3MDD 177\\\n', '< PyMOL>ATOM 7 C PHE A 12 19.514 28.397 -15.861 1.00 23.38 3MDD 178\\\n', '< PyMOL>ATOM 6017 NZ LYS B 395 -4.299 -6.687 15.377 1.00 35.83 3MDD6188\\\n', '< PyMOL>ATOM 6018 OXT LYS B 395 -0.899 -11.439 20.683 1.00 35.32 3MDD6189\\\n', '< PyMOL>END 3MDD6517\\\n', '< PyMOL>HEADER ELECTRON TRANSPORT 02-MAR-92 1MDA 1MDA 2\\\n', '< PyMOL>ATOM 1 N GLU H 1 15.906 81.036 72.025 1.00 50.00 1MDA 307\\\n', '< PyMOL>ATOM 2 CA GLU H 1 17.350 81.236 71.880 1.00 50.00 1MDA 308\\\n', '< PyMOL>ATOM 3 C GLU H 1 17.854 81.695 70.506 1.00 50.00 1MDA 309\\\n', '< PyMOL>ATOM 4 O GLU H 1 17.668 80.983 69.518 1.00 50.00 1MDA 310\\\n', '< PyMOL>ATOM 5 CB GLU H 1 18.222 80.229 72.680 1.00 50.00 1MDA 311\\\n', '< PyMOL>ATOM 6 CG GLU H 1 17.540 78.863 72.954 1.00 50.00 1MDA 312\\\n', '< PyMOL>ATOM 7 CD GLU H 1 17.831 77.718 72.017 1.00 43.59 1MDA 313\\\n', '< PyMOL>ATOM 8 OE1 GLU H 1 18.953 77.453 71.614 1.00 47.42 1MDA 314\\\n', '< PyMOL>ATOM 9 OE2 GLU H 1 16.759 77.049 71.674 1.00 37.68 1MDA 315\\\n', '< PyMOL>ATOM 8568 CG GLU B 105 37.556 38.617 32.271 1.00 15.99 1MDA8874\\\n', '< PyMOL>ATOM 8569 CD GLU B 105 36.485 37.572 32.282 1.00 36.23 1MDA8875\\\n', '< PyMOL>ATOM 8570 OE1 GLU B 105 36.488 36.782 31.231 1.00 50.00 1MDA8876\\\n', '< PyMOL>ATOM 8571 OE2 GLU B 105 35.647 37.508 33.152 1.00 50.00 1MDA8877\\\n', '< PyMOL>ATOM 8572 OXT GLU B 105 41.453 38.354 30.968 1.00 50.00 1MDA8878\\\n', '< PyMOL>END 1MDA8924\\\n', '< PyMOL>""","test")\n', '< PyMOL>print cmd.get_names()\n', "< ['3MDD', '1MDA']\n", '< PyMOL>count_atoms\n', '< count_atoms: 23 atoms\n', '< PyMOL>reinit\n', '< PyMOL>cmd.read_pdbstr("""\\\n', '< PyMOL>ATOM 1 N GLY A 11 22.422 32.842 -15.744 1.00 24.74 3MDD 172\\\n', '< PyMOL>ATOM 2 CA GLY A 11 21.837 32.022 -14.672 1.00 24.52 3MDD 173\\\n', '< PyMOL>ATOM 3 C GLY A 11 21.575 30.609 -15.194 1.00 24.62 3MDD 174\\\n', '< PyMOL>ATOM 4 O GLY A 11 22.036 30.238 -16.285 1.00 24.99 3MDD 175\\\n', '< PyMOL>ATOM 5 N PHE A 12 20.843 29.864 -14.390 1.00 24.29 3MDD 176\\\n', '< PyMOL>ATOM 6 CA PHE A 12 20.481 28.469 -14.679 1.00 24.00 3MDD 177\\\n', '< PyMOL>ATOM 7 C PHE A 12 19.514 28.397 -15.861 1.00 23.38 3MDD 178\\\n', '< PyMOL>ATOM 6017 NZ LYS B 395 -4.299 -6.687 15.377 1.00 35.83 3MDD6188\\\n', '< PyMOL>ATOM 6018 OXT LYS B 395 -0.899 -11.439 20.683 1.00 35.32 3MDD6189\\\n', '< PyMOL>END 3MDD6517\\\n', '< PyMOL>ATOM 1 N GLU H 1 15.906 81.036 72.025 1.00 50.00 1MDA 307\\\n', '< PyMOL>ATOM 2 CA GLU H 1 17.350 81.236 71.880 1.00 50.00 1MDA 308\\\n', '< PyMOL>ATOM 3 C GLU H 1 17.854 81.695 70.506 1.00 50.00 1MDA 309\\\n', '< PyMOL>ATOM 4 O GLU H 1 17.668 80.983 69.518 1.00 50.00 1MDA 310\\\n', '< PyMOL>ATOM 5 CB GLU H 1 18.222 80.229 72.680 1.00 50.00 1MDA 311\\\n', '< PyMOL>ATOM 6 CG GLU H 1 17.540 78.863 72.954 1.00 50.00 1MDA 312\\\n', '< PyMOL>ATOM 7 CD GLU H 1 17.831 77.718 72.017 1.00 43.59 1MDA 313\\\n', '< PyMOL>ATOM 8 OE1 GLU H 1 18.953 77.453 71.614 1.00 47.42 1MDA 314\\\n', '< PyMOL>ATOM 9 OE2 GLU H 1 16.759 77.049 71.674 1.00 37.68 1MDA 315\\\n', '< PyMOL>ATOM 8568 CG GLU B 105 37.556 38.617 32.271 1.00 15.99 1MDA8874\\\n', '< PyMOL>ATOM 8569 CD GLU B 105 36.485 37.572 32.282 1.00 36.23 1MDA8875\\\n', '< PyMOL>ATOM 8570 OE1 GLU B 105 36.488 36.782 31.231 1.00 50.00 1MDA8876\\\n', '< PyMOL>ATOM 8571 OE2 GLU B 105 35.647 37.508 33.152 1.00 50.00 1MDA8877\\\n', '< PyMOL>ATOM 8572 OXT GLU B 105 41.453 38.354 30.968 1.00 50.00 1MDA8878\\\n', '< PyMOL>END 1MDA8924\\\n', '< PyMOL>""","test")\n', '< PyMOL>print cmd.get_names()\n', "< ['test_0001', 'test_0002']\n", '< PyMOL>count_atoms\n', '< count_atoms: 23 atoms\n', '< PyMOL>reinit\n'] run_tests: C0800matrices... run_tests: C0800matrices.log DIFFERS over about 141 lines: ['1,282d0\n', '< PyMOL>load dat/pept.pdb, mol1\n', '< CmdLoad: "dat/pept.pdb" loaded as "mol1".\n', '< PyMOL>load dat/pept.pdb, mol2\n', '< CmdLoad: "dat/pept.pdb" loaded as "mol2".\n', '< PyMOL>load dat/pept.pdb, mol3\n', '< CmdLoad: "dat/pept.pdb" loaded as "mol3".\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [ 0.00 0.00 0.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>translate [2,3,4], object=mol2, object_mode=1\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [ 5.38 0.00 5.38 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>matrix= cmd.get_object_matrix("mol2")\n', '< PyMOL>cmd.transform_object("mol3",matrix, homogenous=1)\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [ 5.38 5.38 0.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dele mol3\n', '< PyMOL>load dat/pept.pdb,mol3\n', '< CmdLoad: "dat/pept.pdb" loaded as "mol3".\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [ 5.38 0.00 5.38 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>matrix_transfer mol1, mol3\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [ 5.38 0.00 5.38 ]\n', '< PyMOL>matrix_transfer mol2, mol3\n', '< PyMOL>dump_lst((cmd.get_distance("mol1///5/ca","mol2///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol1///5/ca","mol3///5/ca"), \\\n', '< PyMOL>cmd.get_distance("mol2///5/ca","mol3///5/ca")))\n', '< [ 5.38 5.38 0.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol2"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("mol3"))\n', '< [ 1.00 0.00 0.00 2.00 \n', '< 0.00 1.00 0.00 3.00 \n', '< 0.00 0.00 1.00 4.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dele all\n', '< PyMOL>load ../data/tut/1hpv.pdb\n', '< HEADER HYDROLASE (ACID PROTEINASE) 18-NOV-94 1HPV 1HPV 2\n', '< COMPND HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478 1HPV 3\n', '< COMPND 2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1- 1HPV 4\n', '< COMPND 3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY- 1HPV 5\n', '< COMPND 4 4-PHENYLBUTANE) 1HPV 6\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "../data/tut/1hpv.pdb" loaded as "1hpv".\n', '< PyMOL>create ligand, organic\n', '< Selector: found 35 atoms.\n', '< Executive: object "ligand" created.\n', '< PyMOL>create protein, polymer\n', '< Selector: found 1516 atoms.\n', '< Executive: object "protein" created.\n', '< PyMOL>delete 1hpv\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [ 6.86 5.47 8.86 ]\n', '< PyMOL>translate [2,3,4], object=protein, object_mode=1\n', '< PyMOL>rotate x, 20, object=protein, object_mode=1\n', '< PyMOL>rotate y, 40, object=protein, object_mode=1\n', '< PyMOL>rotate z, 90, object=protein, object_mode=1\n', '< PyMOL>translate [4,5,6], object=protein, object_mode=1\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [ 22.69 18.69 18.07 ]\n', '< PyMOL>matrix_transfer protein, ligand\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [ 6.86 5.47 8.86 ]\n', '< PyMOL>load ../data/tut/1hpv.pdb, copy\n', '< HEADER HYDROLASE (ACID PROTEINASE) 18-NOV-94 1HPV 1HPV 2\n', '< COMPND HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478 1HPV 3\n', '< COMPND 2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1- 1HPV 4\n', '< COMPND 3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY- 1HPV 5\n', '< COMPND 4 4-PHENYLBUTANE) 1HPV 6\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "../data/tut/1hpv.pdb" loaded as "copy".\n', '< PyMOL>create copy_ligand, copy and organic\n', '< Selector: found 35 atoms.\n', '< Executive: object "copy_ligand" created.\n', '< PyMOL>create copy_protein, copy and polymer\n', '< Selector: found 1516 atoms.\n', '< Executive: object "copy_protein" created.\n', '< PyMOL>create copy_protein2, copy and polymer\n', '< Selector: found 1516 atoms.\n', '< Executive: object "copy_protein2" created.\n', '< PyMOL>delete copy\n', '< PyMOL>matrix_transfer protein, copy_protein2\n', '< PyMOL>fit copy_protein, protein\n', '< Executive: RMS = 0.000 (1516 to 1516 atoms)\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>load ../data/tut/1hpv.pdb, target\n', '< HEADER HYDROLASE (ACID PROTEINASE) 18-NOV-94 1HPV 1HPV 2\n', '< COMPND HIV-1 PROTEASE (E.C.3.4.23.-) COMPLEXED WITH VX-478 1HPV 3\n', '< COMPND 2 (3(S)-N-(3-TETRAHYDROFURANYLOXYCARBONYL) AMINO-1- 1HPV 4\n', '< COMPND 3 (N,N-ISOBUTYL,4-AMINOBENZENESULFONYL) AMINO-2-(S)-HYDROXY- 1HPV 5\n', '< COMPND 4 4-PHENYLBUTANE) 1HPV 6\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "../data/tut/1hpv.pdb" loaded as "target".\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/target/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/target/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /target/1HPV/B/VAL`82/CB")))\n', '< [ 14.32 17.77 18.33 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>matrix_transfer target, ligand\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/target/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/target/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /target/1HPV/B/VAL`82/CB")))\n', '< [ 6.86 5.47 8.86 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>fit protein, target\n', '< Executive: RMS = 0.000 (1516 to 1516 atoms)\n', '< PyMOL>dump_mat(cmd.get_object_matrix("protein"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("ligand"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [ 6.86 5.47 8.86 ]\n', '< PyMOL>matrix_transfer protein, ligand\n', '< PyMOL>dump_lst((cmd.get_distance("ligand////s1","/protein/1HPV/B/ILE`84/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/C4","/protein/1HPV/B/ILE`50/CB"), \\\n', '< PyMOL>cmd.get_distance("/ligand/1HPV//478`200/O3"," /protein/1HPV/B/VAL`82/CB")))\n', '< [ 6.86 5.47 8.86 ]\n', '< PyMOL>dump_lst((cmd.get_distance("/target/1HPV/B/ILE`84/CB","/copy_protein2/1HPV/B/ILE`84/CB"),))\n', '< [ 19.55 ]\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))\n', '< [ 0.00 -0.94 0.34 30.89 \n', '< 0.77 0.22 0.60 11.28 \n', '< -0.64 0.26 0.72 13.10 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>matrix_reset copy_protein2\n', '< PyMOL>dump_mat(cmd.get_object_matrix("copy_protein2"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>dump_lst((cmd.get_distance("/target/1HPV/B/ILE`84/CB","/copy_protein2/1HPV/B/ILE`84/CB"),))\n', '< [ 0.00 ]\n'] run_tests: C1000viewing... run_tests: C1000viewing.log DIFFERS over about 264 lines: ['1,527d0\n', '< PyMOL>bg white\n', '< PyMOL>bg_color black\n', '< PyMOL>bg_color 0\n', '< PyMOL>bg_color 1\n', '< PyMOL>bg_color blue\n', '< PyMOL>bg_color -28374283\n', '< Color-Error: Bad color name.\n', '< PyMOL>bg_color 239283498\n', '< Color-Error: Bad color name.\n', '< PyMOL>bg_color asdfasdf\n', '< Color-Error: Bad color name.\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>clip\n', '< Parsing-Error: missing required argument: mode\n', '< PyMOL>clip near\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>clip near,-5\n', '< PyMOL>clip far,10\n', '< PyMOL>clip near,2\n', '< PyMOL>clip far,-3\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 43.000 93.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER ENTEROTOXIN 20-MAR-96 1TII\n', '< TITLE ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND 3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND 4 SYNONYM: LT-IIB;\n', '< COMPND 5 ENGINEERED: YES;\n', '< COMPND 6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>hide\n', '< PyMOL>show cartoon\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 67216 graphics primitives.\n', '< PyMOL>cartoon rect\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 39552 graphics primitives.\n', '< PyMOL>cartoon loop\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 59232 graphics primitives.\n', '< PyMOL>cartoon tube\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 88720 graphics primitives.\n', '< PyMOL>cartoon oval\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 98720 graphics primitives.\n', '< PyMOL>cartoon arrow\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 39552 graphics primitives.\n', '< PyMOL>cartoon dumbbell\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 138176 graphics primitives.\n', '< PyMOL>cartoon automatic\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 67216 graphics primitives.\n', '< PyMOL>cartoon loop,ss h\n', '< PyMOL>cartoon tube,ss s\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 66876 graphics primitives.\n', '< PyMOL>cartoon skip,resi 1-100\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 10678 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>color\n', '< Parsing-Error: missing required argument: color\n', '< PyMOL>color -123454\n', '< Color-Error: Unknown color.\n', '< PyMOL>color 1023912\n', '< Color-Error: Unknown color.\n', '< PyMOL>color blue\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>color red\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>color 99\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>color blue,pept\n', '< Executive: Colored 107 atoms and 1 object.\n', '< PyMOL>color green,cgo\n', '< Executive: Colored 1 object.\n', '< PyMOL>color red,(all)\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>cgo_tuple = (SPHERE, 0.0, 0.0, 0.0, 1.0)\n', "< PyMOL>cmd.load_cgo(cgo_tuple,'cgo')\n", '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 1 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1\n', '< TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND 3 CHAIN: A, B;\n', '< COMPND 4 ENGINEERED: YES;\n', '< COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 2 symmetry operators.\n', '< CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>disable\n', '< PyMOL>enable pept\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable 3al1\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 1266 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 1432 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable all\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 1432 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable 3al1\n', '< PyMOL>enable pept\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 1432 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>hide\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>show (name ca)\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>show (name c)\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 13 graphics primitives.\n', '< PyMOL>show (all)\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>hide (name ca)\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 115 graphics primitives.\n', '< PyMOL>hide\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>show sticks\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>show spheres,(name ca)\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 179 graphics primitives.\n', '< PyMOL>show surface,(not name n)\n', '< PyMOL>hide (name o)\n', '< PyMOL>ray\n', '< RepSurface: 1319 surface points.\n', '< RepSurface: 2634 triangles.\n', '< RayRenderTest: obtained 2412 graphics primitives.\n', '< PyMOL>hide surf\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 153 graphics primitives.\n', '< PyMOL>hide sph\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 140 graphics primitives.\n', '< PyMOL>hide sticks\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>label (all),resi\n', '< Label: labelled 107 atoms.\n', '< PyMOL>label (name ca),"ca"\n', '< Label: labelled 13 atoms.\n', '< PyMOL>label (name n),"%s-%s-%s"%(chain,resi,resn)\n', '< Label: labelled 13 atoms.\n', "< PyMOL>label (all),''\n", '< Label: labelled 107 atoms.\n', '< PyMOL>label (all)\n', '< Label: labelled 107 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>move\n', '< Parsing-Error: missing required argument: axis\n', '< PyMOL>move x\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>move y\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>move z\n', '< Parsing-Error: missing required argument: distance\n', '< PyMOL>move x,10\n', '< PyMOL>move y,5\n', '< PyMOL>move z,2\n', '< PyMOL>move z,-1\n', '< PyMOL>move x,-10\n', '< PyMOL>move y,2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 7.000 -49.000 0.000 0.000 0.000 39.000 99.