RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux denneed01 3.19.0-31-powerpc64-smp #36~14.04.1-Ubuntu SMP Thu Oct 8 10:49:59 UTC 2015 ppc64 Buildd toolchain package versions: launchpad-buildd_134 python-lpbuildd_134 sbuild_0.65.2-1ubuntu2~ubuntu14.04.1~ppa6 dpkg-dev_1.17.5ubuntu5.4 python-debian_0.1.27ubuntu1~ubuntu14.04.1~ppa1. Syncing the system clock with the buildd NTP service... 15 Dec 03:13:32 ntpdate[16800]: adjust time server 10.211.37.1 offset -0.004397 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-8441450', '/home/buildd/filecache-default/59b2027bd898a08257bdf6a14dda09a63b60b4fb'] Unpacking chroot for build PACKAGEBUILD-8441450 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-8441450'] Mounting chroot for build PACKAGEBUILD-8441450 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-8441450', 'deb http://ppa.launchpad.net/xnox/nonvirt/ubuntu xenial main', '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-8441450 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-8441450', 'powerpc'] Updating debian chroot for build PACKAGEBUILD-8441450 Get:1 http://ftpmaster.internal xenial InRelease [227 kB] Get:2 http://ppa.launchpad.net xenial InRelease [23.9 kB] Ign http://ppa.launchpad.net xenial InRelease Get:3 http://ppa.launchpad.net xenial/main powerpc Packages [10.2 kB] Get:4 http://ppa.launchpad.net xenial/main Translation-en [6977 B] Get:5 http://ftpmaster.internal xenial-security InRelease [73.5 kB] Get:6 http://ftpmaster.internal xenial-updates InRelease [73.5 kB] Get:7 http://ftpmaster.internal xenial-proposed InRelease [227 kB] Get:8 http://ftpmaster.internal xenial/main powerpc Packages [1425 kB] Get:9 http://ftpmaster.internal xenial/universe powerpc Packages [6902 kB] Get:10 http://ftpmaster.internal xenial/main Translation-en [848 kB] Get:11 http://ftpmaster.internal xenial/universe Translation-en [4747 kB] Get:12 http://ftpmaster.internal xenial-security/main powerpc Packages [28 B] Get:13 http://ftpmaster.internal xenial-security/universe powerpc Packages [28 B] Get:14 http://ftpmaster.internal xenial-security/main Translation-en [28 B] Get:15 http://ftpmaster.internal xenial-security/universe Translation-en [28 B] Get:16 http://ftpmaster.internal xenial-updates/main powerpc Packages [28 B] Get:17 http://ftpmaster.internal xenial-updates/universe powerpc Packages [28 B] Get:18 http://ftpmaster.internal xenial-updates/main Translation-en [28 B] Get:19 http://ftpmaster.internal xenial-updates/universe Translation-en [28 B] Get:20 http://ftpmaster.internal xenial-proposed/main powerpc Packages [87.9 kB] Get:21 http://ftpmaster.internal xenial-proposed/universe powerpc Packages [424 kB] Get:22 http://ftpmaster.internal xenial-proposed/main Translation-en [40.0 kB] Get:23 http://ftpmaster.internal xenial-proposed/universe Translation-en [254 kB] Fetched 15.4 MB in 19s (786 kB/s) Reading package lists... W: GPG error: http://ppa.launchpad.net xenial InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 157951FE4031D287 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 NEW packages will be installed: libapt-pkg5.0 libisl15 libprocps4 The following packages will be upgraded: advancecomp apt apt-transport-https base-files binutils bsdutils cpp cpp-5 debconf diffutils dmsetup dpkg dpkg-dev e2fslibs e2fsprogs findutils g++ g++-5 gcc gcc-5 gcc-5-base gnupg gpgv hostname init initscripts libapparmor1 libasan2 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 libidn11 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libmount1 libncurses5 libncursesw5 libpng12-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.0.0 libstdc++-5-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo5 libubsan0 libudev1 libuuid1 linux-libc-dev lsb-base mount multiarch-support ncurses-base ncurses-bin openssl pkg-create-dbgsym pkgbinarymangler procps systemd systemd-sysv sysv-rc sysvinit-utils tar udev util-linux 98 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 260 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ xenial/main base-files powerpc 9.4ubuntu3 [62.2 kB] Get:2 http://ftpmaster.internal/ubuntu/ xenial/main bsdutils powerpc 1:2.27.1-1ubuntu3 [50.9 kB] Get:3 http://ftpmaster.internal/ubuntu/ xenial/main diffutils powerpc 1:3.3-2 [149 kB] Get:4 http://ftpmaster.internal/ubuntu/ xenial/main dpkg powerpc 1.18.3ubuntu1 [2049 kB] Get:5 http://ftpmaster.internal/ubuntu/ xenial/main libc6-dev powerpc 2.21-0ubuntu5 [1793 kB] Get:6 http://ftpmaster.internal/ubuntu/ xenial/main libc-dev-bin powerpc 2.21-0ubuntu5 [61.5 kB] Get:7 http://ftpmaster.internal/ubuntu/ xenial-proposed/main linux-libc-dev powerpc 4.3.0-4.13 [807 kB] Get:8 http://ftpmaster.internal/ubuntu/ xenial/main libcap2 powerpc 1:2.24-12 [12.5 kB] Get:9 http://ftpmaster.internal/ubuntu/ xenial/main libc-bin powerpc 2.21-0ubuntu5 [1272 kB] Get:10 http://ftpmaster.internal/ubuntu/ xenial/main libgomp1 powerpc 5.3.1-3ubuntu1 [51.0 kB] Get:11 http://ftpmaster.internal/ubuntu/ xenial/main libatomic1 powerpc 5.3.1-3ubuntu1 [7188 B] Get:12 http://ftpmaster.internal/ubuntu/ xenial/main libasan2 powerpc 5.3.1-3ubuntu1 [232 kB] Get:13 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5-base powerpc 5.3.1-3ubuntu1 [16.5 kB] Get:14 http://ftpmaster.internal/ubuntu/ xenial/main libgcc1 powerpc 1:5.3.1-3ubuntu1 [27.0 kB] Get:15 http://ftpmaster.internal/ubuntu/ xenial/main libubsan0 powerpc 5.3.1-3ubuntu1 [95.7 kB] Get:16 http://ftpmaster.internal/ubuntu/ xenial/main libisl15 powerpc 0.15-3 [420 kB] Get:17 http://ftpmaster.internal/ubuntu/ xenial/main cpp-5 powerpc 5.3.1-3ubuntu1 [26.5 MB] Get:18 http://ftpmaster.internal/ubuntu/ xenial/main libcc1-0 powerpc 5.3.1-3ubuntu1 [40.7 kB] Get:19 http://ftpmaster.internal/ubuntu/ xenial/main binutils powerpc 2.25.90.20151211-0ubuntu2 [2290 kB] Get:20 http://ftpmaster.internal/ubuntu/ xenial/main g++-5 powerpc 5.3.1-3ubuntu1 [28.6 MB] Get:21 http://ftpmaster.internal/ubuntu/ xenial/main gcc-5 powerpc 5.3.1-3ubuntu1 [26.7 MB] Get:22 http://ftpmaster.internal/ubuntu/ xenial/main libgcc-5-dev powerpc 5.3.1-3ubuntu1 [500 kB] Get:23 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++-5-dev powerpc 5.3.1-3ubuntu1 [1357 kB] Get:24 http://ftpmaster.internal/ubuntu/ xenial/main libstdc++6 powerpc 5.3.1-3ubuntu1 [401 kB] Get:25 http://ftpmaster.internal/ubuntu/ xenial/main libgmp10 powerpc 2:6.1.0+dfsg-2 [199 kB] Get:26 http://ftpmaster.internal/ubuntu/ xenial/main libc6 powerpc 2.21-0ubuntu5 [5095 kB] Get:27 http://ftpmaster.internal/ubuntu/ xenial/main e2fslibs powerpc 1.42.13-1ubuntu1 [187 kB] Get:28 http://ftpmaster.internal/ubuntu/ xenial/main e2fsprogs powerpc 1.42.13-1ubuntu1 [753 kB] Get:29 http://ftpmaster.internal/ubuntu/ xenial/main findutils powerpc 4.4.2-10 [234 kB] Get:30 http://ftpmaster.internal/ubuntu/ xenial/main hostname powerpc 3.16ubuntu2 [11.3 kB] Get:31 http://ftpmaster.internal/ubuntu/ xenial/main init powerpc 1.24ubuntu2 [3982 B] Get:32 http://ftpmaster.internal/ubuntu/ xenial/main libsmartcols1 powerpc 2.27.1-1ubuntu3 [57.5 kB] Get:33 http://ftpmaster.internal/ubuntu/ xenial/main libuuid1 powerpc 2.27.1-1ubuntu3 [15.9 kB] Get:34 http://ftpmaster.internal/ubuntu/ xenial/main libblkid1 powerpc 2.27.1-1ubuntu3 [99.5 kB] Get:35 http://ftpmaster.internal/ubuntu/ xenial/main libfdisk1 powerpc 2.27.1-1ubuntu3 [125 kB] Get:36 http://ftpmaster.internal/ubuntu/ xenial/main debconf all 1.5.58ubuntu1 [136 kB] Get:37 http://ftpmaster.internal/ubuntu/ xenial/main sysvinit-utils powerpc 2.88dsf-59.2ubuntu3 [25.5 kB] Get:38 http://ftpmaster.internal/ubuntu/ xenial/main sysv-rc all 2.88dsf-59.2ubuntu3 [36.1 kB] Get:39 http://ftpmaster.internal/ubuntu/ xenial/main initscripts powerpc 2.88dsf-59.2ubuntu3 [24.8 kB] Get:40 http://ftpmaster.internal/ubuntu/ xenial/main util-linux powerpc 2.27.1-1ubuntu3 [781 kB] Get:41 http://ftpmaster.internal/ubuntu/ xenial/main libudev1 powerpc 228-2ubuntu2 [52.5 kB] Get:42 http://ftpmaster.internal/ubuntu/ xenial/main udev powerpc 228-2ubuntu2 [947 kB] Get:43 http://ftpmaster.internal/ubuntu/ xenial/main libsystemd0 powerpc 228-2ubuntu2 [182 kB] Get:44 http://ftpmaster.internal/ubuntu/ xenial/main systemd powerpc 228-2ubuntu2 [3256 kB] Get:45 http://ftpmaster.internal/ubuntu/ xenial/main libselinux1 powerpc 2.4-3 [50.3 kB] Get:46 http://ftpmaster.internal/ubuntu/ xenial/main libtinfo5 powerpc 6.0+20151024-2ubuntu1 [69.5 kB] Get:47 http://ftpmaster.internal/ubuntu/ xenial/main libncurses5 powerpc 6.0+20151024-2ubuntu1 [80.7 kB] Get:48 http://ftpmaster.internal/ubuntu/ xenial/main libncursesw5 powerpc 6.0+20151024-2ubuntu1 [101 kB] Get:49 http://ftpmaster.internal/ubuntu/ xenial/main libprocps4 powerpc 2:3.3.10-4ubuntu1 [30.2 kB] Get:50 http://ftpmaster.internal/ubuntu/ xenial/main procps powerpc 2:3.3.10-4ubuntu1 [212 