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>orient\n', '< PyMOL>orient (none)\n', '< PyMOL>orient (name ca)\n', '< PyMOL>orient (resi 10)\n', '< PyMOL>orient (name ca and i. 10)\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>origin\n', '< PyMOL>origin (none)\n', '< PyMOL>origin (name ca)\n', '< PyMOL>origin (resi 10)\n', '< PyMOL>origin (name ca and i. 10)\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>show dots\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 6837 graphics primitives.\n', '< PyMOL>alter (all),vdw=5.0\n', '< Alter: modified 107 atoms.\n', '< PyMOL>refresh\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 6837 graphics primitives.\n', '< PyMOL>rebuild\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 1960 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>color shoot\n', '< Color-Error: Unknown color.\n', '< PyMOL>set_color shoot,[1.0,0.9,1.0]\n', '< Color: "shoot" defined as [ 1.000, 0.900, 1.000 ].\n', '< PyMOL>color shoot\n', '< Executive: Colored 107 atoms.\n', '< PyMOL>refresh\n', '< PyMOL>set_color shoot,[1.0,0.0,1.0]\n', '< Color: "shoot" defined as [ 1.000, 0.000, 1.000 ].\n', '< PyMOL>recolor\n', '< PyMOL>refresh\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(v1)\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>turn\n', '< Parsing-Error: missing required argument: axis\n', '< PyMOL>turn x\n', '< Parsing-Error: missing required argument: angle\n', '< PyMOL>turn y\n', '< Parsing-Error: missing required argument: angle\n', '< PyMOL>turn z\n', '< Parsing-Error: missing required argument: angle\n', '< PyMOL>turn x,10\n', '< PyMOL>turn y,5\n', '< PyMOL>turn z,2\n', '< PyMOL>turn z,-1\n', '< PyMOL>turn x,-10\n', '< PyMOL>turn y,2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 0.992 0.002 -0.124 -0.002 1.000 -0.001 0.124 0.001 0.992\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>reset\n', '< PyMOL>view\n', '< Parsing-Error: missing required argument: key\n', '< PyMOL>view 1,store\n', '< view: view stored as "1".\n', '< PyMOL>view 2,store\n', '< view: view stored as "2".\n', '< PyMOL>move x,10\n', '< PyMOL>view 2,st\n', '< view: view stored as "2".\n', '< PyMOL>reset\n', '< PyMOL>move y,-10\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 -10.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>view 1,recall\n', '< view: "1" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 0.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>view 2,rec\n', '< view: "2" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000\n', '< 10.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>turn x,10\n', '< PyMOL>view test,store\n', '< view: view stored as "test".\n', '< PyMOL>turn x,20\n', '< PyMOL>view rest,store\n', '< view: view stored as "rest".\n', '< PyMOL>view test\n', '< view: "test" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 10.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>view rest\n', '< view: "rest" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.866 0.500 0.000 -0.500 0.866\n', '< 10.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>view rest,clear\n', "< view: 'rest' deleted.\n", '< PyMOL>view rest\n', "< Error: unknown view: 'rest'. Choices:\n", '< 1 2 test\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.866 0.500 0.000 -0.500 0.866\n', '< 10.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>view test\n', '< view: "test" recalled.\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 10.000 0.000 -50.000 0.000 0.000 0.000 40.000 100.000 -20.000\n', '< PyMOL>viewport\n', '< PyMOL>viewport 300\n', '< PyMOL>viewport 100,100\n', '< PyMOL>viewport 300,300\n', '< PyMOL>viewport 640,480\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>zoom\n', '< PyMOL>zoom resi 10\n', '< PyMOL>zoom resi 4,5,6\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -14.178 2.395 -9.290 18.016 11.178 17.178 -20.000\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb,m1\n', '< HEADER ENTEROTOXIN 20-MAR-96 1TII\n', '< TITLE ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND 3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND 4 SYNONYM: LT-IIB;\n', '< COMPND 5 ENGINEERED: YES;\n', '< COMPND 6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "dat/1tii.pdb" loaded as "m1".\n', '< PyMOL>load dat/il2.pdb,m1\n', '< CmdLoad: "dat/il2.pdb" appended into object "m1", state 2.\n', '< PyMOL>load dat/pept.pdb,m1\n', '< CmdLoad: "dat/pept.pdb" appended into object "m1", state 3.\n', '< PyMOL>zoom m1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -269.487 39.950 5.709 13.189 212.466 326.509 -20.000\n', '< PyMOL>zoom m1,state=0\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -269.487 39.950 5.709 13.189 212.466 326.509 -20.000\n', '< PyMOL>zoom m1,state=1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -227.278 51.665 11.519 10.196 179.188 275.368 -20.000\n', '< PyMOL>zoom m1,state=2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -149.541 9.985 -9.318 20.976 117.899 181.182 -20.000\n', '< PyMOL>zoom m1,state=3\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>zoom m1,state=4\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>origin m1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 38.726 17.022 -67.659 39.950 5.709 13.189 49.820 76.561 -20.000\n', '< PyMOL>origin m1,state=0\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 38.726 17.022 -67.659 39.950 5.709 13.189 49.820 76.561 -20.000\n', '< PyMOL>origin m1,state=1\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 50.441 23.264 -69.598 51.665 11.519 10.196 49.820 76.561 -20.000\n', '< PyMOL>origin m1,state=2\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 8.761 0.872 -62.600 9.985 -9.318 20.976 49.820 76.561 -20.000\n', '< PyMOL>origin m1,state=3\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>origin m1,state=4\n', '< PyMOL>cmd._dump_floats(cmd.get_view(0))\n', '< 1.000 0.000 0.000 0.000 0.985 0.174 0.000 -0.174 0.985\n', '< 0.000 0.000 -63.191 1.224 -10.279 20.545 49.820 76.561 -20.000\n', '< PyMOL>orient m1\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.924 0.347 0.160 0.338 0.550 0.763 0.177 0.760 0.626\n', '< 0.000 0.000 269.487 39.950 5.709 13.189 212.466 326.509 20.000\n', '< PyMOL>orient m1,state=0\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.924 0.347 0.160 0.338 0.550 0.763 0.177 0.760 0.626\n', '< 0.000 0.000 269.487 39.950 5.709 13.189 212.466 326.509 20.000\n', '< PyMOL>orient m1,state=1\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.899 0.239 0.366 0.288 0.306 0.907 0.329 0.921 0.206\n', '< 0.000 0.000 227.278 51.665 11.519 10.196 179.188 275.368 20.000\n', '< PyMOL>orient m1,state=2\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.288 0.019 0.958 0.301 0.951 0.072 0.909 0.309 0.279\n', '< 0.000 0.000 149.541 9.985 9.318 20.976 117.899 181.182 20.000\n', '< PyMOL>orient m1,state=3\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.537 0.312 0.784 0.841 0.118 0.529 0.072 0.943 0.325\n', '< 0.000 0.000 63.191 1.224 10.279 20.545 49.820 76.561 20.000\n', '< PyMOL>orient m1,state=4\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.537 0.312 0.784 0.841 0.118 0.529 0.072 0.943 0.325\n', '< 0.000 0.000 63.191 1.224 10.279 20.545 49.820 76.561 20.000\n', '< PyMOL>zoom m1,state=-5000\n', '< PyMOL>zoom (none),state=5\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< PyMOL>zoom (all),state=-1\n', '< PyMOL>zoom (all),state=0\n', '< PyMOL>cmd._dump_ufloats(cmd.get_view(0))\n', '< 0.537 0.312 0.784 0.841 0.118 0.529 0.072 0.943 0.325\n', '< 0.000 0.000 269.487 39.950 5.709 13.189 212.466 326.509 20.000\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER ENTEROTOXIN 20-MAR-96 1TII\n', '< TITLE ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND 3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND 4 SYNONYM: LT-IIB;\n', '< COMPND 5 ENGINEERED: YES;\n', '< COMPND 6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii")[0])\n', '< 11.590 -22.877 -28.270\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii")[1])\n', '< 84.681 40.101 47.233\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII")[0])\n', '< 11.590 -22.877 -28.270\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII")[1])\n', '< 84.681 40.101 47.233\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii")[0])\n', '< 11.590 -22.877 -28.270\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii")[1])\n', '< 84.681 40.101 47.233\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii////cA")[0])\n', '< 12.578 -21.622 -23.339\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1tii////ca")[1])\n', '< 81.195 38.760 45.050\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII////cA")[0])\n', '< 12.578 -21.622 -23.339\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1TII////ca")[1])\n', '< 81.195 38.760 45.050\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii////cA")[0])\n', '< 12.578 -21.622 -23.339\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("1Tii////ca")[1])\n', '< 81.195 38.760 45.050\n', '< PyMOL>dist TSt,/1tii//A/TYR`3/CD1, /1tii//F/ARG`12/NE\n', '< Executive: object "TSt" created.\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tst")[0])\n', '< 35.306 24.391 -8.737\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tst")[1])\n', '< 77.385 25.286 6.130\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("TST")[0])\n', '< 35.306 24.391 -8.737\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("TST")[1])\n', '< 77.385 25.286 6.130\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tSt")[0])\n', '< 35.306 24.391 -8.737\n', '< PyMOL>cmd._dump_floats(cmd.get_extent("tSt")[1])\n', '< 77.385 25.286 6.130\n'] run_tests: C1010helping... run_tests: C1010helping.log DIFFERS over about 27 lines: ['1,53d0\n', '< PyMOL>help\n', '< \n', '< COMMANDS\n', '< \n', '< INPUT/OUTPUT load save delete quit\n', '< VIEW turn move clip rock\n', '< show hide enable disable\n', '< reset refresh rebuild \n', '< zoom origin orient \n', '< view get_view set_view\n', '< MOVIES mplay mstop mset mdo\n', '< mpng mmatrix frame\n', '< rewind middle ending\n', '< forward backward\n', '< IMAGING png mpng\n', '< RAY TRACING ray \n', '< MAPS isomesh isodot\n', '< DISPLAY cls viewport splash \n', '< SELECTIONS select mask \n', '< SETTINGS set button\n', '< ATOMS alter alter_state \n', '< EDITING create replace remove h_fill remove_picked\n', '< edit bond unbond h_add fuse \n', '< undo redo protect cycle_valence attach\n', '< FITTING fit rms rms_cur pair_fit \n', '< intra_fit intra_rms intra_rms_cur \n', '< COLORS color set_color\n', '< HELP help commands\n', '< DISTANCES dist \n', '< STEREO stereo\n', '< SYMMETRY symexp\n', '< SCRIPTS @ run\n', '< LANGUAGE alias extend\n', '< \n', '< Try "help ". Also see the following extra topics:\n', '< \n', '< "movies", "keyboard", "mouse", "selections",\n', '< "examples", "launching", "editing", and "api". \n', '< \n', '< PyMOL>help dummy\n', '< \n', '< DESCRIPTION\n', '< \n', '< This is a dummy function which returns None. \n', '< \n', "< PyMOL>cmd.show_help('dummy')\n", '< PyMOL>help dummy\n', '< \n', '< DESCRIPTION\n', '< \n', '< This is a dummy function which returns None. \n', '< \n', '< (Hit ESC to hide)\n'] run_tests: C1020querying... run_tests: C1020querying.log DIFFERS over about 123 lines: ['1,245d0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>count_atoms\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms name ca\n', '< count_atoms: 13 atoms\n', '< PyMOL>count_states\n', '< cmd.count_states: 1 states.\n', '< PyMOL>create pept,(all),1,2\n', '< Selector: found 107 atoms.\n', '< PyMOL>create pept,(all),1,3\n', '< Selector: found 107 atoms.\n', '< PyMOL>create pept,(none),1,2\n', '< Selector: found 0 atoms.\n', '< PyMOL>create cpy,(all),1,1\n', '< Selector: found 107 atoms.\n', '< Executive: object "cpy" created.\n', '< PyMOL>count_states\n', '< cmd.count_states: 3 states.\n', '< PyMOL>count_states pept\n', '< cmd.count_states: 3 states.\n', '< PyMOL>count_states cpy\n', '< cmd.count_states: 1 states.\n', '< PyMOL>count_frames\n', '< cmd.count_frames: 3 frames\n', '< PyMOL>mset 1 x10\n', '< PyMOL>count_frames\n', '< cmd.count_frames: 10 frames\n', '< PyMOL>cmd.count_frames()\n', '< PyMOL>cmd.count_states()\n', '< PyMOL>cmd.count_atoms()\n', '< PyMOL>dist\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>distance\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>select lb,resi 5 and name ca\n', '< Selector: selection "lb" defined with 2 atoms.\n', '< PyMOL>dist\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>select rb,resi 8 and name ca\n', '< Selector: selection "rb" defined with 2 atoms.\n', '< PyMOL>dist\n', "< cmd-Error: The 'pk1' selection is undefined.\n", "< cmd-Error: The 'pk2' selection is undefined.\n", '< PyMOL>dist (lb),resi 10 and name ca\n', '< Executive: object "dist01" created.\n', '< PyMOL>distance resi 6 and name n,resi 9\n', '< Executive: object "dist02" created.\n', '< PyMOL>distance resi 7 and name ca,all,3.0,zoom=1\n', '< Executive: object "dist03" created.\n', '< PyMOL>print "%6.3f"%cmd.distance("resi 1 and name ca","resi 13 and name ca")\n', '< 5.762\n', '< PyMOL>print "%6.3f"%cmd.distance("resi 1 and name ca","resi 14 and name ca")\n', '< -1.000\n', '< PyMOL>print cmd.find_pairs("name o","name n",mode=1,cutoff=3.4)\n', "< [(('cpy', 103), ('pept', 1)), (('pept', 103), ('pept', 1)), (('cpy', 83), ('pept', 15)), (('pept', 83), ('pept', 15)), (('cpy', 59), ('pept', 34)), (('pept', 59), ('pept', 34)), (('cpy', 47), ('pept', 56)), (('cpy', 37), ('pept', 56)), (('pept', 47), ('pept', 56)), (('pept', 37), ('pept', 56)), (('cpy', 18), ('pept', 73)), (('pept', 18), ('pept', 73)), (('cpy', 4), ('pept', 100)), (('pept', 4), ('pept', 100)), (('cpy', 103), ('cpy', 1)), (('pept', 103), ('cpy', 1)), (('cpy', 83), ('cpy', 15)), (('pept', 83), ('cpy', 15)), (('cpy', 59), ('cpy', 34)), (('pept', 59), ('cpy', 34)), (('cpy', 47), ('cpy', 56)), (('cpy', 37), ('cpy', 56)), (('pept', 47), ('cpy', 56)), (('pept', 37), ('cpy', 56)), (('cpy', 18), ('cpy', 73)), (('pept', 18), ('cpy', 73)), (('cpy', 4), ('cpy', 100)), (('pept', 4), ('cpy', 100))]\n", '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_area (none)\n', '< cmd.get_area: 0.000 Angstroms^2.\n', '< PyMOL>get_area\n', '< cmd.get_area: 1381.186 Angstroms^2.\n', '< PyMOL>get_area state=2\n', '< Area-Error: Invalid state.\n', '< PyMOL>get_area name ca\n', '< cmd.get_area: 112.133 Angstroms^2.\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1\n', '< TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND 3 CHAIN: A, B;\n', '< COMPND 4 ENGINEERED: YES;\n', '< COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 2 symmetry operators.\n', '< CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>get_area\n', '< Area-Error: Selection must be within a single object.\n', '< PyMOL>dele all\n', '< PyMOL>print lst\n', "< [('white', 0), ('black', 1), ('blue', 2), ('green', 3), ('red', 4), ('cyan', 5), ('yellow', 6), ('dash', 7), ('magenta', 8), ('salmon', 9)]\n", '< PyMOL>print cmd.get_color_tuple("red")\n', '< (1.0, 0.0, 0.0)\n', '< PyMOL>print cmd.get_color_tuple("blue")\n', '< (0.0, 0.0, 1.0)\n', '< PyMOL>print cmd.get_color_tuple("green")\n', '< (0.0, 1.0, 0.0)\n', '< PyMOL>print cmd.get_color_tuple("white")\n', '< (1.0, 1.0, 1.0)\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_dihedral 1/n,1/ca,1/c,1/o\n', '< cmd.get_dihedral: -8.586 degrees.