kB] Get:51 http://ftpmaster.internal/ubuntu/ xenial/main libapparmor1 powerpc 2.10-0ubuntu8 [27.3 kB] Get:52 http://ftpmaster.internal/ubuntu/ xenial/main libaudit-common all 1:2.4.4-4ubuntu1 [3892 B] Get:53 http://ftpmaster.internal/ubuntu/ xenial/main libaudit1 powerpc 1:2.4.4-4ubuntu1 [34.6 kB] Get:54 http://ftpmaster.internal/ubuntu/ xenial/main libmount1 powerpc 2.27.1-1ubuntu3 [101 kB] Get:55 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libseccomp2 powerpc 2.2.3-2ubuntu2 [35.2 kB] Get:56 http://ftpmaster.internal/ubuntu/ xenial/main libcap2-bin powerpc 1:2.24-12 [19.7 kB] Get:57 http://ftpmaster.internal/ubuntu/ xenial/main lsb-base all 9.20150917ubuntu1 [13.4 kB] Get:58 http://ftpmaster.internal/ubuntu/ xenial/main mount powerpc 2.27.1-1ubuntu3 [115 kB] Get:59 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-bin powerpc 6.0+20151024-2ubuntu1 [129 kB] Get:60 http://ftpmaster.internal/ubuntu/ xenial/main tar powerpc 1.28-2.1 [192 kB] Get:61 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libapt-pkg5.0 powerpc 1.1.5 [654 kB] Get:62 http://ftpmaster.internal/ubuntu/ xenial-proposed/main apt powerpc 1.1.5 [953 kB] Get:63 http://ftpmaster.internal/ubuntu/ xenial/main gpgv powerpc 1.4.19-6ubuntu1 [145 kB] Get:64 http://ftpmaster.internal/ubuntu/ xenial/main gnupg powerpc 1.4.19-6ubuntu1 [579 kB] Get:65 http://ftpmaster.internal/ubuntu/ xenial/main ncurses-base all 6.0+20151024-2ubuntu1 [17.1 kB] Get:66 http://ftpmaster.internal/ubuntu/ xenial/main systemd-sysv powerpc 228-2ubuntu2 [15.1 kB] Get:67 http://ftpmaster.internal/ubuntu/ xenial/main dmsetup powerpc 2:1.02.110-1ubuntu1 [52.4 kB] Get:68 http://ftpmaster.internal/ubuntu/ xenial/main libdevmapper1.02.1 powerpc 2:1.02.110-1ubuntu1 [120 kB] Get:69 http://ftpmaster.internal/ubuntu/ xenial/main libcomerr2 powerpc 1.42.13-1ubuntu1 [65.5 kB] Get:70 http://ftpmaster.internal/ubuntu/ xenial/main libdebconfclient0 powerpc 0.198ubuntu1 [6314 B] Get:71 http://ftpmaster.internal/ubuntu/ xenial/main libgpg-error0 powerpc 1.20-1 [31.9 kB] Get:72 http://ftpmaster.internal/ubuntu/ xenial/main libgcrypt20 powerpc 1.6.4-3 [304 kB] Get:73 http://ftpmaster.internal/ubuntu/ xenial/main libsepol1 powerpc 2.4-2 [155 kB] Get:74 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage-common all 2.4-3 [6744 B] Get:75 http://ftpmaster.internal/ubuntu/ xenial-proposed/main libsemanage1 powerpc 2.4-3 [68.0 kB] Get:76 http://ftpmaster.internal/ubuntu/ xenial/main libss2 powerpc 1.42.13-1ubuntu1 [69.6 kB] Get:77 http://ftpmaster.internal/ubuntu/ xenial/main multiarch-support powerpc 2.21-0ubuntu5 [7182 B] Get:78 http://ftpmaster.internal/ubuntu/ xenial/main libffi6 powerpc 3.2.1-4 [17.0 kB] Get:79 http://ftpmaster.internal/ubuntu/ xenial/main libtasn1-6 powerpc 4.7-2 [39.6 kB] Get:80 http://ftpmaster.internal/ubuntu/ xenial/main libgnutls-deb0-28 powerpc 3.3.18-1ubuntu1 [414 kB] Get:81 http://ftpmaster.internal/ubuntu/ xenial/main libpng12-0 powerpc 1.2.54-1 [110 kB] Get:82 http://ftpmaster.internal/ubuntu/ xenial/main libsqlite3-0 powerpc 3.9.2-1 [348 kB] Get:83 http://ftpmaster.internal/ubuntu/ xenial/main libssl1.0.0 powerpc 1.0.2e-1ubuntu1 [720 kB] Get:84 http://ftpmaster.internal/ubuntu/ xenial/main libgssapi-krb5-2 powerpc 1.13.2+dfsg-4 [102 kB] Get:85 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5-3 powerpc 1.13.2+dfsg-4 [239 kB] Get:86 http://ftpmaster.internal/ubuntu/ xenial/main libkrb5support0 powerpc 1.13.2+dfsg-4 [29.0 kB] Get:87 http://ftpmaster.internal/ubuntu/ xenial/main libk5crypto3 powerpc 1.13.2+dfsg-4 [81.5 kB] Get:88 http://ftpmaster.internal/ubuntu/ xenial/main libkeyutils1 powerpc 1.5.9-8ubuntu1 [9890 B] Get:89 http://ftpmaster.internal/ubuntu/ xenial/main libidn11 powerpc 1.32-3ubuntu1 [42.8 kB] Get:90 http://ftpmaster.internal/ubuntu/ xenial/main libcurl3-gnutls powerpc 7.45.0-1ubuntu1 [165 kB] Get:91 http://ftpmaster.internal/ubuntu/ xenial-proposed/main apt-transport-https powerpc 1.1.5 [25.2 kB] Get:92 http://ftpmaster.internal/ubuntu/ xenial/main libdbus-1-3 powerpc 1.10.6-1ubuntu1 [143 kB] Get:93 http://ftpmaster.internal/ubuntu/ xenial/main openssl powerpc 1.0.2e-1ubuntu1 [465 kB] Get:94 http://ftpmaster.internal/ubuntu/ xenial/main advancecomp powerpc 1.20-1 [143 kB] Get:95 http://ftpmaster.internal/ubuntu/ xenial/main cpp powerpc 4:5.2.1-16ubuntu2 [27.6 kB] Get:96 http://ftpmaster.internal/ubuntu/ xenial/main dpkg-dev all 1.18.3ubuntu1 [583 kB] Get:97 http://ftpmaster.internal/ubuntu/ xenial/main libdpkg-perl all 1.18.3ubuntu1 [195 kB] Get:98 http://ftpmaster.internal/ubuntu/ xenial/main gcc powerpc 4:5.2.1-16ubuntu2 [5228 B] Get:99 http://ftpmaster.internal/ubuntu/ xenial/main g++ powerpc 4:5.2.1-16ubuntu2 [1512 B] Get:100 http://ftpmaster.internal/ubuntu/ xenial/main pkg-create-dbgsym all 0.70 [9046 B] Get:101 http://ftpmaster.internal/ubuntu/ xenial/main pkgbinarymangler all 125 [41.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 114 MB in 1min 7s (1702 kB/s) (Reading database ... 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Updating /etc/profile to current default. Updating /etc/nsswitch.conf to current default. Updating /root/.profile to current default. (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 ... 11513 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.27.1-1ubuntu3_powerpc.deb ... Unpacking bsdutils (1:2.27.1-1ubuntu3) over (1:2.26.2-6ubuntu3) ... Setting up bsdutils (1:2.27.1-1ubuntu3) ... (Reading database ... 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Selecting previously unselected package libisl15:powerpc. Preparing to unpack .../libisl15_0.15-3_powerpc.deb ... Unpacking libisl15:powerpc (0.15-3) ... Preparing to unpack .../cpp-5_5.3.1-3ubuntu1_powerpc.deb ... Unpacking cpp-5 (5.3.1-3ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libcc1-0_5.3.1-3ubuntu1_powerpc.deb ... Unpacking libcc1-0:powerpc (5.3.1-3ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../binutils_2.25.90.20151211-0ubuntu2_powerpc.deb ... Unpacking binutils (2.25.90.20151211-0ubuntu2) over (2.25.1-6ubuntu1) ... Preparing to unpack .../g++-5_5.3.1-3ubuntu1_powerpc.deb ... Unpacking g++-5 (5.3.1-3ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../gcc-5_5.3.1-3ubuntu1_powerpc.deb ... Unpacking gcc-5 (5.3.1-3ubuntu1) over (5.2.1-22ubuntu2) ... Preparing to unpack .../libgcc-5-dev_5.3.1-3ubuntu1_powerpc.deb ... Unpacking libgcc-5-dev:powerpc (5.3.1-3ubuntu1) over (5.2.1-22ubuntu2) ... 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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 ... 11499 files and directories currently installed.) Preparing to unpack .../systemd_228-2ubuntu2_powerpc.deb ... Unpacking systemd (228-2ubuntu2) over (225-1ubuntu9) ... Setting up systemd (228-2ubuntu2) ... 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. (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 ... 11500 files and directories currently installed.) Preparing to unpack .../libselinux1_2.4-3_powerpc.deb ... Unpacking libselinux1:powerpc (2.4-3) over (2.3-2build1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libselinux1:powerpc (2.4-3) ... 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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 ... 11500 files and directories currently installed.) Preparing to unpack .../libncurses5_6.0+20151024-2ubuntu1_powerpc.deb ... Unpacking libncurses5:powerpc (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libncurses5:powerpc (6.0+20151024-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... (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 ... 11500 files and directories currently installed.) Preparing to unpack .../libprocps4_2%3a3.3.10-4ubuntu1_powerpc.deb ... Unpacking libprocps4:powerpc (2:3.3.10-4ubuntu1) ... Preparing to unpack .../procps_2%3a3.3.10-4ubuntu1_powerpc.deb ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Unpacking procps (2:3.3.10-4ubuntu1) over (1:3.3.9-1ubuntu8) ... 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Preparing to unpack .../libaudit-common_1%3a2.4.4-4ubuntu1_all.deb ... Unpacking libaudit-common (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Setting up libaudit-common (1:2.4.4-4ubuntu1) ... (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 ... 11509 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a2.4.4-4ubuntu1_powerpc.deb ... Unpacking libaudit1:powerpc (1:2.4.4-4ubuntu1) over (1:2.4.2-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libaudit1:powerpc (1:2.4.4-4ubuntu1) ... 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 ... 11509 files and directories currently installed.) Preparing to unpack .../libmount1_2.27.1-1ubuntu3_powerpc.deb ... Unpacking libmount1:powerpc (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libmount1:powerpc (2.27.1-1ubuntu3) ... 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 ... 11509 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.2.3-2ubuntu2_powerpc.deb ... Unpacking libseccomp2:powerpc (2.2.3-2ubuntu2) over (2.2.3-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libseccomp2:powerpc (2.2.3-2ubuntu2) ... 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 u8) ... Preparin(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 ... 11509 files and directories currently installed.) Preparing to unpack .../libcap2-bin_1%3a2.24-12_powerpc.deb ... Unpacking libcap2-bin (1:2.24-12) over (1:2.24-9) ... Setting up libcap2-bin (1:2.24-12) ... (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 ... 11509 files and directories currently installed.) Preparing to unpack .../lsb-base_9.20150917ubuntu1_all.deb ... Unpacking lsb-base (9.20150917ubuntu1) over (4.1+Debian11ubuntu8) ... Setting up lsb-base (9.20150917ubuntu1) ... (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 ... 11509 files and directories currently installed.) Preparing to unpack .../mount_2.27.1-1ubuntu3_powerpc.deb ... Unpacking mount (2.27.1-1ubuntu3) over (2.26.2-6ubuntu3) ... Setting up mount (2.27.1-1ubuntu3) ... (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 ... 11509 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.0+20151024-2ubuntu1_powerpc.deb ... Unpacking ncurses-bin (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Setting up ncurses-bin (6.0+20151024-2ubuntu1) ... (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 ... 11505 files and directories currently installed.) Preparing to unpack .../tar_1.28-2.1_powerpc.deb ... Unpacking tar (1.28-2.1) over (1.27.1-2) ... Setting up tar (1.28-2.1) ... (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 ... 11505 files and directories currently installed.) Preparing to unpack .../archives/apt_1.1.5_powerpc.deb ... Unpacking apt (1.1.5) over (1.0.10.2ubuntu1) ... Selecting previously unselected package libapt-pkg5.0:powerpc. Preparing to unpack .../libapt-pkg5.0_1.1.5_powerpc.deb ... Unpacking libapt-pkg5.0:powerpc (1.1.5) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libapt-pkg5.0:powerpc (1.1.5) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../gpgv_1.4.19-6ubuntu1_powerpc.deb ... Unpacking gpgv (1.4.19-6ubuntu1) over (1.4.18-7ubuntu1) ... Setting up gpgv (1.4.19-6ubuntu1) ... (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 ... 11533 files and directories currently installed.) Preparing to unpack .../gnupg_1.4.19-6ubuntu1_powerpc.deb ... Unpacking gnupg (1.4.19-6ubuntu1) over (1.4.18-7ubuntu1) ... Setting up gnupg (1.4.19-6ubuntu1) ... (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 ... 11532 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.0+20151024-2ubuntu1_all.deb ... Unpacking ncurses-base (6.0+20151024-2ubuntu1) over (5.9+20150516-2ubuntu1) ... Setting up ncurses-base (6.0+20151024-2ubuntu1) ... (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 ... 11533 files and directories currently installed.) Preparing to unpack .../systemd-sysv_228-2ubuntu2_powerpc.deb ... Unpacking systemd-sysv (228-2ubuntu2) over (225-1ubuntu9) ... Setting up systemd-sysv (228-2ubuntu2) ... (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 ... 11533 files and directories currently installed.) Preparing to unpack .../dmsetup_2%3a1.02.110-1ubuntu1_powerpc.deb ... Unpacking dmsetup (2:1.02.110-1ubuntu1) over (2:1.02.99-1ubuntu1) ... Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.110-1ubuntu1_powerpc.deb ... Unpacking libdevmapper1.02.1:powerpc (2:1.02.110-1ubuntu1) over (2:1.02.99-1ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libdevmapper1.02.1:powerpc (2:1.02.110-1ubuntu1) ... Setting up dmsetup (2:1.02.110-1ubuntu1) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.42.13-1ubuntu1_powerpc.deb ... Unpacking libcomerr2:powerpc (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libcomerr2:powerpc (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 ... 11533 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.198ubuntu1_powerpc.deb ... Unpacking libdebconfclient0:powerpc (0.198ubuntu1) over (0.192ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libdebconfclient0:powerpc (0.198ubuntu1) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.20-1_powerpc.deb ... Unpacking libgpg-error0:powerpc (1.20-1) over (1.19-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgpg-error0:powerpc (1.20-1) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.6.4-3_powerpc.deb ... Unpacking libgcrypt20:powerpc (1.6.4-3) over (1.6.3-2ubuntu1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libgcrypt20:powerpc (1.6.4-3) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../libsepol1_2.4-2_powerpc.deb ... Unpacking libsepol1:powerpc (2.4-2) over (2.3-2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsepol1:powerpc (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 ... 11533 files and directories currently installed.) Preparing to unpack .../libsemanage-common_2.4-3_all.deb ... Unpacking libsemanage-common (2.4-3) over (2.3-1build2) ... Setting up libsemanage-common (2.4-3) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../libsemanage1_2.4-3_powerpc.deb ... Unpacking libsemanage1:powerpc (2.4-3) over (2.3-1build2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libsemanage1:powerpc (2.4-3) ... 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 ... 11533 files and directories currently installed.) Preparing to unpack .../libss2_1.42.13-1ubuntu1_powerpc.deb ... Unpacking libss2:powerpc (1.42.13-1ubuntu1) over (1.42.12-1ubuntu2) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libss2:powerpc (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 ... 11533 files and directories currently installed.) Preparing to unpack .../multiarch-support_2.21-0ubuntu5_powerpc.deb ... Unpacking multiarch-support (2.21-0ubuntu5) over (2.21-0ubuntu4) ... Setting up multiarch-support (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 ... 11533 files and directories currently installed.) Preparing to unpack .../libffi6_3.2.1-4_powerpc.deb ... Unpacking libffi6:powerpc (3.2.1-4) over (3.2.1-3) ... Preparing to unpack .../libtasn1-6_4.7-2_powerpc.deb ... Unpacking libtasn1-6:powerpc (4.7-2) over (4.5-2) ... Preparing to unpack .../libgnutls-deb0-28_3.3.18-1ubuntu1_powerpc.deb ... Unpacking libgnutls-deb0-28:powerpc (3.3.18-1ubuntu1) over (3.3.15-5ubuntu2) ... Preparing to unpack .../libpng12-0_1.2.54-1_powerpc.deb ... Unpacking libpng12-0:powerpc (1.2.54-1) over (1.2.51-0ubuntu3) ... Preparing to unpack .../libsqlite3-0_3.9.2-1_powerpc.deb ... Unpacking libsqlite3-0:powerpc (3.9.2-1) over (3.8.11.1-1) ... Preparing to unpack .../libssl1.0.0_1.0.2e-1ubuntu1_powerpc.deb ... Unpacking libssl1.0.0:powerpc (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu1) ... Preparing to unpack .../libgssapi-krb5-2_1.13.2+dfsg-4_powerpc.deb ... Unpacking libgssapi-krb5-2:powerpc (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkrb5-3_1.13.2+dfsg-4_powerpc.deb ... Unpacking libkrb5-3:powerpc (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkrb5support0_1.13.2+dfsg-4_powerpc.deb ... Unpacking libkrb5support0:powerpc (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libk5crypto3_1.13.2+dfsg-4_powerpc.deb ... Unpacking libk5crypto3:powerpc (1.13.2+dfsg-4) over (1.13.2+dfsg-2) ... Preparing to unpack .../libkeyutils1_1.5.9-8ubuntu1_powerpc.deb ... Unpacking libkeyutils1:powerpc (1.5.9-8ubuntu1) over (1.5.9-5ubuntu1) ... Preparing to unpack .../libidn11_1.32-3ubuntu1_powerpc.deb ... Unpacking libidn11:powerpc (1.32-3ubuntu1) over (1.28-1ubuntu2) ... Preparing to unpack .../libcurl3-gnutls_7.45.0-1ubuntu1_powerpc.deb ... Unpacking libcurl3-gnutls:powerpc (7.45.0-1ubuntu1) over (7.43.0-1ubuntu2) ... Preparing to unpack .../apt-transport-https_1.1.5_powerpc.deb ... Unpacking apt-transport-https (1.1.5) over (1.0.10.2ubuntu1) ... Preparing to unpack .../libdbus-1-3_1.10.6-1ubuntu1_powerpc.deb ... Unpacking libdbus-1-3:powerpc (1.10.6-1ubuntu1) over (1.10.0-1ubuntu1) ... Preparing to unpack .../openssl_1.0.2e-1ubuntu1_powerpc.deb ... Unpacking openssl (1.0.2e-1ubuntu1) over (1.0.2d-0ubuntu1) ... Preparing to unpack .../advancecomp_1.20-1_powerpc.deb ... Unpacking advancecomp (1.20-1) over (1.19-1) ... Preparing to unpack .../cpp_4%3a5.2.1-16ubuntu2_powerpc.deb ... Unpacking cpp (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../dpkg-dev_1.18.3ubuntu1_all.deb ... Unpacking dpkg-dev (1.18.3ubuntu1) over (1.18.2ubuntu5) ... Preparing to unpack .../libdpkg-perl_1.18.3ubuntu1_all.deb ... Unpacking libdpkg-perl (1.18.3ubuntu1) over (1.18.2ubuntu5) ... Preparing to unpack .../gcc_4%3a5.2.1-16ubuntu2_powerpc.deb ... Removing old gcc doc directory. Unpacking gcc (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../g++_4%3a5.2.1-16ubuntu2_powerpc.deb ... Unpacking g++ (4:5.2.1-16ubuntu2) over (4:5.2.1-3ubuntu1) ... Preparing to unpack .../pkg-create-dbgsym_0.70_all.deb ... Unpacking pkg-create-dbgsym (0.70) over (0.69) ... Preparing to unpack .../pkgbinarymangler_125_all.deb ... Unpacking pkgbinarymangler (125) over (122) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Setting up libc-dev-bin (2.21-0ubuntu5) ... Setting up linux-libc-dev:powerpc (4.3.0-4.13) ... Setting up libc6-dev:powerpc (2.21-0ubuntu5) ... Setting up libgomp1:powerpc (5.3.1-3ubuntu1) ... Setting up libatomic1:powerpc (5.3.1-3ubuntu1) ... Setting up libasan2:powerpc (5.3.1-3ubuntu1) ... Setting up libubsan0:powerpc (5.3.1-3ubuntu1) ... Setting up libgmp10:powerpc (2:6.1.0+dfsg-2) ... Setting up libisl15:powerpc (0.15-3) ... Setting up cpp-5 (5.3.1-3ubuntu1) ... Setting up libcc1-0:powerpc (5.3.1-3ubuntu1) ... Setting up binutils (2.25.90.20151211-0ubuntu2) ... Setting up libgcc-5-dev:powerpc (5.3.1-3ubuntu1) ... Setting up gcc-5 (5.3.1-3ubuntu1) ... Setting up libstdc++-5-dev:powerpc (5.3.1-3ubuntu1) ... Setting up g++-5 (5.3.1-3ubuntu1) ... Setting up libprocps4:powerpc (2:3.3.10-4ubuntu1) ... Setting up procps (2:3.3.10-4ubuntu1) ... 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 (228-2ubuntu2) ... 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 (1.1.5) ... 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 libffi6:powerpc (3.2.1-4) ... Setting up libtasn1-6:powerpc (4.7-2) ... Setting up libgnutls-deb0-28:powerpc (3.3.18-1ubuntu1) ... Setting up libpng12-0:powerpc (1.2.54-1) ... Setting up libsqlite3-0:powerpc (3.9.2-1) ... Setting up libssl1.0.0:powerpc (1.0.2e-1ubuntu1) ... Setting up libkrb5support0:powerpc (1.13.2+dfsg-4) ... Setting up libk5crypto3:powerpc (1.13.2+dfsg-4) ... Setting up libkeyutils1:powerpc (1.5.9-8ubuntu1) ... Setting up libkrb5-3:powerpc (1.13.2+dfsg-4) ... Setting up libgssapi-krb5-2:powerpc (1.13.2+dfsg-4) ... Setting up libidn11:powerpc (1.32-3ubuntu1) ... Setting up libcurl3-gnutls:powerpc (7.45.0-1ubuntu1) ... Setting up apt-transport-https (1.1.5) ... Setting up libdbus-1-3:powerpc (1.10.6-1ubuntu1) ... Setting up openssl (1.0.2e-1ubuntu1) ... Setting up advancecomp (1.20-1) ... Setting up cpp (4:5.2.1-16ubuntu2) ... Setting up libdpkg-perl (1.18.3ubuntu1) ... Setting up dpkg-dev (1.18.3ubuntu1) ... 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 (125) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... Processing triggers for systemd (228-2ubuntu2) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-8441450', 'powerpc', 'xenial', '-c', 'chroot:autobuild', '--arch=powerpc', '--dist=xenial', '--purge=never', '--nolog', 'blasr_0~20150724+git3ca7fe8-1build2.dsc'] Initiating build PACKAGEBUILD-8441450 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.19.0-31-powerpc64-smp #36~14.04.1-Ubuntu SMP Thu Oct 8 10:49:59 UTC 2015 ppc sbuild (Debian sbuild) 0.65.2 (24 Mar 2015) on denneed01.buildd ╔══════════════════════════════════════════════════════════════════════════════╗ ║ blasr 0~20150724+git3ca7fe8-1build2 (powerpc) 15 Dec 2015 03:15 ║ ╚══════════════════════════════════════════════════════════════════════════════╝ Package: blasr Version: 0~20150724+git3ca7fe8-1build2 Source Version: 0~20150724+git3ca7fe8-1build2 Distribution: xenial Machine Architecture: powerpc Host Architecture: powerpc Build Architecture: powerpc I: NOTICE: Log filtering will replace 'build/blasr-FCiw0Q/blasr-0~20150724+git3ca7fe8' with '«PKGBUILDDIR»' I: NOTICE: Log filtering will replace 'build/blasr-FCiw0Q' with '«BUILDDIR»' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-8441450/chroot-autobuild' with '«CHROOT»' ┌──────────────────────────────────────────────────────────────────────────────┐ │ Fetch source files │ └──────────────────────────────────────────────────────────────────────────────┘ Local sources ───────────── blasr_0~20150724+git3ca7fe8-1build2.dsc exists in .; copying to chroot Check architectures ─────────────────── sh: 1: gcc: not found sbuild: warning: couldn't determine gcc system type, falling back to default (native compilation) 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-l_qiHy/apt_archive/sbuild-build-depends-core-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Packages [530 B] Ign:4 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Sources Ign:5 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Packages Get:4 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Sources [208 B] Get:5 file:/«BUILDDIR»/resolver-l_qiHy/apt_archive ./ Packages [530 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-l_qiHy/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-l_qiHy/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 ... 11529 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 (>= 9), python, libhdf5-dev, zlib1g-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 (>= 9), python, libhdf5-dev, zlib1g-dev dpkg-deb: building package 'sbuild-build-depends-blasr-dummy' in '/«BUILDDIR»/resolver-6EsvVX/apt_archive/sbuild-build-depends-blasr-dummy.deb'. Get:1 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ InRelease Ign:1 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ InRelease Get:2 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Release [2119 B] Get:2 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Release [2119 B] Get:3 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Release.gpg Ign:3 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Release.gpg Get:4 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Sources [437 B] Ign:4 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Sources Get:5 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Packages [701 B] Get:4 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Sources [437 B] Ign:5 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Packages Get:5 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Packages [701 B] Reading package lists... W: The repository 'file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ Release' is not signed. Reading package lists... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Install blasr 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: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base hdf5-helpers intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libexpat1 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu55 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libtimedate-perl libunistring0 libxml2 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal zlib1g-dev Suggested packages: wamerican | wordlist whois vacation dh-make gettext-doc groff libhdf5-doc less www-browser libmail-box-perl python-doc python-tk python2.7-doc binfmt-support Recommended packages: curl | wget | lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xdg-user-dirs xml-core libmail-sendmail-perl The following NEW packages will be installed: bsdmainutils debhelper dh-strip-nondeterminism file gettext gettext-base groff-base hdf5-helpers intltool-debian libarchive-zip-perl libasprintf0v5 libcroco3 libexpat1 libfile-stripnondeterminism-perl libgfortran3 libglib2.0-0 libhdf5-10 libhdf5-cpp-11 libhdf5-dev libicu55 libjpeg-dev libjpeg-turbo8 libjpeg-turbo8-dev libjpeg8 libjpeg8-dev libmagic1 libpipeline1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libtimedate-perl libunistring0 libxml2 man-db mime-support po-debconf python python-minimal python2.7 python2.7-minimal sbuild-build-depends-blasr-dummy zlib1g-dev 0 upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 24.2 MB/24.2 MB of archives. After this operation, 107 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! sbuild-build-depends-blasr-dummy Authentication warning overridden. Get:1 file:/«BUILDDIR»/resolver-6EsvVX/apt_archive ./ sbuild-build-depends-blasr-dummy 0.invalid.0 [946 B] Get:2 http://ftpmaster.internal/ubuntu xenial/main powerpc libasprintf0v5 powerpc 0.19.4-1ubuntu3 [6864 B] Get:3 http://ftpmaster.internal/ubuntu xenial/main powerpc groff-base powerpc 1.22.3-4 [1205 kB] Get:4 http://ftpmaster.internal/ubuntu xenial/main powerpc bsdmainutils powerpc 9.0.6ubuntu1 [172 kB] Get:5 http://ftpmaster.internal/ubuntu xenial/main powerpc libpipeline1 powerpc 1.4.1-1 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu xenial/main powerpc man-db powerpc 2.7.5-1 [835 kB] Get:7 http://ftpmaster.internal/ubuntu xenial/main powerpc libjpeg-turbo8 powerpc 1.3.0-0ubuntu2 [85.3 kB] Get:8 http://ftpmaster.internal/ubuntu xenial/main powerpc libunistring0 powerpc 0.9.3-5.2ubuntu1 [254 kB] Get:9 http://ftpmaster.internal/ubuntu xenial/main powerpc