\n', '< -5.188 -20.331 13.157 8.919 0.863 27.058\n', '< -5.063 -17.973 17.858 7.053 -2.295 25.698\n', '< PyMOL>print len(cmd.get_model().atom)\n', '< 107\n', '< PyMOL>print len(cmd.get_model("resi 1").bond)\n', '< 7\n', '< PyMOL>dele all\n', '< PyMOL>print cmd.get_names()\n', '< []\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>print cmd.get_names()\n', "< ['pept']\n", '< PyMOL>edit 4/ca\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>print cmd.get_names("all")\n', "< ['pept', 'pk1', '_pkbase1', '_pkfrag1', '_pkbase2', '_pkfrag2', 'pkmol']\n", '< PyMOL>print cmd.get_names("selections")\n', "< ['pk1', '_pkbase1', '_pkfrag1', '_pkbase2', '_pkfrag2', 'pkmol']\n", '< PyMOL>print cmd.get_names("objects")\n', "< ['pept']\n", '< PyMOL>print cmd.get_names_of_type("object:molecule")\n', "< ['pept']\n", '< PyMOL>print cmd.get_names_of_type("object:map")\n', '< []\n', '< PyMOL>kee = pp.keys()[0]\n', '< PyMOL>print kee\n', "< ('pept', 10)\n", '< PyMOL>cmd._dump_floats(pp[kee])\n', '< -124.163 170.604\n', '< PyMOL>reset\n', '< PyMOL>get_position\n', '< cmd.get_position: [ 1.224, -10.279, 20.545]\n', '< PyMOL>zoom resi 10\n', '< PyMOL>get_position\n', '< cmd.get_position: [ 2.395, -9.290, 18.016]\n', '< PyMOL>get_type\n', '< Parsing-Error: missing required argument: name\n', '< PyMOL>get_type nonexistent\n', '< cmd-Error: unrecognized name.\n', '< PyMOL>get_type pept\n', '< object:molecule\n', '< PyMOL>id_atom none\n', '< cmd-Error: atom none not found by id_atom.\n', '< PyMOL>id_atom all\n', '< cmd-Error: multiple atoms all found by id_atom.\n', '< PyMOL>id_atom 5/ca\n', '< cmd.id_atom: (id 35)\n', '< PyMOL>identify name ca\n', '< cmd.identify: (id 2)\n', '< cmd.identify: (id 10)\n', '< cmd.identify: (id 16)\n', '< cmd.identify: (id 21)\n', '< cmd.identify: (id 35)\n', '< cmd.identify: (id 45)\n', '< cmd.identify: (id 53)\n', '< cmd.identify: (id 57)\n', '< cmd.identify: (id 66)\n', '< cmd.identify: (id 74)\n', '< cmd.identify: (id 81)\n', '< cmd.identify: (id 95)\n', '< cmd.identify: (id 101)\n', '< PyMOL>index name ca\n', '< cmd.index: (pept`2)\n', '< cmd.index: (pept`10)\n', '< cmd.index: (pept`16)\n', '< cmd.index: (pept`21)\n', '< cmd.index: (pept`35)\n', '< cmd.index: (pept`45)\n', '< cmd.index: (pept`53)\n', '< cmd.index: (pept`57)\n', '< cmd.index: (pept`66)\n', '< cmd.index: (pept`74)\n', '< cmd.index: (pept`81)\n', '< cmd.index: (pept`95)\n', '< cmd.index: (pept`101)\n', '< PyMOL>overlap pept,pept\n', '< cmd.overlap: 549.083 Angstroms.\n', '< PyMOL>alter (all),vdw=0.0\n', '< Alter: modified 107 atoms.\n', '< PyMOL>overlap pept,pept\n', '< cmd.overlap: 0.000 Angstroms.\n', '< PyMOL>alter (all),vdw=0.5\n', '< Alter: modified 107 atoms.\n', '< PyMOL>overlap pept,pept\n', '< cmd.overlap: 53.500 Angstroms.\n', '< PyMOL>phi_psi all\n', '< CYS-2: ( -124.2, 170.6 )\n', '< ALA-3: ( -128.4, 140.0 )\n', '< TRP-4: ( -128.5, 135.2 )\n', '< HIS-5: ( -114.1, 109.1 )\n', '< LEU-6: ( 53.9, 41.8 )\n', '< GLY-7: ( 90.4, -28.0 )\n', '< GLU-8: ( -75.5, 138.7 )\n', '< LEU-9: ( -73.5, 125.3 )\n', '< VAL-10: ( -91.9, -61.0 )\n', '< TRP-11: ( -168.2, 159.0 )\n', '< CYS-12: ( -138.9, 133.5 )\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_symmetry\n', '< get_symmetry: No symmetry defined.\n', '< PyMOL>get_symmetry pept\n', '< get_symmetry: No symmetry defined.\n', '< PyMOL>get_symmetry none\n', '< Error: selection must refer to exactly one object.\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1\n', '< TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND 3 CHAIN: A, B;\n', '< COMPND 4 ENGINEERED: YES;\n', '< COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 2 symmetry operators.\n', '< CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>get_symmetry\n', '< Error: selection must refer to exactly one object.\n', '< PyMOL>get_symmetry 3al1\n', '< get_symmetry: A = 20.544 B = 20.859 C = 26.055\n', '< get_symmetry: Alpha = 101.160 Beta = 97.030 Gamma = 118.060\n', '< get_symmetry: SpaceGroup = P -1\n', '< PyMOL>get_symmetry pept\n', '< get_symmetry: No symmetry defined.\n', '< PyMOL>hide\n', '< PyMOL>show cell,pept\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>apply(cmd.set_symmetry,["pept"]+cmd.get_symmetry("3al1"))\n', '< Symmetry: Found 2 symmetry operators.\n', '< PyMOL>get_symmetry pept\n', '< get_symmetry: A = 20.544 B = 20.859 C = 26.055\n', '< get_symmetry: Alpha = 101.160 Beta = 97.030 Gamma = 118.060\n', '< get_symmetry: SpaceGroup = P -1\n', '< PyMOL>get_symmetry 3al1\n', '< get_symmetry: A = 20.544 B = 20.859 C = 26.055\n', '< get_symmetry: Alpha = 101.160 Beta = 97.030 Gamma = 118.060\n', '< get_symmetry: SpaceGroup = P -1\n', '< PyMOL>show cell,pept\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 12 graphics primitives.\n'] run_tests: C1030selecting... run_tests: C1030selecting.log DIFFERS over about 62 lines: ['1,123d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>select (resi trp)\n', '< Selector: selection "sel01" defined with 0 atoms.\n', '< PyMOL>indicate (name ca)\n', '< PyMOL>deselect\n', '< PyMOL>select 1/o\n', '< Selector: selection "sel02" defined with 1 atoms.\n', '< PyMOL>select 1/o+ca+n\n', '< Selector: selection "sel03" defined with 3 atoms.\n', '< PyMOL>select /pept\n', '< Selector: selection "sel04" defined with 107 atoms.\n', '< PyMOL>select bb = (name ca or name c or name n)\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (name ca,c,n)\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = */ca+c+n\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (*/ca,c,n)\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (not (not (name ca or name c or name n)))\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (not (not (n. c|n. ca|n. n)))\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (not (not (not (not (not (not (not (not (not (not (not (not (not (not (*/ca,c,n)))))))))))))))\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = (all and all and all and (not (not all)) and (not none) and all and not (not (n;ca,c,n)))\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb,(name ca or (n;c | (n. n) | (*/n)))\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb, \\\n', '< PyMOL>name ca \\\n', '< PyMOL>or name c \\\n', '< PyMOL>or name n\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = bb\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select bb = not not bb\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>select cc = not bb\n', '< Selector: selection "cc" defined with 68 atoms.\n', '< PyMOL>select bb = not cc\n', '< Selector: selection "bb" defined with 39 atoms.\n', '< PyMOL>enable\n', '< PyMOL>enable bb\n', '< PyMOL>enable cc\n', '< PyMOL>disable cc\n', '< PyMOL>hide lines,cc\n', '< PyMOL>hide lines,bb\n', '< PyMOL>show (bb)\n', '< PyMOL>set ray_default_renderer=2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 63 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/1tii.pdb\n', '< HEADER ENTEROTOXIN 20-MAR-96 1TII\n', '< TITLE ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: HEAT LABILE ENTEROTOXIN TYPE IIB;\n', '< COMPND 3 CHAIN: D, E, F, G, H, A, C;\n', '< COMPND 4 SYNONYM: LT-IIB;\n', '< COMPND 5 ENGINEERED: YES;\n', '< COMPND 6 OTHER_DETAILS: LATENT/INACTIVE FORM\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 6 symmetry operators.\n', '< CmdLoad: "dat/1tii.pdb" loaded as "1tii".\n', '< PyMOL>count_atoms 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+23+24+25+26+27+28+29+30+31+32+33+34+35+36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230/\n', '< count_atoms: 5655 atoms\n', '< PyMOL>print cmd.count_atoms("resi 1+2+3+4+5+6+7+8+9+10+11+12+13+14+15+16+17+18+19+20+21+22+23+24+25+26+27+28+29+30+31+32+33+34+35+36+37+38+39+40+41+42+43+44+45+46+47+48+49+50+51+52+53+54+55+56+57+58+59+60+61+62+63+64+65+66+67+68+69+70+71+72+73+74+75+76+77+78+79+80+81+82+83+84+85+86+87+88+89+90+91+92+93+94+95+96+97+98+99+100+101+102+103+104+105+106+107+108+109+110+111+112+113+114+115+116+117+118+119+120+121+122+123+124+125+126+127+128+129+130+131+132+133+134+135+136+137+138+139+140+141+142+143+144+145+146+147+148+149+150+151+152+153+154+155+156+157+158+159+160+161+162+163+164+165+166+167+168+169+170+171+172+173+174+175+176+177+178+179+180+181+182+183+184+185+186+187+195+196+197+198+199+200+201+202+203+204+205+206+207+208+209+210+211+212+213+214+215+216+217+218+219+220+221+222+223+224+225+226+227+228+229+230")\n', '< 5655\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/tiny.pdb, model\n', '< Executive-Warning: name "model" collides with a selection language keyword.\n', '< CmdLoad: "dat/tiny.pdb" loaded as "model".\n', '< PyMOL>load dat/small01.mol, test+me\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "test+me", through state 1.\n', '< PyMOL>load dat/small02.pdb, mymodel\n', '< CmdLoad: "dat/small02.pdb" loaded as "mymodel".\n', '< PyMOL>load dat/small03.mol2, model2\n', '< ObjectMoleculeReadStr: read through molecule 1.\n', '< ObjectMoleculeReadStr: read through molecule 2.\n', '< ObjectMoleculeReadStr: read through molecule 3.\n', '< ObjectMoleculeReadStr: read through molecule 4.\n', '< ObjectMoleculeReadStr: read through molecule 5.\n', '< ObjectMoleculeReadStr: read through molecule 6.\n', '< ObjectMoleculeReadStr: read through molecule 7.\n', '< ObjectMoleculeReadStr: read through molecule 8.\n', '< ObjectMoleculeReadStr: read through molecule 9.\n', '< ObjectMoleculeReadStr: read through molecule 10.\n', '< ExecutiveLoad: "dat/small03.mol2" loaded as "model2", through state 16.\n', '< PyMOL>count_atoms model\n', '< Selector-Error: Misplaced ).\n', '< Selector-Error: Malformed selection.\n', '< ( model )<--\n', '< count_atoms: -1 atoms\n', '< PyMOL>count_atoms model model\n', '< count_atoms: 37 atoms\n', '< PyMOL>count_atoms /model\n', '< count_atoms: 37 atoms\n', '< PyMOL>count_atoms pept\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms model model pept\n', '< count_atoms: 144 atoms\n', '< PyMOL>count_atoms /model+pept\n', '< count_atoms: 144 atoms\n', '< PyMOL>count_atoms /pept+model\n', '< count_atoms: 144 atoms\n', '< PyMOL>count_atoms /test+\\me\n', '< count_atoms: 36 atoms\n', '< PyMOL>count_atoms /pept+model+test\\+me\n', '< count_atoms: 180 atoms\n', '< PyMOL>count_atoms test+me\n', '< count_atoms: 36 atoms\n', '< PyMOL>count_atoms test+me model model\n', '< count_atoms: 73 atoms\n', '< PyMOL>count_atoms mymodel\n', '< count_atoms: 36 atoms\n', '< PyMOL>count_atoms model2\n', '< count_atoms: 389 atoms\n'] run_tests: C1035wildcards... run_tests: C1035wildcards.log DIFFERS over about 53 lines: ['1,106d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>count_atoms name C*\n', '< count_atoms: 69 atoms\n', '< PyMOL>count_atoms */C*\n', '< count_atoms: 69 atoms\n', '< PyMOL>count_atoms A*/\n', '< count_atoms: 13 atoms\n', '< PyMOL>count_atoms A*/O*\n', '< count_atoms: 4 atoms\n', "< PyMOL>alter all,segi='FOUR'\n", '< Alter: modified 107 atoms.\n', "< PyMOL>alter 1-5/,segi='FIRE'\n", '< Alter: modified 43 atoms.\n', "< PyMOL>alter 6-7/,segi='SORE'\n", '< Alter: modified 12 atoms.\n', '< PyMOL>count_atoms F*///\n', '< count_atoms: 95 atoms\n', '< PyMOL>count_atoms F*R*///\n', '< count_atoms: 95 atoms\n', '< PyMOL>count_atoms F*R///\n', '< count_atoms: 52 atoms\n', '< PyMOL>count_atoms *R*///\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms *IRE///\n', '< count_atoms: 43 atoms\n', '< PyMOL>count_atoms *RE///\n', '< count_atoms: 55 atoms\n', '< PyMOL>count_atoms *E///\n', '< count_atoms: 55 atoms\n', '< PyMOL>count_atoms *O*///\n', '< count_atoms: 64 atoms\n', '< PyMOL>count_atoms chain E\n', '< count_atoms: 107 atoms\n', "< PyMOL>alter 1-3/,chain='A'\n", '< Alter: modified 19 atoms.\n', "< PyMOL>alter 6-9/,chain='B'\n", '< Alter: modified 29 atoms.\n', "< PyMOL>alter 10-11/,chain='G'\n", '< Alter: modified 21 atoms.\n', '< PyMOL>count_atoms chain A\n', '< count_atoms: 19 atoms\n', '< PyMOL>count_atoms chain A:B\n', '< count_atoms: 48 atoms\n', '< PyMOL>count_atoms chain B:F\n', '< count_atoms: 67 atoms\n', '< PyMOL>count_atoms chain A:Z\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms chain A+E\n', '< count_atoms: 57 atoms\n', '< PyMOL>count_atoms chain A+F\n', '< count_atoms: 19 atoms\n', '< PyMOL>count_atoms */*/*/*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms */*/*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms */*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms */*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms *\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*/*/*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*/*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*/*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms /*\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atom /*/*RE\n', '< count_atoms: 55 atoms\n', '< PyMOL>count_atom /*////ca\n', '< count_atoms: 13 atoms\n', '< PyMOL>count_atom *////ca\n', '< count_atoms: 13 atoms\n', '< PyMOL>count_atom /////ca\n', '< count_atoms: 13 atoms\n', '< PyMOL>create pap,pept and not elem o\n', '< Selector: found 88 atoms.\n', '< Executive: object "pap" created.\n', '< PyMOL>create abt,pept and not elem n\n', '< Selector: found 90 atoms.\n', '< Executive: object "abt" created.\n', '< PyMOL>count_atoms p*\n', '< count_atoms: 195 atoms\n', '< PyMOL>count_atoms *t\n', '< count_atoms: 197 atoms\n', '< PyMOL>count_atoms *pt\n', '< count_atoms: 107 atoms\n', '< PyMOL>count_atoms p*p\n', '< count_atoms: 88 atoms\n', '< PyMOL>count_atoms p*p*\n', '< count_atoms: 195 atoms\n', '< PyMOL>count_atoms a*\n', '< count_atoms: 90 atoms\n', '< PyMOL>count_atoms /p*/*RE\n', '< count_atoms: 101 atoms\n', '< PyMOL>count_atoms /*t/*O*\n', '< count_atoms: 119 atoms\n', '< PyMOL>count_atoms /*pt//A:E\n', '< count_atoms: 86 atoms\n', '< PyMOL>count_atoms /p*/*RE/E/h*/c*\n', '< count_atoms: 12 atoms\n'] run_tests: C1040editing... run_tests: C1040editing.log DIFFERS over about 260 lines: ['1,519d0\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>alter (elem n,o),vdw=4.0\n', '< Alter: modified 36 atoms.\n', '< PyMOL>show dots\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 2032 graphics primitives.\n', '< PyMOL>alter_state 1,(all),x=x+y\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>hide\n', '< PyMOL>show lines\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" appended into object "pept", state 2.\n', '< PyMOL>alter_state -1,(all),x=x+y\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>alter_state 0,(all), x=x+y\n', '< AlterState: modified 214 atom coordinate states.\n', '< PyMOL>alter_state 1,(all), x=x+y\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>alter_state 2,(all), x=x+y\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>alter_state 3,(all), x=x+y\n', '< AlterState: modified 0 atom coordinate states.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>remove hydro\n', '< Remove: eliminated 20 atoms in model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>remove id 17\n', '< Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>count_atoms\n', '< count_atoms: 35 atoms\n', '< PyMOL>edit id 3\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>attach X,4,2\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>edit elem X\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>remove_picked\n', '< Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>unpick\n', '< PyMOL>print cmd.get_names()\n', "< ['small01']\n", '< PyMOL>count_atoms\n', '< count_atoms: 35 atoms\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>unbond id 1,id 2\n', '< Unbond: 1 bonds removed from model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 38 atoms\n', '< PyMOL>remove hydro\n', '< Remove: eliminated 22 atoms in model "small01".\n', '< PyMOL>bond id 1,id 2\n', '< Bond: 1 bonds added to model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>edit id 6,id 10\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>cycle_valence\n', '< Remove: eliminated 2 atoms in model "small01".\n', '< Remove: eliminated 2 atoms in model "small01".\n', '< PyMOL>count_atoms\n', '< count_atoms: 34 atoms\n', '< PyMOL>cycle_valence\n', '< Remove: eliminated 1 atoms in model "small01".\n', '< Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>count_atoms\n', '< count_atoms: 32 atoms\n', '< PyMOL>remove_picked\n', '< PyMOL>bond id 6,id 10,2\n', '< Bond: 1 bonds added to model "small01".