libpython2.7-minimal powerpc 2.7.11-2 [333 kB] Get:10 http://ftpmaster.internal/ubuntu xenial/main powerpc python2.7-minimal powerpc 2.7.11-2 [1244 kB] Get:11 http://ftpmaster.internal/ubuntu xenial/main powerpc python-minimal powerpc 2.7.11-1 [28.1 kB] Get:12 http://ftpmaster.internal/ubuntu xenial/main powerpc mime-support all 3.59ubuntu1 [31.0 kB] Get:13 http://ftpmaster.internal/ubuntu xenial/main powerpc libexpat1 powerpc 2.1.0-7 [63.8 kB] Get:14 http://ftpmaster.internal/ubuntu xenial/main powerpc libpython2.7-stdlib powerpc 2.7.11-2 [1862 kB] Get:15 http://ftpmaster.internal/ubuntu xenial/main powerpc python2.7 powerpc 2.7.11-2 [216 kB] Get:16 http://ftpmaster.internal/ubuntu xenial/main powerpc libpython-stdlib powerpc 2.7.11-1 [7666 B] Get:17 http://ftpmaster.internal/ubuntu xenial/main powerpc python powerpc 2.7.11-1 [137 kB] Get:18 http://ftpmaster.internal/ubuntu xenial/main powerpc libmagic1 powerpc 1:5.25-2ubuntu1 [214 kB] Get:19 http://ftpmaster.internal/ubuntu xenial/main powerpc file powerpc 1:5.25-2ubuntu1 [21.1 kB] Get:20 http://ftpmaster.internal/ubuntu xenial/main powerpc gettext-base powerpc 0.19.4-1ubuntu3 [45.3 kB] Get:21 http://ftpmaster.internal/ubuntu xenial/main powerpc libglib2.0-0 powerpc 2.47.3-3 [962 kB] Get:22 http://ftpmaster.internal/ubuntu xenial/main powerpc libicu55 powerpc 55.1-6ubuntu1 [7464 kB] Get:23 http://ftpmaster.internal/ubuntu xenial/main powerpc libxml2 powerpc 2.9.2+zdfsg1-4ubuntu2 [573 kB] Get:24 http://ftpmaster.internal/ubuntu xenial/main powerpc libcroco3 powerpc 0.6.9-1 [69.9 kB] Get:25 http://ftpmaster.internal/ubuntu xenial/main powerpc gettext powerpc 0.19.4-1ubuntu3 [798 kB] Get:26 http://ftpmaster.internal/ubuntu xenial/main powerpc intltool-debian all 0.35.0+20060710.4 [24.9 kB] Get:27 http://ftpmaster.internal/ubuntu xenial/main powerpc po-debconf all 1.0.18 [234 kB] Get:28 http://ftpmaster.internal/ubuntu xenial/main powerpc libarchive-zip-perl all 1.53-1 [87.0 kB] Get:29 http://ftpmaster.internal/ubuntu xenial/main powerpc libfile-stripnondeterminism-perl all 0.014-1 [10.1 kB] Get:30 http://ftpmaster.internal/ubuntu xenial/main powerpc libtimedate-perl all 2.3000-2 [37.5 kB] Get:31 http://ftpmaster.internal/ubuntu xenial/main powerpc dh-strip-nondeterminism all 0.014-1 [5596 B] Get:32 http://ftpmaster.internal/ubuntu xenial/main powerpc debhelper all 9.20151126ubuntu1 [741 kB] Get:33 http://ftpmaster.internal/ubuntu xenial-proposed/universe powerpc hdf5-helpers powerpc 1.8.16+docs-1 [12.6 kB] Get:34 http://ftpmaster.internal/ubuntu xenial/main powerpc libgfortran3 powerpc 5.3.1-3ubuntu1 [188 kB] Get:35 http://ftpmaster.internal/ubuntu xenial-proposed/universe powerpc libhdf5-10 powerpc 1.8.16+docs-1 [792 kB] Get:36 http://ftpmaster.internal/ubuntu xenial-proposed/universe powerpc libhdf5-cpp-11 powerpc 1.8.16+docs-1 [97.3 kB] Get:37 http://ftpmaster.internal/ubuntu xenial/main powerpc zlib1g-dev powerpc 1:1.2.8.dfsg-2ubuntu4 [163 kB] Get:38 http://ftpmaster.internal/ubuntu xenial/main powerpc libjpeg-turbo8-dev powerpc 1.3.0-0ubuntu2 [215 kB] Get:39 http://ftpmaster.internal/ubuntu xenial/main powerpc libjpeg8 powerpc 8c-2ubuntu8 [2200 B] Get:40 http://ftpmaster.internal/ubuntu xenial/main powerpc libjpeg8-dev powerpc 8c-2ubuntu8 [1550 B] Get:41 http://ftpmaster.internal/ubuntu xenial/main powerpc libjpeg-dev powerpc 8c-2ubuntu8 [1550 B] Get:42 http://ftpmaster.internal/ubuntu xenial-proposed/universe powerpc libhdf5-dev powerpc 1.8.16+docs-1 [4949 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 24.2 MB in 11s (2124 kB/s) Selecting previously unselected package libasprintf0v5:powerpc. (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 ... 11529 files and directories currently installed.) Preparing to unpack .../libasprintf0v5_0.19.4-1ubuntu3_powerpc.deb ... Unpacking libasprintf0v5:powerpc (0.19.4-1ubuntu3) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.3-4_powerpc.deb ... Unpacking groff-base (1.22.3-4) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../bsdmainutils_9.0.6ubuntu1_powerpc.deb ... Unpacking bsdmainutils (9.0.6ubuntu1) ... Selecting previously unselected package libpipeline1:powerpc. Preparing to unpack .../libpipeline1_1.4.1-1_powerpc.deb ... Unpacking libpipeline1:powerpc (1.4.1-1) ... Selecting previously unselected package man-db. Preparing to unpack .../man-db_2.7.5-1_powerpc.deb ... Unpacking man-db (2.7.5-1) ... Selecting previously unselected package libjpeg-turbo8:powerpc. Preparing to unpack .../libjpeg-turbo8_1.3.0-0ubuntu2_powerpc.deb ... Unpacking libjpeg-turbo8:powerpc (1.3.0-0ubuntu2) ... Selecting previously unselected package libunistring0:powerpc. Preparing to unpack .../libunistring0_0.9.3-5.2ubuntu1_powerpc.deb ... Unpacking libunistring0:powerpc (0.9.3-5.2ubuntu1) ... Selecting previously unselected package libpython2.7-minimal:powerpc. Preparing to unpack .../libpython2.7-minimal_2.7.11-2_powerpc.deb ... Unpacking libpython2.7-minimal:powerpc (2.7.11-2) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../python2.7-minimal_2.7.11-2_powerpc.deb ... Unpacking python2.7-minimal (2.7.11-2) ... Selecting previously unselected package python-minimal. Preparing to unpack .../python-minimal_2.7.11-1_powerpc.deb ... Unpacking python-minimal (2.7.11-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../mime-support_3.59ubuntu1_all.deb ... Unpacking mime-support (3.59ubuntu1) ... Selecting previously unselected package libexpat1:powerpc. Preparing to unpack .../libexpat1_2.1.0-7_powerpc.deb ... Unpacking libexpat1:powerpc (2.1.0-7) ... Selecting previously unselected package libpython2.7-stdlib:powerpc. Preparing to unpack .../libpython2.7-stdlib_2.7.11-2_powerpc.deb ... Unpacking libpython2.7-stdlib:powerpc (2.7.11-2) ... Selecting previously unselected package python2.7. Preparing to unpack .../python2.7_2.7.11-2_powerpc.deb ... Unpacking python2.7 (2.7.11-2) ... Selecting previously unselected package libpython-stdlib:powerpc. Preparing to unpack .../libpython-stdlib_2.7.11-1_powerpc.deb ... Unpacking libpython-stdlib:powerpc (2.7.11-1) ... Setting up libpython2.7-minimal:powerpc (2.7.11-2) ... Setting up python2.7-minimal (2.7.11-2) ... Setting up python-minimal (2.7.11-1) ... Selecting previously unselected package python. (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 ... 12817 files and directories currently installed.) Preparing to unpack .../python_2.7.11-1_powerpc.deb ... Unpacking python (2.7.11-1) ... Selecting previously unselected package libmagic1:powerpc. Preparing to unpack .../libmagic1_1%3a5.25-2ubuntu1_powerpc.deb ... Unpacking libmagic1:powerpc (1:5.25-2ubuntu1) ... Selecting previously unselected package file. Preparing to unpack .../file_1%3a5.25-2ubuntu1_powerpc.deb ... Unpacking file (1:5.25-2ubuntu1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../gettext-base_0.19.4-1ubuntu3_powerpc.deb ... Unpacking gettext-base (0.19.4-1ubuntu3) ... Selecting previously unselected package libglib2.0-0:powerpc. Preparing to unpack .../libglib2.0-0_2.47.3-3_powerpc.deb ... Unpacking libglib2.0-0:powerpc (2.47.3-3) ... Selecting previously unselected package libicu55:powerpc. Preparing to unpack .../libicu55_55.1-6ubuntu1_powerpc.deb ... Unpacking libicu55:powerpc (55.1-6ubuntu1) ... Selecting previously unselected package libxml2:powerpc. Preparing to unpack .../libxml2_2.9.2+zdfsg1-4ubuntu2_powerpc.deb ... Unpacking libxml2:powerpc (2.9.2+zdfsg1-4ubuntu2) ... Selecting previously unselected package libcroco3:powerpc. Preparing to unpack .../libcroco3_0.6.9-1_powerpc.deb ... Unpacking libcroco3:powerpc (0.6.9-1) ... Selecting previously unselected package gettext. Preparing to unpack .../gettext_0.19.4-1ubuntu3_powerpc.deb ... Unpacking gettext (0.19.4-1ubuntu3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../intltool-debian_0.35.0+20060710.4_all.deb ... Unpacking intltool-debian (0.35.0+20060710.4) ... Selecting previously unselected package po-debconf. Preparing to unpack .../po-debconf_1.0.18_all.deb ... Unpacking po-debconf (1.0.18) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../libarchive-zip-perl_1.53-1_all.deb ... Unpacking libarchive-zip-perl (1.53-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. 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Selecting previously unselected package libhdf5-10:powerpc. Preparing to unpack .../libhdf5-10_1.8.16+docs-1_powerpc.deb ... Unpacking libhdf5-10:powerpc (1.8.16+docs-1) ... Selecting previously unselected package libhdf5-cpp-11:powerpc. Preparing to unpack .../libhdf5-cpp-11_1.8.16+docs-1_powerpc.deb ... Unpacking libhdf5-cpp-11:powerpc (1.8.16+docs-1) ... Selecting previously unselected package zlib1g-dev:powerpc. Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-2ubuntu4_powerpc.deb ... Unpacking zlib1g-dev:powerpc (1:1.2.8.dfsg-2ubuntu4) ... Selecting previously unselected package libjpeg-turbo8-dev:powerpc. Preparing to unpack .../libjpeg-turbo8-dev_1.3.0-0ubuntu2_powerpc.deb ... Unpacking libjpeg-turbo8-dev:powerpc (1.3.0-0ubuntu2) ... Selecting previously unselected package libjpeg8:powerpc. Preparing to unpack .../libjpeg8_8c-2ubuntu8_powerpc.deb ... Unpacking libjpeg8:powerpc (8c-2ubuntu8) ... Selecting previously unselected package libjpeg8-dev:powerpc. 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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:powerpc (1.4.1-1) ... Setting up man-db (2.7.5-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libjpeg-turbo8:powerpc (1.3.0-0ubuntu2) ... Setting up libunistring0:powerpc (0.9.3-5.2ubuntu1) ... Setting up mime-support (3.59ubuntu1) ... Setting up libexpat1:powerpc (2.1.0-7) ... Setting up libpython2.7-stdlib:powerpc (2.7.11-2) ... Setting up python2.7 (2.7.11-2) ... Setting up libpython-stdlib:powerpc (2.7.11-1) ... Setting up python (2.7.11-1) ... Setting up libmagic1:powerpc (1:5.25-2ubuntu1) ... Setting up file (1:5.25-2ubuntu1) ... Setting up gettext-base (0.19.4-1ubuntu3) ... Setting up libglib2.0-0:powerpc (2.47.3-3) ... No schema files found: doing nothing. Setting up libicu55:powerpc (55.1-6ubuntu1) ... Setting up libxml2:powerpc (2.9.2+zdfsg1-4ubuntu2) ... Setting up libcroco3:powerpc (0.6.9-1) ... Setting up gettext (0.19.4-1ubuntu3) ... Setting up intltool-debian (0.35.0+20060710.4) ... Setting up po-debconf (1.0.18) ... Setting up libarchive-zip-perl (1.53-1) ... Setting up libfile-stripnondeterminism-perl (0.014-1) ... Setting up libtimedate-perl (2.3000-2) ... Setting up hdf5-helpers (1.8.16+docs-1) ... Setting up libgfortran3:powerpc (5.3.1-3ubuntu1) ... Setting up libhdf5-10:powerpc (1.8.16+docs-1) ... Setting up libhdf5-cpp-11:powerpc (1.8.16+docs-1) ... Setting up zlib1g-dev:powerpc (1:1.2.8.dfsg-2ubuntu4) ... Setting up libjpeg-turbo8-dev:powerpc (1.3.0-0ubuntu2) ... Setting up libjpeg8:powerpc (8c-2ubuntu8) ... Setting up libjpeg8-dev:powerpc (8c-2ubuntu8) ... Setting up libjpeg-dev:powerpc (8c-2ubuntu8) ... Setting up libhdf5-dev (1.8.16+docs-1) ... update-alternatives: using /usr/lib/powerpc-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/powerpc-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up debhelper (9.20151126ubuntu1) ... Setting up sbuild-build-depends-blasr-dummy (0.invalid.0) ... Setting up dh-strip-nondeterminism (0.014-1) ... Processing triggers for libc-bin (2.21-0ubuntu5) ... ┌──────────────────────────────────────────────────────────────────────────────┐ │ Build environment │ └──────────────────────────────────────────────────────────────────────────────┘ Kernel: Linux 3.19.0-31-powerpc64-smp powerpc (ppc) Toolchain package versions: binutils_2.25.90.20151211-0ubuntu2 dpkg-dev_1.18.3ubuntu1 g++-5_5.3.1-3ubuntu1 gcc-5_5.3.1-3ubuntu1 libc6-dev_2.21-0ubuntu5 libstdc++-5-dev_5.3.1-3ubuntu1 libstdc++6_5.3.1-3ubuntu1 linux-libc-dev_4.3.0-4.13 Package versions: adduser_3.113+nmu3ubuntu4 advancecomp_1.20-1 apt_1.1.5 apt-transport-https_1.1.5 base-files_9.4ubuntu3 base-passwd_3.5.38 bash_4.3-14ubuntu1 binutils_2.25.90.20151211-0ubuntu2 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_5.3.1-3ubuntu1 dash_0.5.7-4ubuntu2 debconf_1.5.58ubuntu1 debhelper_9.20151126ubuntu1 debianutils_4.5.1 dh-strip-nondeterminism_0.014-1 diffutils_1:3.3-2 dmsetup_2:1.02.110-1ubuntu1 dpkg_1.18.3ubuntu1 dpkg-dev_1.18.3ubuntu1 e2fslibs_1.42.13-1ubuntu1 e2fsprogs_1.42.13-1ubuntu1 fakeroot_1.20.2-1ubuntu1 file_1:5.25-2ubuntu1 findutils_4.4.2-10 g++_4:5.2.1-16ubuntu2 g++-5_5.3.1-3ubuntu1 gcc_4:5.2.1-16ubuntu2 gcc-5_5.3.1-3ubuntu1 gcc-5-base_5.3.1-3ubuntu1 gettext_0.19.4-1ubuntu3 gettext-base_0.19.4-1ubuntu3 gnupg_1.4.19-6ubuntu1 gpgv_1.4.19-6ubuntu1 grep_2.21-2 groff-base_1.22.3-4 gzip_1.6-4ubuntu1 hdf5-helpers_1.8.16+docs-1 hostname_3.16ubuntu2 init_1.24ubuntu2 initscripts_2.88dsf-59.2ubuntu3 insserv_1.14.0-5ubuntu3 intltool-debian_0.35.0+20060710.4 libacl1_2.2.52-2 libapparmor1_2.10-0ubuntu8 libapt-pkg4.16_1.0.10.2ubuntu1 libapt-pkg5.0_1.1.5 libarchive-zip-perl_1.53-1 libasan2_5.3.1-3ubuntu1 libasn1-8-heimdal_1.6~rc2+dfsg-10ubuntu1 libasprintf0v5_0.19.4-1ubuntu3 libatomic1_5.3.1-3ubuntu1 libattr1_1:2.4.47-2 libaudit-common_1:2.4.4-4ubuntu1 libaudit1_1:2.4.4-4ubuntu1 libblkid1_2.27.1-1ubuntu3 libbz2-1.0_1.0.6-8 libc-bin_2.21-0ubuntu5 libc-dev-bin_2.21-0ubuntu5 libc6_2.21-0ubuntu5 libc6-dev_2.21-0ubuntu5 libcap2_1:2.24-12 libcap2-bin_1:2.24-12 libcc1-0_5.3.1-3ubuntu1 libcomerr2_1.42.13-1ubuntu1 libcroco3_0.6.9-1 libcryptsetup4_2:1.6.6-5ubuntu2 libcurl3-gnutls_7.45.0-1ubuntu1 libdb5.3_5.3.28-11 libdbus-1-3_1.10.6-1ubuntu1 libdebconfclient0_0.198ubuntu1 libdevmapper1.02.1_2:1.02.110-1ubuntu1 libdpkg-perl_1.18.3ubuntu1 libexpat1_2.1.0-7 libfakeroot_1.20.2-1ubuntu1 libfdisk1_2.27.1-1ubuntu3 libffi6_3.2.1-4 libfile-stripnondeterminism-perl_0.014-1 libgcc-5-dev_5.3.1-3ubuntu1 libgcc1_1:5.3.1-3ubuntu1 libgcrypt20_1.6.4-3 libgdbm3_1.8.3-13.1 libgfortran3_5.3.1-3ubuntu1 libglib2.0-0_2.47.3-3 libgmp10_2:6.1.0+dfsg-2 libgnutls-deb0-28_3.3.18-1ubuntu1 libgomp1_5.3.1-3ubuntu1 libgpg-error0_1.20-1 libgssapi-krb5-2_1.13.2+dfsg-4 libgssapi3-heimdal_1.6~rc2+dfsg-10ubuntu1 libhcrypto4-heimdal_1.6~rc2+dfsg-10ubuntu1 libhdf5-10_1.8.16+docs-1 libhdf5-cpp-11_1.8.16+docs-1 libhdf5-dev_1.8.16+docs-1 libheimbase1-heimdal_1.6~rc2+dfsg-10ubuntu1 libheimntlm0-heimdal_1.6~rc2+dfsg-10ubuntu1 libhogweed4_3.1.1-4 libhx509-5-heimdal_1.6~rc2+dfsg-10ubuntu1 libicu55_55.1-6ubuntu1 libidn11_1.32-3ubuntu1 libisl13_0.14-2 libisl15_0.15-3 libjpeg-dev_8c-2ubuntu8 libjpeg-turbo8_1.3.0-0ubuntu2 libjpeg-turbo8-dev_1.3.0-0ubuntu2 libjpeg8_8c-2ubuntu8 libjpeg8-dev_8c-2ubuntu8 libk5crypto3_1.13.2+dfsg-4 libkeyutils1_1.5.9-8ubuntu1 libkmod2_21-1ubuntu1 libkrb5-26-heimdal_1.6~rc2+dfsg-10ubuntu1 libkrb5-3_1.13.2+dfsg-4 libkrb5support0_1.13.2+dfsg-4 libldap-2.4-2_2.4.41+dfsg-1ubuntu2 liblockfile-bin_1.09-6ubuntu1 liblockfile1_1.09-6ubuntu1 liblzma5_5.1.1alpha+20120614-2ubuntu2 libmagic1_1:5.25-2ubuntu1 libmount1_2.27.1-1ubuntu3 libmpc3_1.0.3-1 libmpfr4_3.1.3-1 libncurses5_6.0+20151024-2ubuntu1 libncursesw5_6.0+20151024-2ubuntu1 libnettle6_3.1.1-4 libnih-dbus1_1.0.3-4ubuntu27 libnih1_1.0.3-4ubuntu27 libp11-kit0_0.23.1-3 libpam-modules_1.1.8-3.1ubuntu3 libpam-modules-bin_1.1.8-3.1ubuntu3 libpam-runtime_1.1.8-3.1ubuntu3 libpam0g_1.1.8-3.1ubuntu3 libpcre3_2:8.35-7.1ubuntu1 libpipeline1_1.4.1-1 libpng12-0_1.2.54-1 libprocps3_1:3.3.9-1ubuntu8 libprocps4_2:3.3.10-4ubuntu1 libpython-stdlib_2.7.11-1 libpython2.7-minimal_2.7.11-2 libpython2.7-stdlib_2.7.11-2 libreadline6_6.3-8ubuntu1 libroken18-heimdal_1.6~rc2+dfsg-10ubuntu1 librtmp1_2.4+20150115.gita107cef-1build1 libsasl2-2_2.1.26.dfsg1-14 libsasl2-modules-db_2.1.26.dfsg1-14 libseccomp2_2.2.3-2ubuntu2 libselinux1_2.4-3 libsemanage-common_2.4-3 libsemanage1_2.4-3 libsepol1_2.4-2 libslang2_2.3.0-2ubuntu1 libsmartcols1_2.27.1-1ubuntu3 libsqlite3-0_3.9.2-1 libss2_1.42.13-1ubuntu1 libssl1.0.0_1.0.2e-1ubuntu1 libstdc++-5-dev_5.3.1-3ubuntu1 libstdc++6_5.3.1-3ubuntu1 libsystemd0_228-2ubuntu2 libtasn1-6_4.7-2 libtimedate-perl_2.3000-2 libtinfo5_6.0+20151024-2ubuntu1 libubsan0_5.3.1-3ubuntu1 libudev1_228-2ubuntu2 libunistring0_0.9.3-5.2ubuntu1 libusb-0.1-4_2:0.1.12-27 libustr-1.0-1_1.0.4-5 libuuid1_2.27.1-1ubuntu3 libwind0-heimdal_1.6~rc2+dfsg-10ubuntu1 libxml2_2.9.2+zdfsg1-4ubuntu2 linux-libc-dev_4.3.0-4.13 lockfile-progs_0.1.17 login_1:4.1.5.1-1.1ubuntu7 lsb-base_9.20150917ubuntu1 make_4.0-8.2 man-db_2.7.5-1 mawk_1.3.3-17ubuntu2 mime-support_3.59ubuntu1 mount_2.27.1-1ubuntu3 multiarch-support_2.21-0ubuntu5 ncurses-base_6.0+20151024-2ubuntu1 ncurses-bin_6.0+20151024-2ubuntu1 openssl_1.0.2e-1ubuntu1 optipng_0.7.5-1 passwd_1:4.1.5.1-1.1ubuntu7 patch_2.7.5-1 perl_5.20.2-6 perl-base_5.20.2-6 perl-modules_5.20.2-6 pkg-create-dbgsym_0.70 pkgbinarymangler_125 po-debconf_1.0.18 policyrcd-script-zg2_0.1-2 procps_2:3.3.10-4ubuntu1 python_2.7.11-1 python-minimal_2.7.11-1 python2.7_2.7.11-2 python2.7-minimal_2.7.11-2 readline-common_6.3-8ubuntu1 sbuild-build-depends-blasr-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.2-6.1 sensible-utils_0.0.9 systemd_228-2ubuntu2 systemd-sysv_228-2ubuntu2 sysv-rc_2.88dsf-59.2ubuntu3 sysvinit-utils_2.88dsf-59.2ubuntu3 tar_1.28-2.1 tzdata_2015g-1 ubuntu-keyring_2012.05.19 udev_228-2ubuntu2 util-linux_2.27.1-1ubuntu3 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 Tue Dec 15 08:12:43 2015 UTC using RSA key ID CD2CA5F9 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./blasr_0~20150724+git3ca7fe8-1build2.dsc dpkg-source: info: extracting blasr in blasr-0~20150724+git3ca7fe8 dpkg-source: info: unpacking blasr_0~20150724+git3ca7fe8.orig.tar.xz dpkg-source: info: unpacking blasr_0~20150724+git3ca7fe8-1build2.debian.tar.xz dpkg-source: info: applying selective-static-linking Check disc space ──────────────── Sufficient free space for build User Environment ──────────────── DEB_BUILD_OPTIONS=parallel=8 HOME=/home/buildd LANG=C 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=/«BUILDDIR»/blasr-0~20150724+git3ca7fe8 SHELL=/bin/sh SUDO_COMMAND=/usr/sbin/chroot /«CHROOT» su buildd -s /bin/sh -c cd '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' && 'env' SUDO_GID=2501 SUDO_UID=2001 SUDO_USER=buildd TERM=unknown USER=buildd USERNAME=root dpkg-buildpackage ───────────────── dpkg-buildpackage: source package blasr dpkg-buildpackage: source version 0~20150724+git3ca7fe8-1build2 dpkg-buildpackage: source distribution xenial dpkg-source --before-build blasr-0~20150724+git3ca7fe8 dpkg-buildpackage: host architecture powerpc fakeroot debian/rules clean dh clean dh_testdir debian/rules override_dh_auto_clean make[1]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' ./configure.py --no-pbbam --submodules writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/defines.mk' """ LIBBLASR_LIBFLAGS ?