\n', '< PyMOL>h_add\n', '< PyMOL>set valence=0.05\n', '< Setting: valence set to on.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 59 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>protect resi 1-6\n', '< Protect: 51 atoms protected from movement.\n', '< PyMOL>edit 2/sg,12/sg\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>torsion 90\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -10.445, -22.170, 11.965]\n', '< cmd.extent: max: [ 6.787, 0.863, 27.058]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>redo\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -10.445, -22.170, 11.965]\n', '< cmd.extent: max: [ 6.787, 0.863, 27.058]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>deprotect\n', '< Protect: 107 atoms deprotected.\n', '< PyMOL>edit 2/sg,12/sg\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< PyMOL>torsion 90\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -15.562, -22.170, 11.965]\n', '< cmd.extent: max: [ 5.893, -8.073, 25.808]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>flag ignore,(!*/ca,c,n,o,cb)\n', '< Flag: flag 25 is set in 43 of 107 atoms.\n', '< PyMOL>flag exfoliate,(*/cb)\n', '< Flag: flag 24 is set in 12 of 107 atoms.\n', '< PyMOL>show surf\n', '< PyMOL>ray\n', '< RepSurface: 921 surface points.\n', '< RepSurface: 1838 triangles.\n', '< RayRenderTest: obtained 1529 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol,m1\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "m1", through state 1.\n', '< PyMOL>load dat/small01.mol,m2\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "m2", through state 1.\n', '< PyMOL>fuse m1 and id 31,m2 and id 31\n', '< PyMOL>dele m1\n', '< PyMOL>zoom\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 144 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol,m1\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "m1", through state 1.\n', '< PyMOL>load dat/small01.mol,m2\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "m2", through state 1.\n', '< PyMOL>remove id 30\n', '< Remove: eliminated 1 atoms in model "m1".\n', '< Remove: eliminated 1 atoms in model "m2".\n', '< PyMOL>fuse m1 and id 12,m2 and id 12\n', '< PyMOL>dele m1\n', '< PyMOL>zoom\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 144 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>edit id 2,id 6, id 5\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< Selector: selection "pk2" defined with 1 atoms.\n', '< Selector: selection "pk3" defined with 1 atoms.\n', '< PyMOL>invert\n', '< Editor: Inverted atom.\n', '< PyMOL>print "%8.3f"%cmd.dist("id 28","id 17")\n', '< 1.957\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>iterate (name n),print resi\n', '< 1\n', '< 2\n', '< 3\n', '< 4\n', '< 5\n', '< 6\n', '< 7\n', '< 8\n', '< 9\n', '< 10\n', '< 11\n', '< 12\n', '< 13\n', '< Iterate: iterated over 13 atoms.\n', '< PyMOL>iterate_state 1,(name o),print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '< 4.456 -15.889 23.517\n', '< 3.025 -12.039 25.188\n', '< 1.332 -9.867 21.362\n', '< 0.752 -5.592 23.297\n', '< -2.092 -3.870 19.914\n', '< -5.181 -3.100 20.933\n', '< -5.188 -7.669 21.049\n', '< -1.643 -7.529 19.691\n', '< -0.699 -9.660 16.692\n', '< 2.708 -11.019 16.296\n', '< 3.449 -13.097 20.534\n', '< 5.278 -17.322 18.998\n', '< 5.962 -19.432 22.570\n', '< IterateState: iterated over 13 atom coordinate states.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>stored.sum = 0\n', '< PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x\n', '< IterateState: iterated over 2084 atom coordinate states.\n', '< PyMOL>print "%8.3f"%stored.sum\n', '< 20809.421\n', '< PyMOL>push_undo (il2)\n', '< PyMOL>alter_state 1,(il2),x=0.0\n', '< AlterState: modified 2084 atom coordinate states.\n', '< PyMOL>rebuild\n', '< PyMOL>stored.sum = 0\n', '< PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x\n', '< IterateState: iterated over 2084 atom coordinate states.\n', '< PyMOL>print "%8.3f"%stored.sum\n', '< 0.000\n', '< PyMOL>edit il2`1\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>undo\n', '< PyMOL>stored.sum = 0\n', '< PyMOL>iterate_state 1,(il2),stored.sum=stored.sum+x\n', '< IterateState: iterated over 2084 atom coordinate states.\n', '< PyMOL>print "%8.3f"%stored.sum\n', '< 20809.421\n', '< PyMOL>rebuild\n', '< PyMOL>show dots\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 111433 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>iterate (all),print name\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< C\n', '< O\n', '< O\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< H\n', '< Iterate: iterated over 36 atoms.\n', '< PyMOL>rename small01\n', '< Rename: renamed 33 atoms.\n', '< PyMOL>iterate (all),print name\n', '< C01\n', '< C02\n', '< C03\n', '< C04\n', '< C05\n', '< C06\n', '< C07\n', '< C08\n', '< C09\n', '< C10\n', '< C11\n', '< C12\n', '< C13\n', '< C\n', '< O14\n', '< O\n', '< H15\n', '< H16\n', '< H17\n', '< H18\n', '< H19\n', '< H20\n', '< H21\n', '< H22\n', '< H23\n', '< H24\n', '< H25\n', '< H26\n', '< H27\n', '< H28\n', '< H29\n', '< H30\n', '< H31\n', '< H32\n', '< H33\n', '< H\n', '< Iterate: iterated over 36 atoms.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>edit id 3\n', '< Selector: selection "pk1" defined with 1 atoms.\n', '< PyMOL>replace N,3,3\n', '< Remove: eliminated 1 atoms in model "small01".\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>origin pept,object=pept\n', '< PyMOL>rotate x,-45,object=pept\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -18.391, 12.126]\n', '< cmd.extent: max: [ 8.919, -1.236, 29.153]\n', '< PyMOL>reset\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -18.391, 12.126]\n', '< cmd.extent: max: [ 8.919, -1.236, 29.153]\n', '< PyMOL>rotate x,45,pept\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_dihedral 1/n,1/ca,1/c,1/o\n', '< cmd.get_dihedral: -8.586 degrees.\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>set_dihedral 1/n,1/ca,1/c,1/o,180\n', '< SetDihedral: adjusted to 180.000\n', '< PyMOL>get_dihedral 1/n,1/ca,1/c,1/o\n', '< cmd.get_dihedral: 180.000 degrees.\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -1.282, -17.809, 6.314]\n', '< cmd.extent: max: [ 10.270, -4.939, 29.070]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>remove not id 3\n', '< Remove: eliminated 35 atoms in model "small01".\n', '< PyMOL>zoom\n', '< PyMOL>count_atoms\n', '< count_atoms: 1 atoms\n', '< PyMOL>set_geometry (id 3),4,4\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 5 atoms\n', '< PyMOL>remove hydro\n', '< Remove: eliminated 4 atoms in model "small01".\n', '< PyMOL>set_geometry (id 3),3,3\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 4 atoms\n', '< PyMOL>remove hydro\n', '< Remove: eliminated 3 atoms in model "small01".\n', '< PyMOL>set_geometry (id 3),2,2\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 3 atoms\n', '< PyMOL>remove hydro\n', '< Remove: eliminated 2 atoms in model "small01".\n', '< PyMOL>set_geometry (id 3),4,2\n', '< PyMOL>h_add\n', '< PyMOL>count_atoms\n', '< count_atoms: 3 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>alter (all),resi = (999-int(resi)-ID/4)\n', '< Alter: modified 107 atoms.\n', '< PyMOL>sort\n', '< PyMOL>show sph,(byres id 10)\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 210 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>cmd.edit("(pept`95)",pkresi=1)\n', '< PyMOL>cmd.push_undo("pept",1)\n', '< PyMOL>cmd.edit("(pept`10)",pkresi=1)\n', '< PyMOL>cmd.push_undo("pept",1)\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.124, -31.391, 12.760]\n', '< cmd.extent: max: [ 8.919, -12.759, 27.469]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>cmd.edit("(small01`3)",pkresi=1)\n', '< PyMOL>cmd.edit_mode()\n', '< PyMOL>cmd.push_undo("small01",1)\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -15.344, -2.159, -3.683]\n', '< cmd.extent: max: [ -3.585, 2.683, 3.171]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -8.369, -2.595, -4.337]\n', '< cmd.extent: max: [ 2.256, 2.247, 2.517]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -8.369, -2.595, -4.337]\n', '< cmd.extent: max: [ 2.256, 2.247, 2.517]\n', "< PyMOL>cmd.set('valence','0.0500')\n", '< PyMOL>cmd.edit_mode()\n', '< PyMOL>cmd.push_undo("small01",1)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.120608196, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202755, -0.160811022, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.120608196, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202755, -0.160811022, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.120608196, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, -0.020101367, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.060304098, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.040202733, -0.160810933, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.000000000, -0.040202733, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", -0.020101367, 0.000000000, 0.000000000,1,1,0)\n', '< PyMOL>cmd.translate_atom("/small01////C`", 0.020101367, 0.000000000, 0.000000000,1,1,0)\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -8.369, -3.896, -4.337]\n', '< cmd.extent: max: [ 2.256, 2.247, 2.517]\n', '< PyMOL>undo\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -8.369, -2.595, -4.337]\n', '< cmd.extent: max: [ 2.256, 2.247, 2.517]\n', '< PyMOL>dele all\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>get_extent\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n', '< PyMOL>load dat/pept.pdb,sav\n', '< CmdLoad: "dat/pept.pdb" loaded as "sav".\n', '< PyMOL>alter_state 1,(pept),x=1;y=2;z=3;\n', '< AlterState: modified 107 atom coordinate states.\n', '< PyMOL>rebuild\n', '< PyMOL>get_extent pept\n', '< cmd.extent: min: [ 1.000, 2.000, 3.000]\n', '< cmd.extent: max: [ 1.000, 2.000, 3.000]\n', '< PyMOL>update pept,sav\n', '< Update: coordinates updated for 107 atoms.\n', '< PyMOL>get_extent pept\n', '< cmd.extent: min: [ -5.188, -20.331, 13.157]\n', '< cmd.extent: max: [ 8.919, 0.863, 27.058]\n'] run_tests: C1050fitting... run_tests: C1050fitting.log DIFFERS over about 77 lines: ['1,153d0\n', '< the 1st random number should be 0.052\n', '< otherwise the rest of the test is meaningless...\n', '< \n', '< Selector: found 107 atoms.\n', '< Executive: object "trg" created.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< Selector: found 107 atoms.\n', '< AlterState: modified 107 atom coordinate states.\n', '< 0.080\n', '< 1 0.073 0.080 0.198\n', '< 2 0.058 0.080 0.220\n', '< 3 0.053 0.080 0.320\n', '< 4 0.088 0.080 0.105\n', '< 5 0.052 0.080 0.138\n', '< 6 0.081 0.080 0.147\n', '< 7 0.035 0.080 1.396\n', '< 8 0.059 0.080 0.108\n', '< 9 0.098 0.080 0.113\n', '< 10 0.072 0.080 0.121\n', '< 11 0.056 0.080 0.119\n', '< 12 0.075 0.080 0.203\n', '< 13 0.078 0.080 0.341\n', '< 0.080\n', '< 1 0.073 0.080 0.198\n', '< 2 0.058 0.080 0.220\n', '< 3 0.053 0.080 0.320\n', '< 4 0.088 0.080 0.105\n', '< 5 0.052 0.080 0.138\n', '< 6 0.081 0.080 0.147\n', '< 7 0.035 0.080 1.396\n', '< 8 0.059 0.080 0.108\n', '< 9 0.098 0.080 0.113\n', '< 10 0.072 0.080 0.121\n', '< 11 0.056 0.080 0.119\n', '< 12 0.075 0.080 0.203\n', '< 13 0.078 0.080 0.341\n', '< 0.080\n', '< -1.000 0.274 0.302 0.275 0.256 0.305 0.351 0.266 0.260\n', '< 0.329\n', '< -1.000 0.372 0.356 0.340 0.338 0.346 0.346 0.355 0.354\n', '< 0.358\n', '< -1.000 1.672 1.481 0.691 1.952 2.292 1.546 1.670 1.143\n', '< 1.372\n', '< 0.274 -1.000 0.305 0.308 0.227 0.329 0.320 0.309 0.269\n', '< 0.266\n', '< 0.372 -1.000 0.355 0.364 0.357 0.341 0.346 0.358 0.358\n', '< 0.357\n', '< 1.672 -1.000 0.740 1.325 0.924 0.842 1.237 0.692 0.872\n', '< 0.853\n', '< 0.302 0.305 -1.000 0.223 0.254 0.289 0.376 0.329 0.303\n', '< 0.355\n', '< 0.356 0.355 -1.000 0.363 0.338 0.343 0.331 0.362 0.343\n', '< 0.348\n', '< 1.481 0.740 -1.000 1.077 0.487 1.003 0.555 0.982 0.837\n', '< 0.963\n', '< 0.275 0.308 0.223 -1.000 0.211 0.325 0.358 0.303 0.271\n', '< 0.359\n', '< 0.340 0.364 0.363 -1.000 0.344 0.355 0.366 0.361 0.353\n', '< 0.356\n', '< 0.691 1.325 1.077 -1.000 1.309 1.795 0.834 1.378 0.874\n', '< 1.113\n', '< 0.256 0.227 0.254 0.211 -1.000 0.259 0.234 0.263 0.240\n', '< 0.300\n', '< 0.338 0.357 0.338 0.344 -1.000 0.346 0.334 0.344 0.338\n', '< 0.341\n', '< 1.952 0.924 0.487 1.309 -1.000 0.802 0.783 1.259 1.299\n', '< 1.292\n', '< 0.305 0.329 0.289 0.325 0.259 -1.000 0.280 0.359 0.292\n', '< 0.304\n', '< 0.346 0.341 0.343 0.355 0.346 -1.000 0.334 0.356 0.340\n', '< 0.346\n', '< 2.292 0.842 1.003 1.795 0.802 -1.000 1.352 1.063 1.420\n', '< 1.249\n', '< 0.351 0.320 0.376 0.358 0.234 0.280 -1.000 0.365 0.321\n', '< 0.301\n', '< 0.346 0.346 0.331 0.366 0.334 0.334 -1.000 0.352 0.357\n', '< 0.350\n', '< 1.546 1.237 0.555 0.834 0.783 1.352 -1.000 1.471 1.244\n', '< 1.364\n', '< 0.266 0.309 0.329 0.303 0.263 0.359 0.365 -1.000 0.262\n', '< 0.342\n', '< 0.355 0.358 0.362 0.361 0.344 0.356 0.352 -1.000 0.351\n', '< 0.350\n', '< 1.670 0.692 0.982 1.378 1.259 1.063 1.471 -1.000 0.748\n', '< 0.473\n', '< 0.260 0.269 0.303 0.271 0.240 0.292 0.321 0.262 -1.000\n', '< 0.354\n', '< 0.354 0.358 0.343 0.353 0.338 0.340 0.357 0.351 -1.000\n', '< 0.354\n', '< 1.143 0.872 0.837 0.874 1.299 1.420 1.244 0.748 -1.000\n', '< 0.526\n', '< 0.329 0.266 0.355 0.359 0.300 0.304 0.301 0.342 0.354\n', '< -1.000\n', '< 0.358 0.357 0.348 0.356 0.341 0.346 0.350 0.350 0.354\n', '< -1.000\n', '< 1.372 0.853 0.963 1.113 1.292 1.249 1.364 0.473 0.526\n', '< -1.000\n', '< PyMOL>intra_fit (trg),10\n', '< cmd.intra_fit: 0.358 in state 1 vs state 10\n', '< cmd.intra_fit: 0.357 in state 2 vs state 10\n', '< cmd.intra_fit: 0.348 in state 3 vs state 10\n', '< cmd.intra_fit: 0.356 in state 4 vs state 10\n', '< cmd.intra_fit: 0.341 in state 5 vs state 10\n', '< cmd.intra_fit: 0.346 in state 6 vs state 10\n', '< cmd.intra_fit: 0.350 in state 7 vs state 10\n', '< cmd.intra_fit: 0.350 in state 8 vs state 10\n', '< cmd.intra_fit: 0.354 in state 9 vs state 10\n', '< PyMOL>intra_fit (trg and resi 1),10\n', '< cmd.intra_fit: 0.329 in state 1 vs state 10\n', '< cmd.intra_fit: 0.266 in state 2 vs state 10\n', '< cmd.intra_fit: 0.355 in state 3 vs state 10\n', '< cmd.intra_fit: 0.359 in state 4 vs state 10\n', '< cmd.intra_fit: 0.300 in state 5 vs state 10\n', '< cmd.intra_fit: 0.304 in state 6 vs state 10\n', '< cmd.intra_fit: 0.301 in state 7 vs state 10\n', '< cmd.intra_fit: 0.342 in state 8 vs state 10\n', '< cmd.intra_fit: 0.354 in state 9 vs state 10\n', '< PyMOL>intra_rms (trg),10\n', '< cmd.intra_rms: 0.358 in state 1 vs state 10\n', '< cmd.intra_rms: 0.357 in state 2 vs state 10\n', '< cmd.intra_rms: 0.348 in state 3 vs state 10\n', '< cmd.intra_rms: 0.356 in state 4 vs state 10\n', '< cmd.intra_rms: 0.341 in state 5 vs state 10\n', '< cmd.intra_rms: 0.346 in state 6 vs state 10\n', '< cmd.intra_rms: 0.350 in state 7 vs state 10\n', '< cmd.intra_rms: 0.350 in state 8 vs state 10\n', '< cmd.intra_rms: 0.354 in state 9 vs state 10\n', '< PyMOL>intra_rms_cur (trg),10\n', '< cmd.intra_rms_cur: 1.372 in state 1 vs state 10\n', '< cmd.intra_rms_cur: 0.853 in state 2 vs state 10\n', '< cmd.intra_rms_cur: 0.963 in state 3 vs state 10\n', '< cmd.intra_rms_cur: 1.113 in state 4 vs state 10\n', '< cmd.intra_rms_cur: 1.292 in state 5 vs state 10\n', '< cmd.intra_rms_cur: 1.249 in state 6 vs state 10\n', '< cmd.intra_rms_cur: 1.364 in state 7 vs state 10\n', '< cmd.intra_rms_cur: 0.473 in state 8 vs state 10\n', '< cmd.intra_rms_cur: 0.526 in state 9 vs state 10\n'] run_tests: C1060controlling... run_tests: C1060controlling.log DIFFERS over about 7 lines: ['1,13d0\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n', '< None\n'] run_tests: C1070exporting... run_tests: C1070exporting.log DIFFERS over about 29 lines: ['1,58d0\n', '< PyMOL>load dat/small01.mol\n', '< ExecutiveLoad: "dat/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>save tmp/small01.mol\n', '< chempy: writing "tmp/small01.mol".