= -Wl,-Bstatic -lblasr SHELL ?= bash LIBPBIHDF_INCLUDE ?= ${ROOT}/libcpp/hdf DL_LIBFLAGS ?= -Wl,-Bdynamic -ldl LIBPBDATA_INCLUDE ?= ${ROOT}/libcpp/pbdata LIBPBIHDF_LIBFLAGS ?= -Wl,-Bstatic -lpbihdf LIBPBDATA_LIB ?= ${ROOT}/libcpp/pbdata LIBBLASR_INCLUDE ?= ${ROOT}/libcpp/alignment LIBBLASR_LIB ?= ${ROOT}/libcpp/alignment HDF5_LIB ?= /usr/lib/powerpc-linux-gnu/hdf5/serial HDF5_LIBFLAGS ?= -Wl,-Bdynamic -lhdf5_cpp -lhdf5 LIBPBDATA_LIBFLAGS ?= -Wl,-Bstatic -lpbdata ZLIB_LIBFLAGS ?= -Wl,-Bdynamic -lz HDF5_INCLUDE ?= /usr/include/hdf5/serial PTHREAD_LIBFLAGS ?= -Wl,-Bdynamic -lpthread LIBPBIHDF_LIB ?= ${ROOT}/libcpp/hdf LDFLAGS+=-static SUB_CONF_FLAGS+=--shared """ libcpp/configure.py writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk' """ HDF5_INCLUDE:=/usr/include/hdf5/serial HDF5_LIB:=/usr/lib/powerpc-linux-gnu/hdf5/serial #CPPFLAGS+=-I../pbdata -I../hdf -I../alignment LIBPBDATA_INCLUDE ?=../pbdata LIBPBIHDF_INCLUDE ?=../hdf LIBBLASR_INCLUDE ?=../alignment LIBPBDATA_LIB ?=../pbdata/libpbdata.so LIBPBIHDF_LIB ?=../hdf/libpbihdf.so LIBBLASR_LIB ?=../alignment/libblasr.so """ writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata/libconfig.h' """ """ NOT2 /usr/bin/make cleanall make[2]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' /usr/bin/make -C libcpp clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp' /usr/bin/make -C pbdata clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' /usr/bin/make -C hdf clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf' ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf' /usr/bin/make -C alignment clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment' ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment' #@/usr/bin/make -C unittest clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp' rm -f blasr Blasr.o Blasr.d blasr.d ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. /usr/bin/make -C utils clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils' ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils' /usr/bin/make -C extrautils clean ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/extrautils' ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/extrautils' make[2]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' # This is created by configure.py rm -f defines.mk # These are created by libcpp/configure.py rm -f libcpp/defines.mk libcpp/pbdata/libconfig.h make[1]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' dh_clean debian/rules build-arch dh build-arch dh_testdir -a debian/rules override_dh_auto_configure make[1]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' ./configure.py --no-pbbam --submodules writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/defines.mk' """ LIBBLASR_LIBFLAGS ?= -Wl,-Bstatic -lblasr SHELL ?= bash LIBPBIHDF_INCLUDE ?= ${ROOT}/libcpp/hdf DL_LIBFLAGS ?= -Wl,-Bdynamic -ldl LIBPBDATA_INCLUDE ?= ${ROOT}/libcpp/pbdata LIBPBIHDF_LIBFLAGS ?= -Wl,-Bstatic -lpbihdf LIBPBDATA_LIB ?= ${ROOT}/libcpp/pbdata LIBBLASR_INCLUDE ?= ${ROOT}/libcpp/alignment LIBBLASR_LIB ?= ${ROOT}/libcpp/alignment HDF5_LIB ?= /usr/lib/powerpc-linux-gnu/hdf5/serial HDF5_LIBFLAGS ?= -Wl,-Bdynamic -lhdf5_cpp -lhdf5 LIBPBDATA_LIBFLAGS ?= -Wl,-Bstatic -lpbdata ZLIB_LIBFLAGS ?= -Wl,-Bdynamic -lz HDF5_INCLUDE ?= /usr/include/hdf5/serial PTHREAD_LIBFLAGS ?= -Wl,-Bdynamic -lpthread LIBPBIHDF_LIB ?= ${ROOT}/libcpp/hdf LDFLAGS+=-static SUB_CONF_FLAGS+=--shared """ libcpp/configure.py writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk' """ HDF5_INCLUDE:=/usr/include/hdf5/serial HDF5_LIB:=/usr/lib/powerpc-linux-gnu/hdf5/serial #CPPFLAGS+=-I../pbdata -I../hdf -I../alignment LIBPBDATA_INCLUDE ?=../pbdata LIBPBIHDF_INCLUDE ?=../hdf LIBBLASR_INCLUDE ?=../alignment LIBPBDATA_LIB ?=../pbdata/libpbdata.so LIBPBIHDF_LIB ?=../hdf/libpbihdf.so LIBBLASR_LIB ?=../alignment/libblasr.so """ writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata/libconfig.h' """ """ NOT2 make[1]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' debian/rules override_dh_auto_build make[1]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' /usr/bin/make build-submodule make[2]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' # DON'T use pbbam which is not on github. cd libcpp && NOPBBAM=true HDF5_LIB=/usr/lib/powerpc-linux-gnu/hdf5/serial/libhdf5.so HDF5_INCLUDE=/usr/include/hdf5/serial ./configure.py writing to '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/defines.mk' """ HDF5_INCLUDE:=/usr/include/hdf5/serial HDF5_LIB:=/usr/lib/powerpc-linux-gnu/hdf5/serial/libhdf5.so #CPPFLAGS+=-I../pbdata -I../hdf -I../alignment LIBPBDATA_INCLUDE ?=../pbdata LIBPBIHDF_INCLUDE ?=../hdf LIBBLASR_INCLUDE ?=../alignment LIBPBDATA_LIB ?=../pbdata/libpbdata.so LIBPBIHDF_LIB ?=../hdf/libpbihdf.so LIBBLASR_LIB ?=../alignment/libblasr.so """ /usr/bin/make -C libcpp make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp' /usr/bin/make -C pbdata all make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"GFFFile.d" -MT"GFFFile.o GFFFile.d" -c GFFFile.cpp -o GFFFile.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"ChangeListID.d" -MT"ChangeListID.o ChangeListID.d" -c ChangeListID.cpp -o ChangeListID.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"StringUtils.d" -MT"StringUtils.o StringUtils.d" -c StringUtils.cpp -o StringUtils.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTASequence.d" -MT"FASTASequence.o FASTASequence.d" -c FASTASequence.cpp -o FASTASequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"MD5Utils.d" -MT"MD5Utils.o MD5Utils.d" -c MD5Utils.cpp -o MD5Utils.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTAReader.d" -MT"FASTAReader.o FASTAReader.d" -c FASTAReader.cpp -o FASTAReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"CommandLineParser.d" -MT"CommandLineParser.o CommandLineParser.d" -c CommandLineParser.cpp -o CommandLineParser.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"CCSSequence.d" -MT"CCSSequence.o CCSSequence.d" -c CCSSequence.cpp -o CCSSequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTQReader.d" -MT"FASTQReader.o FASTQReader.d" -c FASTQReader.cpp -o FASTQReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"ReverseCompressIndex.d" -MT"ReverseCompressIndex.o ReverseCompressIndex.d" -c ReverseCompressIndex.cpp -o ReverseCompressIndex.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"PackedDNASequence.d" -MT"PackedDNASequence.o PackedDNASequence.d" -c PackedDNASequence.cpp -o PackedDNASequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"SMRTSequence.d" -MT"SMRTSequence.o SMRTSequence.d" -c SMRTSequence.cpp -o SMRTSequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"NucConversion.d" -MT"NucConversion.o NucConversion.d" -c NucConversion.cpp -o NucConversion.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"DNASequence.d" -MT"DNASequence.o DNASequence.d" -c DNASequence.cpp -o DNASequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"FASTQSequence.d" -MT"FASTQSequence.o FASTQSequence.d" -c FASTQSequence.cpp -o FASTQSequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/RegionTable.d" -MT"reads/RegionTable.o reads/RegionTable.d" -c reads/RegionTable.cpp -o reads/RegionTable.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/ReadType.d" -MT"reads/ReadType.o reads/ReadType.d" -c reads/ReadType.cpp -o reads/ReadType.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/ScanData.d" -MT"reads/ScanData.o reads/ScanData.d" -c reads/ScanData.cpp -o reads/ScanData.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/BaseFile.d" -MT"reads/BaseFile.o reads/BaseFile.d" -c reads/BaseFile.cpp -o reads/BaseFile.