\n', '< Save: wrote "tmp/small01.mol".\n', '< PyMOL>save tmp/small01.pkl\n', '< Save: wrote "tmp/small01.pkl".\n', '< PyMOL>save tmp/small02.pkl,format=pkla\n', '< Save: wrote "tmp/small02.pkl".\n', '< PyMOL>save tmp/small01.mmod\n', '< chempy: writing "tmp/small01.mmod".\n', '< Save: wrote "tmp/small01.mmod".\n', '< PyMOL>save tmp/small01.mmd\n', '< chempy: writing "tmp/small01.mmd".\n', '< Save: wrote "tmp/small01.mmd".\n', '< PyMOL>save tmp/small01.pdb\n', '< Save: wrote "tmp/small01.pdb".\n', '< PyMOL>multisave tmp/small01.pmo,small01\n', "< Multisave: wrote 1 object(s) to 'tmp/small01.pmo'.\n", '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.pmo\n', '< CmdLoad: "tmp/small01.pmo" loaded as "small01".\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.pdb\n', '< CmdLoad: "tmp/small01.pdb" loaded as "small01".\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.mmd\n', '< CmdLoad: "tmp/small01.mmd" loaded as "small01".\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.mmod\n', '< CmdLoad: "tmp/small01.mmod" loaded as "small01".\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.pkl\n', '< Executive: object "small01" created.\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small02.pkl\n', '< Executive: object "small02" created.\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>dele all\n', '< PyMOL>load tmp/small01.mol\n', '< ExecutiveLoad: "tmp/small01.mol" loaded as "small01", through state 1.\n', '< PyMOL>count_atoms\n', '< count_atoms: 36 atoms\n', '< PyMOL>feedback disable,ray,details\n', '< PyMOL>ray\n', '< PyMOL>png tmp/tmp.png\n', '< ScenePNG: wrote 640x480 pixel image to file "tmp/tmp.png".\n', '< PyMOL>load_png tmp/tmp.png\n', "< Scene: loaded image from 'tmp/tmp.png'.\n"] run_tests: C1080isomore... run_tests: C1080isomore.log DIFFERS over about 142 lines: ['1,283d0\n', '< PyMOL>load dat/pept.pdb,obj\n', '< CmdLoad: "dat/pept.pdb" loaded as "obj".\n', '< PyMOL>load dat/il2.pdb,obj\n', '< CmdLoad: "dat/il2.pdb" appended into object "obj", state 2.\n', '< PyMOL>load dat/3al1.pdb,obj,state=4\n', '< HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1\n', '< TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND 3 CHAIN: A, B;\n', '< COMPND 4 ENGINEERED: YES;\n', '< COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 2 symmetry operators.\n', '< CmdLoad: "dat/3al1.pdb" appended into object "obj", state 4.\n', '< PyMOL>map_new tst1,gaussian,1.0,state=-3\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 2870 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.049654 & stdev = 0.212673.\n', '< Executive: object "tst1" created.\n', '< PyMOL>map_new tst2,gaussian,1.0,state=2\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 2084 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.074412 & stdev = 0.213934.\n', '< Executive: object "tst2" created.\n', '< PyMOL>map_new tst2,gaussian,1.0,state=4\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 679 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.076772 & stdev = 0.351954.\n', '< PyMOL>map_new tst3,gaussian,1.0,state=-4\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.003829 & stdev = 0.054910.\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 2084 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.036107 & stdev = 0.153608.\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 0 atom positions.\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 679 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.009718 & stdev = 0.133319.\n', '< Executive: object "tst3" created.\n', '< PyMOL>map_new tst4,gaussian,1.0,state=3\n', '< Executive: object "tst4" created.\n', '< PyMOL>map_new tst5,gaussian,1.0,state=4\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 679 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.076772 & stdev = 0.351954.\n', '< Executive: object "tst5" created.\n', '< PyMOL>map_new tst6,gaussian,1.0\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079928 & stdev = 0.237612.\n', '< Executive: object "tst6" created.\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 2084 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.074412 & stdev = 0.213934.\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 679 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.076772 & stdev = 0.351954.\n', '< PyMOL>frame 4\n', '< PyMOL>isomesh m8,tst2,state=-1\n', '< Executive: object "m8" created.\n', '< Isomesh: created "m8", setting level to 1.000\n', '< PyMOL>frame 3\n', '< PyMOL>isomesh m9,tst1,state=-1,source_state=1\n', '< Executive: object "m9" created.\n', '< Isomesh: created "m9", setting level to 1.000\n', '< PyMOL>isomesh m7,tst1,state=4,source_state=1\n', '< Executive: object "m7" created.\n', '< Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m8".\n', '< IsosurfVolume: Surface generated using 6969 lines.\n', '< ObjectMesh: updating "m9".\n', '< IsosurfVolume: Surface generated using 37701 lines.\n', '< ObjectMesh: updating "m7".\n', '< IsosurfVolume: Surface generated using 37701 lines.\n', '< PyMOL>isomesh m7,tst6,state=3,source_state=1\n', '< Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m7".\n', '< IsosurfVolume: Surface generated using 2975 lines.\n', '< PyMOL>isomesh m7,tst5,state=2,source_state=4\n', '< Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m7".\n', '< IsosurfVolume: Surface generated using 6969 lines.\n', '< PyMOL>isomesh m7,tst2,state=1,source_state=2\n', '< Isomesh: created "m7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m7".\n', '< IsosurfVolume: Surface generated using 29064 lines.\n', '< PyMOL>isomesh m1,tst1\n', '< Executive: object "m1" created.\n', '< Isomesh: created "m1", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m1".\n', '< IsosurfVolume: Surface generated using 37701 lines.\n', '< PyMOL>isomesh m2,tst2\n', '< Executive: object "m2" created.\n', '< Isomesh: created "m2", setting level to 1.000\n', '< Isomesh: created "m2", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m2".\n', '< IsosurfVolume: Surface generated using 29064 lines.\n', '< ObjectMesh: updating "m2".\n', '< IsosurfVolume: Surface generated using 6969 lines.\n', '< PyMOL>isomesh m3,tst3\n', '< Executive: object "m3" created.\n', '< Isomesh: created "m3", setting level to 1.000\n', '< Isomesh: created "m3", setting level to 1.000\n', '< Isomesh: created "m3", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m3".\n', '< IsosurfVolume: Surface generated using 3487 lines.\n', '< ObjectMesh: updating "m3".\n', '< IsosurfVolume: Surface generated using 29781 lines.\n', '< ObjectMesh: updating "m3".\n', '< IsosurfVolume: Surface generated using 9095 lines.\n', '< PyMOL>isomesh m4,tst4\n', '< PyMOL>refresh\n', '< PyMOL>isomesh m5a,tst5,source_state=1\n', '< Isomesh-Warning: state 1 not present in map "tst5".\n', '< PyMOL>refresh\n', '< PyMOL>isomesh m5b,tst5\n', '< Executive: object "m5b" created.\n', '< Isomesh: created "m5b", setting level to 1.000\n', '< PyMOL>isomesh m6,tst6\n', '< Executive: object "m6" created.\n', '< Isomesh: created "m6", setting level to 1.000\n', '< Isomesh: created "m6", setting level to 1.000\n', '< Isomesh: created "m6", setting level to 1.000\n', '< PyMOL>isosurface s1,tst1\n', '< Executive: object "s1" created.\n', '< Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m5b".\n', '< IsosurfVolume: Surface generated using 6969 lines.\n', '< ObjectMesh: updating "m6".\n', '< IsosurfVolume: Surface generated using 2975 lines.\n', '< ObjectMesh: updating "m6".\n', '< IsosurfVolume: Surface generated using 29064 lines.\n', '< ObjectMesh: updating "m6".\n', '< IsosurfVolume: Surface generated using 6969 lines.\n', '< ObjectSurface: updating "s1".\n', '< TetsurfVolume: Surface generated using 106172 triangles.\n', '< PyMOL>isosurface s2,tst2\n', '< Executive: object "s2" created.\n', '< Isosurface: created "s2", setting level to 1.000\n', '< Isosurface: created "s2", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s2".\n', '< TetsurfVolume: Surface generated using 82044 triangles.\n', '< ObjectSurface: updating "s2".\n', '< TetsurfVolume: Surface generated using 18780 triangles.\n', '< PyMOL>isosurface s3,tst3\n', '< Executive: object "s3" created.\n', '< Isosurface: created "s3", setting level to 1.000\n', '< Isosurface: created "s3", setting level to 1.000\n', '< Isosurface: created "s3", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s3".\n', '< TetsurfVolume: Surface generated using 10220 triangles.\n', '< ObjectSurface: updating "s3".\n', '< TetsurfVolume: Surface generated using 84672 triangles.\n', '< ObjectSurface: updating "s3".\n', '< TetsurfVolume: Surface generated using 25480 triangles.\n', '< PyMOL>isosurface s4,tst4\n', '< PyMOL>refresh\n', '< PyMOL>isosurface s4,tst5\n', '< Executive: object "s4" created.\n', '< Isosurface: created "s4", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s4".\n', '< TetsurfVolume: Surface generated using 18780 triangles.\n', '< PyMOL>isosurface s5a,tst5,source_state=1\n', '< Isosurface-Warning: state 1 not present in map "tst5".\n', '< PyMOL>refresh\n', '< PyMOL>isosurface s5b,tst5\n', '< Executive: object "s5b" created.\n', '< Isosurface: created "s5b", setting level to 1.000\n', '< PyMOL>isosurface s6,tst6\n', '< Executive: object "s6" created.\n', '< Isosurface: created "s6", setting level to 1.000\n', '< Isosurface: created "s6", setting level to 1.000\n', '< Isosurface: created "s6", setting level to 1.000\n', '< PyMOL>isosurface s7,tst1,state=4,source_state=1\n', '< Executive: object "s7" created.\n', '< Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s5b".\n', '< TetsurfVolume: Surface generated using 18780 triangles.\n', '< ObjectSurface: updating "s6".\n', '< TetsurfVolume: Surface generated using 8492 triangles.\n', '< ObjectSurface: updating "s6".\n', '< TetsurfVolume: Surface generated using 82044 triangles.\n', '< ObjectSurface: updating "s6".\n', '< TetsurfVolume: Surface generated using 18780 triangles.\n', '< ObjectSurface: updating "s7".\n', '< TetsurfVolume: Surface generated using 106172 triangles.\n', '< PyMOL>isosurface s7,tst6,state=3,source_state=1\n', '< Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s7".\n', '< TetsurfVolume: Surface generated using 8492 triangles.\n', '< PyMOL>isosurface s7,tst5,state=2,source_state=4\n', '< Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s7".\n', '< TetsurfVolume: Surface generated using 18780 triangles.\n', '< PyMOL>isosurface s7,tst2,state=1,source_state=2\n', '< Isosurface: created "s7", setting level to 1.000\n', '< PyMOL>refresh\n', '< ObjectSurface: updating "s7".\n', '< TetsurfVolume: Surface generated using 82044 triangles.\n', '< PyMOL>frame 4\n', '< PyMOL>isosurface s8,tst2,state=-1\n', '< Executive: object "s8" created.\n', '< Isosurface: created "s8", setting level to 1.000\n', '< PyMOL>frame 3\n', '< PyMOL>isosurface s9,tst1,state=-1,source_state=1\n', '< Executive: object "s9" created.\n', '< Isosurface: created "s9", setting level to 1.000\n', '< PyMOL>reinit\n', '< PyMOL>load dat/pept.pdb,obj\n', '< CmdLoad: "dat/pept.pdb" loaded as "obj".\n', '< PyMOL>alter all, b=10\n', '< Alter: modified 107 atoms.\n', '< PyMOL>map_new m1, gaussian, 1.0, obj\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '< Executive: object "m1" created.\n', '< PyMOL>map_new m2, gaussian, 1.0, obj, clamp=[-5, 5]\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '< Executive: object "m2" created.\n', '< PyMOL>map_new m3, gaussian, 1.0, obj, clamp=[-3, 3]\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '< Executive: object "m3" created.\n', '< PyMOL>map_new m4, gaussian, 1.0, obj, clamp=[-2, 2]\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '< Executive: object "m4" created.\n', '< PyMOL>map_new m5, gaussian, 1.0, obj, clamp=[-0.9, 0.9]\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079569 & stdev = 0.336150.\n', '< Executive: object "m5" created.\n', '< PyMOL>isosurface s1, m1\n', '< Executive: object "s1" created.\n', '< Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>isosurface s2, m2\n', '< Executive: object "s2" created.\n', '< Isosurface: created "s2", setting level to 1.000\n', '< PyMOL>isosurface s3, m3\n', '< Executive: object "s3" created.\n', '< Isosurface: created "s3", setting level to 1.000\n', '< PyMOL>isosurface s4, m4\n', '< Executive: object "s4" created.\n', '< Isosurface: created "s4", setting level to 1.000\n', '< PyMOL>isosurface s5, m5\n', '< Executive: object "s5" created.\n', '< Isosurface: created "s5", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectSurface: updating "s1".\n', '< TetsurfVolume: Surface generated using 7120 triangles.\n', '< ObjectSurface: updating "s2".\n', '< TetsurfVolume: Surface generated using 7120 triangles.\n', '< ObjectSurface: updating "s3".\n', '< TetsurfVolume: Surface generated using 7120 triangles.\n', '< ObjectSurface: updating "s4".\n', '< TetsurfVolume: Surface generated using 7120 triangles.\n', '< ObjectSurface: updating "s5".\n', '< TetsurfVolume: Surface generated using 0 triangles.\n', '< RayRenderTest: obtained 28646 graphics primitives.\n', '< PyMOL>print "END-LOG"\n'] run_tests: C1090coulomb... run_tests: C1090coulomb.log DIFFERS over about 23 lines: ['1,45d0\n', '< PyMOL>set auto_zoom,0\n', '< Setting: auto_zoom set to 0.\n', '< PyMOL>fragment phe\n', '< Executive: object "phe" created.\n', '< PyMOL>map_new t1,coulomb,0.5,phe,5\n', '< ObjectMap: Map created.\n', '< SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '< SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '< Executive: object "t1" created.\n', '< PyMOL>fragment phe,phe\n', '< CmdLoad: ChemPy-model appended into object "phe", state 2.\n', '< PyMOL>map_new t2,coulomb,0.5,phe,5\n', '< ObjectMap: Map created.\n', '< SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '< SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '< Executive: object "t2" created.\n', '< ObjectMap: Map created.\n', '< SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '< SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '< PyMOL>map_new t3,coulomb,0.5,phe,5,state=-3\n', '< ObjectMap: Map created.\n', '< SelectorMapCoulomb: Total charge is 0.000 for 40 points (40 atoms).\n', '< SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '< Executive: object "t3" created.\n', '< PyMOL>isomesh m1,t1,5\n', '< Executive: object "m1" created.\n', '< Isomesh: created "m1", setting level to 5.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m1".\n', '< IsosurfVolume: Surface generated using 3351 lines.\n', '< PyMOL>isomesh m2,t2,5\n', '< Executive: object "m2" created.\n', '< Isomesh: created "m2", setting level to 5.000\n', '< Isomesh: created "m2", setting level to 5.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m2".\n', '< IsosurfVolume: Surface generated using 3351 lines.\n', '< ObjectMesh: updating "m2".\n', '< IsosurfVolume: Surface generated using 3351 lines.\n', '< PyMOL>isomesh m3,t3,5\n', '< Executive: object "m3" created.\n', '< Isomesh: created "m3", setting level to 5.000\n', '< PyMOL>refresh\n', '< ObjectMesh: updating "m3".\n', '< IsosurfVolume: Surface generated using 3351 lines.\n'] run_tests: C1095slice... run_tests: C1095slice.log DIFFERS over about 33 lines: ['1,65d0\n', '< PyMOL>set auto_zoom,0\n', '< Setting: auto_zoom set to 0.\n', '< PyMOL>fragment phe\n', '< Executive: object "phe" created.\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 31 graphics primitives.\n', '< PyMOL>map_new pot,coulomb,0.5,phe,5\n', '< ObjectMap: Map created.\n', '< SelectorMapCoulomb: Total charge is 0.000 for 20 points (20 atoms).\n', '< SelectorMapCoulomb: Evaluating Coulomb potential for grid (no cutoff)...\n', '< Executive: object "pot" created.\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 31 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot\n', '< Executive: object "ramp" created.\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 116 graphics primitives.\n', '< PyMOL>slice_new slice, pot\n', '< Executive: object "slice" created.\n', '< SliceMap: created "slice".\n', '< PyMOL>color ramp,slice\n', '< Executive: Colored 1 object.\n', '< PyMOL>set ray_default_renderer,2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>refresh\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 5780 graphics primitives.\n', '< PyMOL>set slice_track_camera, on\n', '< Setting: slice_track_camera set to on.\n', '< PyMOL>turn x,45\n', '< PyMOL>turn z,45\n', '< PyMOL>refresh\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 7337 graphics primitives.\n', '< PyMOL>set slice_track_camera,off\n', '< Setting: slice_track_camera set to off.\n', '< PyMOL>refresh\n', '< PyMOL>reset\n', '< PyMOL>turn y,45\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 7337 graphics primitives.\n', '< PyMOL>set slice_height_map\n', '< Setting: slice_height_map set to on.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 7337 graphics primitives.\n', '< PyMOL>set slice_grid, 1\n', '< Setting: slice_grid set to 1.00000.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 716 graphics primitives.\n', '< PyMOL>set slice_grid, 0.2\n', '< Setting: slice_grid set to 0.20000.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 16622 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot, color=sludge\n', '< Executive: object "ramp" created.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 16656 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot, color=rainbow\n', '< Executive: object "ramp" created.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 16656 graphics primitives.\n', '< PyMOL>ramp_new ramp, pot, color=rainbow, selection=none\n', '< Executive: object "ramp" created.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 16642 graphics primitives.\n'] run_tests: C1100do... run_tests: C1100do.log DIFFERS over about 40 lines: ['1,79d0\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>show sticks,pept\n', '< PyMOL>set ray_default_renderer=2\n', '< Setting: ray_default_renderer set to 2.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 166 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/il2.pdb\n', '< CmdLoad: "dat/il2.pdb" loaded as "il2".\n', '< PyMOL>show dots,il2\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 111078 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>load dat/3al1.pdb\n', '< HEADER STRUCTURAL PROTEIN 26-OCT-98 3AL1\n', '< TITLE DESIGNED PEPTIDE ALPHA-1, RACEMIC P1BAR FORM\n', '< COMPND MOL_ID: 1;\n', '< COMPND 2 MOLECULE: D, L-ALPHA-1;\n', '< COMPND 3 CHAIN: A, B;\n', '< COMPND 4 ENGINEERED: YES;\n', '< COMPND 5 OTHER_DETAILS: N TERMINI ARE ACETYLATED\n', '< ObjectMolecule: Read secondary structure assignments.\n', '< ObjectMolecule: Read crystal symmetry information.\n', '< Symmetry: Found 2 symmetry operators.\n', '< CmdLoad: "dat/3al1.pdb" loaded as "3al1".\n', '< PyMOL>show sph,3al1\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 1945 graphics primitives.\n', '< PyMOL>dele all\n', '< PyMOL>fragment arg\n', '< Executive: object "arg" created.\n', '< PyMOL>ray\n', '< RayRenderTest: obtained 42 graphics primitives.\n', '< PyMOL>for a in range(1,10):\\\n', '< PyMOL> print a\\\n', '< PyMOL> print a+10\n', '< 1\n', '< 11\n', '< 2\n', '< 12\n', '< 3\n', '< 13\n', '< 4\n', '< 14\n', '< 5\n', '< 15\n', '< 6\n', '< 16\n', '< 7\n', '< 17\n', '< 8\n', '< 18\n', '< 9\n', '< 19\n', '< PyMOL>for a in range(11,21):\\\n', '< PyMOL> print a\\\n', '< PyMOL> print a+10\n', '< 11\n', '< 21\n', '< 12\n', '< 22\n', '< 13\n', '< 23\n', '< 14\n', '< 24\n', '< 15\n', '< 25\n', '< 16\n', '< 26\n', '< 17\n', '< 27\n', '< 18\n', '< 28\n', '< 19\n', '< 29\n', '< 20\n', '< 30\n', '< PyMOL> \n'] run_tests: C1110matrix_mode... run_tests: C1110matrix_mode.log DIFFERS over about 127 lines: ['1,253d0\n', '< PyMOL>reinit\n', '< PyMOL>set matrix_mode, 0\n', '< Setting: matrix_mode set to 0.\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>remove not resi 5\n', '< Remove: eliminated 97 atoms in model "pept".\n', '< PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '< -0.135 -5.634 21.235\n', '< -0.006 -4.205 21.043\n', '< -1.408 -3.636 20.918\n', '< -2.092 -3.870 19.914\n', '< 0.791 -3.871 19.783\n', '< 0.939 -2.396 19.549\n', '< 0.582 -1.619 18.499\n', '< 1.470 -1.542 20.495\n', '< 1.431 -0.303 20.038\n', '< 0.896 -0.322 18.831\n', '< IterateState: iterated over 10 atom coordinate states.\n', '< PyMOL>rotate x, 53, object=pept\n', '< PyMOL>rotate y, 27, object=pept\n', '< PyMOL>rotate z, 6, object=pept\n', '< PyMOL>translate [1,2,3], object=pept\n', '< PyMOL>save tmp/C1110a.pdb\n', '< Save: wrote "tmp/C1110a.pdb".\n', '< PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N \n', '< END\n', '< PyMOL>save tmp/C1110b.pdb, ref=pept\n', '< Save: wrote "tmp/C1110b.pdb".\n', '< PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N \n', '< END\n', '< PyMOL>load dat/pept.pdb, tmp\n', '< CmdLoad: "dat/pept.pdb" loaded as "tmp".\n', '< PyMOL>remove tmp and not resi 5\n', '< Remove: eliminated 97 atoms in model "tmp".\n', '< PyMOL>matrix_transfer pept, tmp\n', '< PyMOL>save tmp/C1110c.pdb, tmp,\n', '< Save: wrote "tmp/C1110c.pdb".\n', '< PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N \n', '< END\n', '< PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp\n', '< Save: wrote "tmp/C1110d.pdb".\n', '< PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N \n', '< END\n', '< PyMOL>reinit\n', '< PyMOL>set matrix_mode, 1\n', '< Setting: matrix_mode set to 1.\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>remove not resi 5\n', '< Remove: eliminated 97 atoms in model "pept".\n', '< PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '< -0.135 -5.634 21.235\n', '< -0.006 -4.205 21.043\n', '< -1.408 -3.636 20.918\n', '< -2.092 -3.870 19.914\n', '< 0.791 -3.871 19.783\n', '< 0.939 -2.396 19.549\n', '< 0.582 -1.619 18.499\n', '< 1.470 -1.542 20.495\n', '< 1.431 -0.303 20.038\n', '< 0.896 -0.322 18.831\n', '< IterateState: iterated over 10 atom coordinate states.\n', '< PyMOL>rotate x, 53, object=pept\n', '< PyMOL>rotate y, 27, object=pept\n', '< PyMOL>rotate z, 6, object=pept\n', '< PyMOL>translate [1,2,3], object=pept\n', '< PyMOL>save tmp/C1110a.pdb\n', '< Save: wrote "tmp/C1110a.pdb".\n', '< PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N \n', '< END\n', '< PyMOL>save tmp/C1110b.pdb, ref=pept\n', '< Save: wrote "tmp/C1110b.pdb".\n', '< PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N \n', '< END\n', '< PyMOL>load dat/pept.pdb, tmp\n', '< CmdLoad: "dat/pept.pdb" loaded as "tmp".\n', '< PyMOL>remove tmp and not resi 5\n', '< Remove: eliminated 97 atoms in model "tmp".\n', '< PyMOL>matrix_transfer pept, tmp\n', '< PyMOL>save tmp/C1110c.pdb, tmp,\n', '< Save: wrote "tmp/C1110c.pdb".\n', '< PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N \n', '< END\n', '< PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp\n', '< Save: wrote "tmp/C1110d.pdb".\n', '< PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N \n', '< END\n', '< PyMOL>reinit\n', '< PyMOL>set matrix_mode, 2\n', '< Setting: matrix_mode set to 2.\n', '< PyMOL>load dat/pept.pdb\n', '< CmdLoad: "dat/pept.pdb" loaded as "pept".\n', '< PyMOL>remove not resi 5\n', '< Remove: eliminated 97 atoms in model "pept".\n', '< PyMOL>iterate_state 1,all,print "%8.3f %8.3f %8.3f"%(x,y,z)\n', '< -0.135 -5.634 21.235\n', '< -0.006 -4.205 21.043\n', '< -1.408 -3.636 20.918\n', '< -2.092 -3.870 19.914\n', '< 0.791 -3.871 19.783\n', '< 0.939 -2.396 19.549\n', '< 0.582 -1.619 18.499\n', '< 1.470 -1.542 20.495\n', '< 1.431 -0.303 20.038\n', '< 0.896 -0.322 18.831\n', '< IterateState: iterated over 10 atom coordinate states.\n', '< PyMOL>rotate x, 53, object=pept, object_mode=1\n', '< PyMOL>rotate y, 27, object=pept, object_mode=1\n', '< PyMOL>rotate z, 6, object=pept, object_mode=1\n', '< PyMOL>translate [1,2,3], object=pept, object_mode=1\n', '< PyMOL>save tmp/C1110a.pdb\n', '< Save: wrote "tmp/C1110a.pdb".\n', '< PyMOL>for a in open("tmp/C1110a.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N \n', '< END\n', '< PyMOL>save tmp/C1110b.pdb, ref=pept\n', '< Save: wrote "tmp/C1110b.pdb".\n', '< PyMOL>for a in open("tmp/C1110b.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N \n', '< END\n', '< PyMOL>load dat/pept.pdb, tmp\n', '< CmdLoad: "dat/pept.pdb" loaded as "tmp".\n', '< PyMOL>remove tmp and not resi 5\n', '< Remove: eliminated 97 atoms in model "tmp".\n', '< PyMOL>matrix_transfer pept, tmp\n', '< PyMOL>save tmp/C1110c.pdb, tmp,\n', '< Save: wrote "tmp/C1110c.pdb".\n', '< PyMOL>for a in open("tmp/C1110c.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 2.647 -5.977 27.838 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 3.119 -4.909 28.693 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 2.002 -4.582 29.667 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 0.969 -4.026 29.273 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 3.477 -3.657 27.893 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 3.964 -2.526 28.750 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 3.506 -1.261 28.902 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 5.025 -2.657 29.624 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 5.197 -1.522 30.278 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 4.288 -0.660 29.860 1.00 29.87 E N \n', '< END\n', '< PyMOL>save tmp/C1110d.pdb, tmp, ref=tmp\n', '< Save: wrote "tmp/C1110d.pdb".\n', '< PyMOL>for a in open("tmp/C1110d.pdb").readlines(): print a,\n', '< ATOM 1 N HIS E 5 -0.135 -5.634 21.235 1.00 32.18 E N \n', '< ATOM 2 CA HIS E 5 -0.006 -4.205 21.043 1.00 32.91 E C \n', '< ATOM 3 C HIS E 5 -1.408 -3.636 20.918 1.00 34.58 E C \n', '< ATOM 4 O HIS E 5 -2.092 -3.870 19.914 1.00 35.87 E O \n', '< ATOM 5 CB HIS E 5 0.791 -3.871 19.783 1.00 33.02 E C \n', '< ATOM 6 CG HIS E 5 0.939 -2.396 19.549 1.00 32.86 E C \n', '< ATOM 7 CD2 HIS E 5 0.582 -1.619 18.499 1.00 31.48 E C \n', '< ATOM 8 ND1 HIS E 5 1.470 -1.542 20.495 1.00 29.87 E N \n', '< ATOM 9 CE1 HIS E 5 1.431 -0.303 20.038 1.00 29.68 E C \n', '< ATOM 10 NE2 HIS E 5 0.896 -0.322 18.831 1.00 29.87 E N \n', '< END\n', '< PyMOL>print "END-LOG"\n'] run_tests: C1200matrix_maps... run_tests: C1200matrix_maps.log DIFFERS over about 60 lines: ['1,119d0\n', '< PyMOL>load dat/pept.pdb,prot\n', '< CmdLoad: "dat/pept.pdb" loaded as "prot".\n', '< PyMOL>map_new map1,gaussian,1.0,state=-3\n', '< ObjectMap: Map created.\n', '< ObjectMap: Computing Gaussian map for 107 atom positions.\n', '< ObjectMap: Normalizing: mean = 0.079928 & stdev = 0.237612.\n', '< Executive: object "map1" created.\n', '< PyMOL>translate [10,20,30], object=prot, object_mode=1\n', '< PyMOL>rotate x,30,prot,object=prot,object_mode=1\n', '< PyMOL>rotate y,30,prot,object=prot,object_mode=1\n', '< PyMOL>rotate z,30,prot,object=prot,object_mode=1\n', '< PyMOL>zoom prot\n', '< PyMOL>dump44(cmd.get_object_matrix("map1"))\n', '< [ 1.00 0.00 0.00 0.00 \n', '< 0.00 1.00 0.00 0.00 \n', '< 0.00 0.00 1.00 0.00 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>matrix_transfer prot, map1\n', '< PyMOL>dump44(cmd.get_object_matrix("map1"))\n', '< [ 0.75 -0.22 0.62 7.79 \n', '< 0.43 0.88 -0.22 17.71 \n', '< -0.50 0.43 0.75 36.18 \n', '< 0.00 0.00 0.00 1.00 ]\n', '< PyMOL>isomesh m1, map1, 1.0, 5/, carve=2.1\n', '< Executive: object "m1" created.\n', '< Isomesh: created "m1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m1".\n', '< RayRenderTest: obtained 464 graphics primitives.\n', '< PyMOL>isosurf s1, map1, 1.0, 5/, carve=2.1\n', '< Executive: object "s1" created.\n', '< Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectSurface: updating "s1".\n', '< RayRenderTest: obtained 1284 graphics primitives.\n', '< PyMOL>translate [5,-10,2], object=prot, object_mode=1\n', '< PyMOL>rotate x,60,prot,object=prot,object_mode=1\n', '< PyMOL>rotate z,20,prot,object=prot,object_mode=1\n', '< PyMOL>rotate y,30,prot,object=prot,object_mode=1\n', '< PyMOL>matrix_transfer prot, map1\n', '< PyMOL>isomesh m1, map1, 1.0, 5/, carve=3\n', '< Isomesh: created "m1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m1".\n', '< RayRenderTest: obtained 1404 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isosurf s1, map1, 1.0, 5/, carve=3\n', '< Isosurface: created "s1", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< RayRenderTest: obtained 0 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isomesh m2, map1, 1.0, 5/, 3\n', '< Executive: object "m2" created.\n', '< Isomesh: created "m2", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m2".\n', '< RayRenderTest: obtained 1468 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isosurf s2, map1, 1.0, 5/, 3\n', '< Executive: object "s2" created.\n', '< Isosurface: created "s2", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectSurface: updating "s2".\n', '< RayRenderTest: obtained 4096 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isomesh m3, map1\n', '< Executive: object "m3" created.\n', '< Isomesh: created "m3", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m3".\n', '< RayRenderTest: obtained 2908 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isosurf s3, map1\n', '< Executive: object "s3" created.\n', '< Isosurface: created "s3", setting level to 1.000\n', '< PyMOL>ray renderer=2\n', '< ObjectSurface: updating "s3".\n', '< RayRenderTest: obtained 8492 graphics primitives.\n', '< PyMOL>enable\n', '< PyMOL>ray renderer=2\n', '< ObjectSurface: updating "s1".\n', '< RayRenderTest: obtained 18753 graphics primitives.\n', '< PyMOL>save tmp/C1200.pse\n', '< Save: wrote "tmp/C1200.pse".\n', '< PyMOL>reinit\n', '< PyMOL>load tmp/C1200.pse\n', '< Executive: Loading version 1.20 session...\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m1".\n', '< ObjectSurface: updating "s1".\n', '< ObjectMesh: updating "m2".\n', '< ObjectSurface: updating "s2".\n', '< ObjectMesh: updating "m3".\n', '< ObjectSurface: updating "s3".\n', '< RayRenderTest: obtained 18753 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>isomesh m4, map1, 2.0, 2/, 4\n', '< Executive: object "m4" created.\n', '< Isomesh: created "m4", setting level to 2.000\n', '< PyMOL>isosurf s4, map1, 2.0, 2/, 4\n', '< Executive: object "s4" created.\n', '< Isosurface: created "s4", setting level to 2.000\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m4".\n', '< ObjectSurface: updating "s4".\n', '< RayRenderTest: obtained 6533 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable m1\n', '< PyMOL>isolevel m1, 3\n', '< PyMOL>ray renderer=2\n', '< ObjectMesh: updating "m1".\n', '< RayRenderTest: obtained 288 graphics primitives.\n', '< PyMOL>disable\n', '< PyMOL>enable s1\n', '< PyMOL>isolevel s1, 5\n', '< PyMOL>ray renderer=2\n', '< ObjectSurface: updating "s1".\n', '< RayRenderTest: obtained 168 graphics primitives.\n', '< PyMOL>print "END-LOG"\n'] run_tests: C1300extras... run_tests: C1300extras.log DIFFERS over about 38 lines: ['1,76d0\n', '< PyMOL>delete all\n', '< PyMOL>fragment methane\n', '< Executive: object "methane" created.\n', '< PyMOL>remove hydro and not first hydro\n', '< Remove: eliminated 3 atoms in model "methane".\n', "< PyMOL>alter all,segi='METH'\n", '< Alter: modified 2 atoms.\n', "< PyMOL>alter hydro, alt='A'\n", '< Alter: modified 1 atoms.\n', "< PyMOL>alter hydro, text_type='Htype'\n", '< Alter: modified 1 atoms.\n', "< PyMOL>alter all, ss='L'\n", '< Alter: modified 2 atoms.\n', '< PyMOL>alter all, b=rank\n', '< Alter: modified 2 atoms.\n', '< PyMOL>alter all, q=index\n', '< Alter: modified 2 atoms.\n', '< PyMOL>alter all, elec_radius = vdw+1.0\n', '< Alter: modified 2 atoms.\n', '< PyMOL>cmd.label2("all","\'some text\'")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'some text'\n", "< H01 -> 'some text'\n", '< PyMOL>cmd.label2("all","\'some text \'+\'more text\'")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'some text more text'\n", "< H01 -> 'some text more text'\n", '< PyMOL>cmd.label2("all"," \'some text \' + \'more text\' ")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'some text more text'\n", "< H01 -> 'some text more text'\n", '< PyMOL>cmd.label2("all","model")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'methane'\n", "< H01 -> 'methane'\n", '< PyMOL>cmd.label2("all","resv")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '9'\n", "< H01 -> '9'\n", '< PyMOL>cmd.label2("all","model+\' index:\'+index+ \' type:\' +type")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'methane index:1 type:ATOM'\n", "< H01 -> 'methane index:2 type:ATOM'\n", '< PyMOL>cmd.label2("all","segi+\' \'+chain+\' \'+resi+\'`\'+resn+\' \'+str(resv)+name+\'`\'+alt")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'METH E 9`LEU 9C01`'\n", "< H01 -> 'METH E 9`LEU 9H01`A'\n", '< PyMOL>cmd.label2("all","str(index)+\' \'+str(rank)+\' \'+str(ID)")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '1 0 0'\n", "< H01 -> '2 1 1'\n", '< PyMOL>cmd.label2("all","flags")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '8000000'\n", "< H01 -> '8000000'\n", '< PyMOL>cmd.label2("all","str(numeric_type)+text_type")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '0'\n", "< H01 -> '0Htype'\n", '< PyMOL>cmd.label2("all","str(formal_charge) + \' \' + str(partial_charge)")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '0 0.000'\n", "< H01 -> '0 0.000'\n", '< PyMOL>cmd.label2("all","ss + str(cartoon) + str(color)")\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> 'L026'\n", "< H01 -> 'L029'\n", '< PyMOL>cmd.label2("all",\'str(valence) + " " + str(geom)\')\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '4 4'\n", "< H01 -> '1 1'\n", '< PyMOL>cmd.label2("all",\'str(elec_radius)+" "+str(vdw)+" "+b+" "+q+" "+elem\')\n', '< PyMOL>cmd.iterate("all",r"print name +\' -> \' + \'\\\'\' + label + \'\\\'\'")\n', "< C01 -> '2.80 1.80 0.00 1.00 C'\n", "< H01 -> '2.10 1.10 1.00 2.00 H'\n", '< PyMOL>print "END-LOG"\n'] run_tests: C2000returns... run_tests: C2000returns.log DIFFERS over about 121 lines: ['1,242d0\n', '< cmd.load("dat/pept.pdb")\n', '< None\n', '< cmd.load("dat/nonexistent.pdb")\n', "< ExecutiveProcessPDBFile-Error: Unable to open file 'dat/nonexistent.pdb'.\n", '< -1\n', "< ExecutiveProcessPDBFile-Error: Unable to open file 'dat/nonexistent.pdb'.\n", '< CmdException raised.\n', '< cmd.load("dat/small01.mol")\n', '< None\n', '< cmd.load("dat/nonexistent.mol")\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol'.\n", '< -1\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol'.\n", '< CmdException raised.\n', '< cmd.load("dat/ligs3d.sdf")\n', '< None\n', '< cmd.load("dat/nonexistent.sdf")\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.sdf'.\n", '< -1\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.sdf'.\n", '< CmdException raised.\n', '< cmd.load("dat/small03.mol2")\n', '< None\n', '< cmd.load("dat/nonexistent.mol2")\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol2'.\n", '< -1\n', "< ExecutiveLoad-Error: Unable to open file 'dat/nonexistent.mol2'.\n", '< CmdException raised.\n', '< cmd.load("dat/pept.r3d")\n', '< None\n', '< cmd.load("dat/nonexistent.r3d")\n', "< Load-Error: Unable to open file 'dat/nonexistent.r3d'.\n", '< -1\n', "< Load-Error: Unable to open file 'dat/nonexistent.r3d'.\n", '< CmdException raised.\n', '< cmd.load("dat/pept.pkl")\n', '< None\n', '< cmd.load("dat/nonexistent.pkl")\n', "< Load-Error: Unable to load file 'dat/nonexistent.pkl'.\n", '< -1\n', "< Load-Error: Unable to load file 'dat/nonexistent.pkl'.\n", '< CmdException raised.\n', '< cmd.get_names()\n', "< ['small01', 'ligs3d', 'small03', 'pept']\n", '< cmd.delete("all")\n', '< None\n', '< cmd.get_names()\n', '< []\n', '< cmd.get_model("nonexistent")\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< CmdException raised.\n', '< cmd.space("cmyk")\n', "< Color: loaded table '/Users/delwarl/pymol/data/pymol/cmyk.png'.\n", '< None\n', '< cmd.space("unknown")\n', "< Error: unknown color space 'unknown'.\n", '< -1\n', "< Error: unknown color space 'unknown'.\n", '< CmdException raised.\n', '< cmd.space("rgb")\n', '< Color: purged table; restoring RGB colors.\n', '< None\n', '< cmd.space()\n', '< None\n', '< chempy.models.Indexed\n', '< 107\n', '< chempy.models.Indexed\n', '< 0\n', '< cmd.get_model("nonexistent")\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< CmdException raised.\n', '< cmd.create("test","none",quiet=0)\n', '< Selector: found 0 atoms.\n', '< Executive: object "test" created.\n', '< None\n', '< cmd.create("test2","nonexistent")\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "nonexistent".\n', '< ( nonexistent )<--\n', '< CmdException raised.\n', '< cmd.create("test3","?allowed",quiet=0)\n', '< Selector: found 0 atoms.\n', '< Executive: object "test3" created.\n', '< None\n', '< cmd.fragment("arg")\n', '< None\n', '< cmd.fragment("nonexistent")\n', "< Error: unable to load fragment 'nonexistent'.\n", '< -1\n', "< Error: unable to load fragment 'nonexistent'.\n", '< CmdException raised.\n', '< cmd.distance("none","none","none")\n', '< -1.0\n', '< cmd.distance("none","invalid1","none")\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< CmdException raised.\n', '< cmd.distance("none","none","invalid2")\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< CmdException raised.\n', '< cmd.distance("none","invalid1","invalid2")\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid1".\n', '< ( invalid1 )<--\n', '< Selector-Error: Invalid selection name "invalid2".\n', '< ( invalid2 )<--\n', '< CmdException raised.\n', '< cmd.index("none")\n', '< []\n', '< cmd.index("first pept")\n', "< [('pept', 1)]\n", '< cmd.index("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.identify("none")\n', '< []\n', '< cmd.identify("first pept")\n', '< [1]\n', '< cmd.identify("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.identify("none",mode=1)\n', '< []\n', '< cmd.identify("first pept",mode=1)\n', "< [('pept', 1)]\n", '< cmd.identify("invalid",mode=1)\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.count_atoms("none")\n', '< 0\n', '< cmd.count_atoms()\n', '< 107\n', '< cmd.count_atoms("pept")\n', '< 107\n', '< cmd.count_atoms("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.count_frames()\n', '< 1\n', '< cmd.count_states()\n', '< 1\n', '< cmd.count_states("all")\n', '< 1\n', '< cmd.count_states("none")\n', '< 0\n', '< cmd.count_states("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< CmdException raised.\n', '< cmd.get_area()\n', '< 1381.18615723\n', '< cmd.get_area("resi 1")\n', '< 107.905807495\n', '< cmd.get_area("none")\n', '< 0.0\n', '< cmd.get_area("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1.0\n', '< cmd.get_chains()\n', "< ['E']\n", '< cmd.get_chains("pept")\n', "< ['E']\n", '< cmd.get_chains("resi 1")\n', "< ['E']\n", '< cmd.get_chains("none")\n', '< []\n', '< cmd.get_chains("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< ( invalid )<--\n', '< CmdException raised.\n', '< cmd.zoom()\n', '< None\n', '< cmd.zoom("pept")\n', '< None\n', '< cmd.zoom("none")\n', "< ExecutiveWindowZoom-Warning: selection doesn't specify any coordinates.\n", '< None\n', '< cmd.zoom("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< QuietException raised.\n', '< cmd.center()\n', '< None\n', '< cmd.center("pept")\n', '< None\n', '< cmd.center("none")\n', "< ExecutiveCenter-Warning: selection doesn't specify any coordinates.\n", '< None\n', '< cmd.center("invalid")\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< -1\n', '< Selector-Error: Invalid selection name "invalid".\n', '< invalid<--\n', '< QuietException raised.\n'] make[1]: Leaving directory '/«PKGBUILDDIR»' fakeroot debian/rules binary-arch dh binary-arch --with python2 --parallel dh_testroot -a -O--parallel dh_prep -a -O--parallel dh_installdirs -a -O--parallel dh_auto_install -a -O--parallel python setup.py install --force --root=/«PKGBUILDDIR»/debian/pymol --no-compile -O0 --install-layout=deb running install running build running build_py running build_ext running install_lib creating /«PKGBUILDDIR»/debian/pymol/usr/lib creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7 creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/volume.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/PMGApp.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/Demo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/demo copying build/lib.linux-armv7l-2.7/pmg_tk/skins/demo/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/demo copying build/lib.linux-armv7l-2.7/pmg_tk/skins/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal copying build/lib.linux-armv7l-2.7/pmg_tk/skins/normal/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal copying build/lib.linux-armv7l-2.7/pmg_tk/skins/normal/builder.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal copying build/lib.linux-armv7l-2.7/pmg_tk/skins/normal/ModalWindow.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/skins/normal creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup copying build/lib.linux-armv7l-2.7/pmg_tk/startup/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup copying build/lib.linux-armv7l-2.7/pmg_tk/startup/apbs_tools.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup copying build/lib.linux-armv7l-2.7/pmg_tk/startup/remote_pdb_load.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk/startup copying build/lib.linux-armv7l-2.7/pmg_tk/PyMOLMapLoad.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/TextEditor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/SetEditor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/ColorEditor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk copying build/lib.linux-armv7l-2.7/pmg_tk/Setting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_tk creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web copying build/lib.linux-armv7l-2.7/web/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web copying build/lib.linux-armv7l-2.7/web/pymolhttpd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web/examples copying build/lib.linux-armv7l-2.7/web/examples/justhttpd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web/examples copying build/lib.linux-armv7l-2.7/web/examples/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/web/examples creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/povray.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/cmd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/internal.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/locking.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/commanding.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/vfont.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/util.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/xray.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/checking.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/controlling.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/headering.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/creating.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/_cmd.so -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/menu.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/viewing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/parsing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/xwin.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/feedingback.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins copying build/lib.linux-armv7l-2.7/pymol/plugins/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins copying build/lib.linux-armv7l-2.7/pymol/plugins/legacysupport.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins copying build/lib.linux-armv7l-2.7/pymol/plugins/installation.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins copying build/lib.linux-armv7l-2.7/pymol/plugins/repository.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins copying build/lib.linux-armv7l-2.7/pymol/plugins/managergui.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/plugins copying build/lib.linux-armv7l-2.7/pymol/gui.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/fitting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/dragging.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/charge.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/stereodemo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/density.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/renaming.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/annotation.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/security.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/measurement.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/demo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/toggle.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/cleanup.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/label.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/pseudoatom.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/message.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/filter.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/pair_fit.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/fedora.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/benchmark.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/distance.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/sculpting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/appearance.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/box.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/wizard/mutagenesis.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/wizard copying build/lib.linux-armv7l-2.7/pymol/externing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/completing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/selecting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/constants.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/keyboard.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/moving.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/editor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/exporting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/computing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/monitoring.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/preset.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl copying build/lib.linux-armv7l-2.7/pymol/opengl/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glu copying build/lib.linux-armv7l-2.7/pymol/opengl/glu/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glu creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/gl copying build/lib.linux-armv7l-2.7/pymol/opengl/gl/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/gl creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glut copying build/lib.linux-armv7l-2.7/pymol/opengl/glut/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/opengl/glut copying build/lib.linux-armv7l-2.7/pymol/movie.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/api.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed copying build/lib.linux-armv7l-2.7/pymol/embed/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/epymol copying build/lib.linux-armv7l-2.7/pymol/embed/epymol/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/epymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/wxpymol copying build/lib.linux-armv7l-2.7/pymol/embed/wxpymol/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/embed/wxpymol copying build/lib.linux-armv7l-2.7/pymol/constants_palette.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/selector.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/importing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/wizarding.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/helping.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/shortcut.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/m4x.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/parser.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/editing.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/experimenting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/querying.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/rpc.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/keywords.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/colorramping.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/invocation.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/cgo.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol copying build/lib.linux-armv7l-2.7/pymol/callback.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/contrib copying build/lib.linux-armv7l-2.7/pymol/contrib/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol/contrib copying build/lib.linux-armv7l-2.7/pymol/setting.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/arc.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/lst.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ copying build/lib.linux-armv7l-2.7/chempy/champ/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ copying build/lib.linux-armv7l-2.7/chempy/champ/_champ.so -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ copying build/lib.linux-armv7l-2.7/chempy/champ/amber99.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ copying build/lib.linux-armv7l-2.7/chempy/champ/assign.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ copying build/lib.linux-armv7l-2.7/chempy/champ/formal_charges.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/champ copying build/lib.linux-armv7l-2.7/chempy/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/brick.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/protein_amber99.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/map.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/charge.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/dictdb.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/cif.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/bond_mmff.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/models.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/pkl.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/hetatm.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/place.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/cpv.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/sdf.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/bond_amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fragments copying build/lib.linux-armv7l-2.7/chempy/fragments/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fragments copying build/lib.linux-armv7l-2.7/chempy/water_amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/water_residues.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/protein_mmff.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/mmd.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fast copying build/lib.linux-armv7l-2.7/chempy/fast/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/fast creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker copying build/lib.linux-armv7l-2.7/chempy/tinker/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker copying build/lib.linux-armv7l-2.7/chempy/tinker/state.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker copying build/lib.linux-armv7l-2.7/chempy/tinker/keyword.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker copying build/lib.linux-armv7l-2.7/chempy/tinker/realtime.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker copying build/lib.linux-armv7l-2.7/chempy/tinker/amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/tinker copying build/lib.linux-armv7l-2.7/chempy/pdb.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/cex.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/neighbor.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/solvate.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/bonds.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/protein.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/io.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/mol.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/gamess1.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/mass.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/cc1.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/xyz.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/protein_amber.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/mol2.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/mae.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/gms.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy copying build/lib.linux-armv7l-2.7/chempy/protein_residues.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin copying build/lib.linux-armv7l-2.7/chempy/bmin/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin copying build/lib.linux-armv7l-2.7/chempy/bmin/state.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin copying build/lib.linux-armv7l-2.7/chempy/bmin/util.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin copying build/lib.linux-armv7l-2.7/chempy/bmin/realtime.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin copying build/lib.linux-armv7l-2.7/chempy/bmin/commands.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/chempy/bmin creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2 copying build/lib.linux-armv7l-2.7/pymol2/cmd2.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2 copying build/lib.linux-armv7l-2.7/pymol2/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2 copying build/lib.linux-armv7l-2.7/pymol2/make_cmd2.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol2 creating /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_wx copying build/lib.linux-armv7l-2.7/pmg_wx/__init__.py -> /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pmg_wx running install_egg_info Writing /«PKGBUILDDIR»/debian/pymol/usr/lib/python2.7/dist-packages/pymol-1.7.2.1.egg-info copying pymol -> /«PKGBUILDDIR»/debian/pymol/usr/bin debian/rules override_dh_install make[1]: Entering directory '/«PKGBUILDDIR»' pdflatex -output-directory debian -jobname pymol-ref-card debian/pymolRef.tex This is pdfTeX, Version 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./debian/pymolRef.tex LaTeX2e <2015/10/01> patch level 2 Babel <3.9n> and hyphenation patterns for 2 languages loaded. (/usr/share/texlive/texmf-dist/tex/latex/base/article.cls Document Class: article 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo)) (/usr/share/texlive/texmf-dist/tex/latex/tools/multicol.sty) No file pymol-ref-card.aux. Underfull \hbox (badness 10000) in paragraph at lines 78--79 [1{/var/lib/texmf/fonts/map/pdftex/updmap/pdftex.map}] (/usr/share/texlive/texmf-dist/tex/latex/base/omscmr.fd) [2] (debian/pymol-ref-card.aux) ) (see the transcript file for additional information) Output written on debian/pymol-ref-card.pdf (2 pages, 108274 bytes). Transcript written on debian/pymol-ref-card.log. sed -e s/@PYTHON_VERSION@/2.7/g < debian/pymol.launch.in > debian/pymol.launch dh_numpy dh_install data/shaders usr/lib/python2.7/dist-packages/pymol/data/ install -m 755 debian/pymol.launch debian/pymol/usr/bin/pymol make[1]: Leaving directory '/«PKGBUILDDIR»' dh_installdocs -a -O--parallel dh_installchangelogs -a -O--parallel dh_installexamples -a -O--parallel dh_installman -a -O--parallel dh_python2 -a -O--parallel I: dh_python2 fs:328: renaming _cmd.so to _cmd.arm-linux-gnueabihf.so I: dh_python2 fs:328: renaming _champ.so to _champ.arm-linux-gnueabihf.so dh_installmenu -a -O--parallel dh_installmime -a -O--parallel dh_perl -a -O--parallel dh_link -a -O--parallel dh_strip_nondeterminism -a -O--parallel debian/rules override_dh_compress make[1]: Entering directory '/«PKGBUILDDIR»' dh_compress -Xpdb make[1]: Leaving directory '/«PKGBUILDDIR»' dh_fixperms -a -O--parallel dh_strip -a -O--parallel dh_strip debug symbol extraction: enabling -a due to Build-Debug-Symbols: yes in /CurrentlyBuilding dh_strip debug symbol extraction: all non-arch-all packages for this build platform armhf: pymol dh_strip debug symbol extraction: packages to act on: pymol dh_strip debug symbol extraction: ignored packages: dpkg-gencontrol: warning: -is is deprecated; it is without effect dpkg-gencontrol: warning: -ip is deprecated; it is without effect dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dpkg-gencontrol: warning: package pymol: unused substitution variable ${python:Depends} /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a -O--parallel dh_shlibdeps -a -O--parallel dh_installdeb -a -O--parallel dh_gencontrol -a -O--parallel dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_gencontrol debug symbol wrapper: all non-arch-all packages for this build platform armhf: pymol dh_gencontrol debug symbol wrapper: packages to act on: pymol dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package pymol (pkgdir debian/pymol, ddeb package dir debian/pymol-dbgsym) dh_gencontrol debug symbol wrapper: building pymol-dbgsym_1.7.2.1-2.2_armhf.ddeb dpkg-deb: building package 'pymol-dbgsym' in '../pymol-dbgsym_1.7.2.1-2.2_armhf.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile pymol-dbgsym_1.7.2.1-2.2_armhf.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a -O--parallel dh_builddeb -a -O--parallel INFO: pkgstriptranslations version 129 pkgstriptranslations: processing pymol (in debian/pymol); do_strip: , oemstrip: debian/pymol/usr/share/applications/pymol.desktop: does not have gettext domain, not stripping pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/pymol/DEBIAN/control, package pymol, directory debian/pymol pkgstripfiles: Truncating usr/share/doc/pymol/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package pymol ... oo pkgstripfiles: PNG optimization (2/0) for package pymol took 40 s dpkg-deb: building package 'pymol' in '../pymol_1.7.2.1-2.2_armhf.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../pymol_1.7.2.1-2.2_armhf.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build pymol-1.7.2.1 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20160127-2331 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ pymol_1.7.2.1-2.2_armhf.changes: ──────────────────────────────── Format: 1.8 Date: Fri, 22 Jan 2016 11:04:44 +0100 Source: pymol Binary: pymol Architecture: armhf Version: 1.7.2.1-2.2 Distribution: xenial-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Gianfranco Costamagna Description: pymol - Molecular Graphics System Closes: 809840 Changes: pymol (1.7.2.1-2.2) unstable; urgency=medium . * Non-maintainer upload. * Change libpng12-0-dev build-dependency to libpng-dev, to ease libpng transition. (Closes: #809840) Checksums-Sha1: dc9d2dd085ca7de5f44aa13f85f8d2d897a1c14a 3108856 pymol-dbgsym_1.7.2.1-2.2_armhf.ddeb b0e9639c5eabcf604eb94c4bfac0aae675257136 4367326 pymol_1.7.2.1-2.2_armhf.deb Checksums-Sha256: e2c5ba0d73bfe44d24fd368ab42b4e2e24868617963281322f446f8490329e31 3108856 pymol-dbgsym_1.7.2.1-2.2_armhf.ddeb 31b1853e4ba6985baec620537144fd1e7c780399271ec19dc02656723a027b47 4367326 pymol_1.7.2.1-2.2_armhf.deb Files: 8eb8c2fc8f76465ee6f594333e8dffca 3108856 science extra pymol-dbgsym_1.7.2.1-2.2_armhf.ddeb e25f0b2b2c5f3f38e707cdec3da9f566 4367326 science optional pymol_1.7.2.1-2.2_armhf.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ pymol_1.7.2.1-2.2_armhf.deb ─────────────────────────── new debian package, version 2.0. size 4367326 bytes: control archive= 12726 bytes. 1281 bytes, 26 lines control 36828 bytes, 437 lines md5sums 403 bytes, 18 lines * postinst #!/bin/sh 160 bytes, 5 lines * postrm #!/bin/sh 245 bytes, 14 lines * prerm #!/bin/sh Package: pymol Version: 1.7.2.1-2.2 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debichem Team Installed-Size: 15881 Depends: python-numpy (>= 1:1.10.0~b1), python-pmw, python-tk, python-numpy-abi9, python (<< 2.8), python (>= 2.7~), python:any (>= 2.7.5-5~), freeglut3, libc6 (>= 2.15), libfreetype6 (>= 2.2.1), libgcc1 (>= 1:3.5), libgl1-mesa-glx | libgl1, libglew1.13 (>= 1.12.0), libglu1-mesa | libglu1, libpng12-0 (>= 1.2.13-4), libstdc++6 (>= 5.2) Recommends: apbs Section: science Priority: optional Homepage: http://www.pymol.org Description: Molecular Graphics System PyMOL is a molecular graphics system targeted at medium to large biomolecules like proteins. It can generate high-quality publication-ready molecular graphics images and animations. . Features include: * Visualization of molecules, molecular trajectories and surfaces of crystallography data or orbitals * Molecular builder and sculptor * Internal raytracer and movie generator * Fully extensible and scriptable via a Python interface . File formats PyMOL can read include PDB, XYZ, CIF, MDL Molfile, ChemDraw, CCP4 maps, XPLOR maps and Gaussian cube maps. Python-Version: 2.7 drwxr-xr-x root/root 0 2016-01-27 23:30 ./ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/bin/ -rwxr-xr-x root/root 469 2016-01-27 23:29 ./usr/bin/pymol drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/mime/ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/mime/packages/ -rw-r--r-- root/root 136 2014-09-14 13:40 ./usr/lib/mime/packages/pymol drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/python2.7/ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/python2.7/dist-packages/ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/python2.7/dist-packages/chempy/ -rw-r--r-- root/root 15010 2014-08-26 17:41 ./usr/lib/python2.7/dist-packages/chempy/__init__.py -rw-r--r-- root/root 1376 2014-08-26 17:41 ./usr/lib/python2.7/dist-packages/chempy/arc.py drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/lib/python2.7/dist-packages/chempy/bmin/ -rw-r--r-- root/root 1419 2014-08-26 17:41 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./usr/share/pymol/scripts/metaphorics/alignment.pml -rw-r--r-- root/root 1246 2014-08-26 17:41 ./usr/share/pymol/scripts/metaphorics/annotate.pml -rw-r--r-- root/root 1356 2014-08-26 17:41 ./usr/share/pymol/scripts/metaphorics/fedora.pml drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/share/python/ drwxr-xr-x root/root 0 2016-01-27 23:29 ./usr/share/python/runtime.d/ -rwxr-xr-x root/root 123 2016-01-27 23:29 ./usr/share/python/runtime.d/pymol.rtupdate ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: armhf Build-Space: 113412 Build-Time: 416 Distribution: xenial-proposed Host Architecture: armhf Install-Time: 280 Job: pymol_1.7.2.1-2.2.dsc Machine Architecture: armhf Package: pymol Package-Time: 707 Source-Version: 1.7.2.1-2.2 Space: 113412 Status: successful Version: 1.7.2.1-2.2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20160127-2331 Build needed 00:11:47, 113412k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8905283'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8905283/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8905283'] Unmounting chroot for build PACKAGEBUILD-8905283... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8905283'] Removing build PACKAGEBUILD-8905283