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/ZMWGroupEntry.d" -MT"reads/ZMWGroupEntry.o reads/ZMWGroupEntry.d" -c reads/ZMWGroupEntry.cpp -o reads/ZMWGroupEntry.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/PulseBaseCommon.d" -MT"reads/PulseBaseCommon.o reads/PulseBaseCommon.d" -c reads/PulseBaseCommon.cpp -o reads/PulseBaseCommon.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/HoleXY.d" -MT"reads/HoleXY.o reads/HoleXY.d" -c reads/HoleXY.cpp -o reads/HoleXY.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"reads/PulseFile.d" -MT"reads/PulseFile.o reads/PulseFile.d" -c reads/PulseFile.cpp -o reads/PulseFile.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"metagenome/TitleTable.d" -MT"metagenome/TitleTable.o metagenome/TitleTable.d" -c metagenome/TitleTable.cpp -o metagenome/TitleTable.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"qvs/QualityTransform.d" -MT"qvs/QualityTransform.o qvs/QualityTransform.d" -c qvs/QualityTransform.cpp -o qvs/QualityTransform.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"qvs/QualityValue.d" -MT"qvs/QualityValue.o qvs/QualityValue.d" -c qvs/QualityValue.cpp -o qvs/QualityValue.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/AlnGroup.d" -MT"saf/AlnGroup.o saf/AlnGroup.d" -c saf/AlnGroup.cpp -o saf/AlnGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/RefInfo.d" -MT"saf/RefInfo.o saf/RefInfo.d" -c saf/RefInfo.cpp -o saf/RefInfo.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/RefGroup.d" -MT"saf/RefGroup.o saf/RefGroup.d" -c saf/RefGroup.cpp -o saf/RefGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"saf/MovieInfo.d" -MT"saf/MovieInfo.o saf/MovieInfo.d" -c saf/MovieInfo.cpp -o saf/MovieInfo.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"utils/BitUtils.d" -MT"utils/BitUtils.o utils/BitUtils.d" -c utils/BitUtils.cpp -o utils/BitUtils.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"utils/SMRTTitle.d" -MT"utils/SMRTTitle.o utils/SMRTTitle.d" -c utils/SMRTTitle.cpp -o utils/SMRTTitle.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"utils/SMRTReadUtils.d" -MT"utils/SMRTReadUtils.o utils/SMRTReadUtils.d" -c utils/SMRTReadUtils.cpp -o utils/SMRTReadUtils.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"loadpulses/MetricField.d" -MT"loadpulses/MetricField.o loadpulses/MetricField.d" -c loadpulses/MetricField.cpp -o loadpulses/MetricField.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"loadpulses/MovieAlnIndexLookupTable.d" -MT"loadpulses/MovieAlnIndexLookupTable.o loadpulses/MovieAlnIndexLookupTable.d" -c loadpulses/MovieAlnIndexLookupTable.cpp -o loadpulses/MovieAlnIndexLookupTable.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"alignment/CmpAlignment.d" -MT"alignment/CmpAlignment.o alignment/CmpAlignment.d" -c alignment/CmpAlignment.cpp -o alignment/CmpAlignment.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"amos/AfgBasWriter.d" -MT"amos/AfgBasWriter.o amos/AfgBasWriter.d" -c amos/AfgBasWriter.cpp -o amos/AfgBasWriter.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/ReferenceSequence.d" -MT"sam/ReferenceSequence.o sam/ReferenceSequence.d" -c sam/ReferenceSequence.cpp -o sam/ReferenceSequence.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/SAMAlignment.d" -MT"sam/SAMAlignment.o sam/SAMAlignment.d" -c sam/SAMAlignment.cpp -o sam/SAMAlignment.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/SAMHeader.d" -MT"sam/SAMHeader.o sam/SAMHeader.d" -c sam/SAMHeader.cpp -o sam/SAMHeader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/ReadGroup.d" -MT"sam/ReadGroup.o sam/ReadGroup.d" -c sam/ReadGroup.cpp -o sam/ReadGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -MF"sam/SAMKeywordValuePair.d" -MT"sam/SAMKeywordValuePair.o sam/SAMKeywordValuePair.d" -c sam/SAMKeywordValuePair.cpp -o sam/SAMKeywordValuePair.o ar rc libpbdata.a GFFFile.o ChangeListID.o StringUtils.o FASTASequence.o MD5Utils.o FASTAReader.o CommandLineParser.o CCSSequence.o FASTQReader.o ReverseCompressIndex.o PackedDNASequence.o SMRTSequence.o NucConversion.o DNASequence.o FASTQSequence.o reads/RegionTable.o reads/ReadType.o reads/ScanData.o reads/BaseFile.o reads/ZMWGroupEntry.o reads/PulseBaseCommon.o reads/HoleXY.o reads/PulseFile.o metagenome/TitleTable.o qvs/QualityTransform.o qvs/QualityValue.o saf/AlnGroup.o saf/RefInfo.o saf/RefGroup.o saf/MovieInfo.o utils/BitUtils.o utils/SMRTTitle.o utils/SMRTReadUtils.o loadpulses/MetricField.o loadpulses/MovieAlnIndexLookupTable.o alignment/CmpAlignment.o amos/AfgBasWriter.o sam/ReferenceSequence.o sam/SAMAlignment.o sam/SAMHeader.o sam/ReadGroup.o sam/SAMKeywordValuePair.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"GFFFile.shared.d" -MT"GFFFile.shared.o GFFFile.shared.d" -c GFFFile.cpp -o GFFFile.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"ChangeListID.shared.d" -MT"ChangeListID.shared.o ChangeListID.shared.d" -c ChangeListID.cpp -o ChangeListID.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"StringUtils.shared.d" -MT"StringUtils.shared.o StringUtils.shared.d" -c StringUtils.cpp -o StringUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTASequence.shared.d" -MT"FASTASequence.shared.o FASTASequence.shared.d" -c FASTASequence.cpp -o FASTASequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"MD5Utils.shared.d" -MT"MD5Utils.shared.o MD5Utils.shared.d" -c MD5Utils.cpp -o MD5Utils.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTAReader.shared.d" -MT"FASTAReader.shared.o FASTAReader.shared.d" -c FASTAReader.cpp -o FASTAReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"CommandLineParser.shared.d" -MT"CommandLineParser.shared.o CommandLineParser.shared.d" -c CommandLineParser.cpp -o CommandLineParser.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"CCSSequence.shared.d" -MT"CCSSequence.shared.o CCSSequence.shared.d" -c CCSSequence.cpp -o CCSSequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTQReader.shared.d" -MT"FASTQReader.shared.o FASTQReader.shared.d" -c FASTQReader.cpp -o FASTQReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"ReverseCompressIndex.shared.d" -MT"ReverseCompressIndex.shared.o ReverseCompressIndex.shared.d" -c ReverseCompressIndex.cpp -o ReverseCompressIndex.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"PackedDNASequence.shared.d" -MT"PackedDNASequence.shared.o PackedDNASequence.shared.d" -c PackedDNASequence.cpp -o PackedDNASequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"SMRTSequence.shared.d" -MT"SMRTSequence.shared.o SMRTSequence.shared.d" -c SMRTSequence.cpp -o SMRTSequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"NucConversion.shared.d" -MT"NucConversion.shared.o NucConversion.shared.d" -c NucConversion.cpp -o NucConversion.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"DNASequence.shared.d" -MT"DNASequence.shared.o DNASequence.shared.d" -c DNASequence.cpp -o DNASequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"FASTQSequence.shared.d" -MT"FASTQSequence.shared.o FASTQSequence.shared.d" -c FASTQSequence.cpp -o FASTQSequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/RegionTable.shared.d" -MT"reads/RegionTable.shared.o reads/RegionTable.shared.d" -c reads/RegionTable.cpp -o reads/RegionTable.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/ReadType.shared.d" -MT"reads/ReadType.shared.o reads/ReadType.shared.d" -c reads/ReadType.cpp -o reads/ReadType.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/ScanData.shared.d" -MT"reads/ScanData.shared.o reads/ScanData.shared.d" -c reads/ScanData.cpp -o reads/ScanData.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/BaseFile.shared.d" -MT"reads/BaseFile.shared.o reads/BaseFile.shared.d" -c reads/BaseFile.cpp -o reads/BaseFile.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/ZMWGroupEntry.shared.d" -MT"reads/ZMWGroupEntry.shared.o reads/ZMWGroupEntry.shared.d" -c reads/ZMWGroupEntry.cpp -o reads/ZMWGroupEntry.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/PulseBaseCommon.shared.d" -MT"reads/PulseBaseCommon.shared.o reads/PulseBaseCommon.shared.d" -c reads/PulseBaseCommon.cpp -o reads/PulseBaseCommon.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/HoleXY.shared.d" -MT"reads/HoleXY.shared.o reads/HoleXY.shared.d" -c reads/HoleXY.cpp -o reads/HoleXY.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"reads/PulseFile.shared.d" -MT"reads/PulseFile.shared.o reads/PulseFile.shared.d" -c reads/PulseFile.cpp -o reads/PulseFile.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"metagenome/TitleTable.shared.d" -MT"metagenome/TitleTable.shared.o metagenome/TitleTable.shared.d" -c metagenome/TitleTable.cpp -o metagenome/TitleTable.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"qvs/QualityTransform.shared.d" -MT"qvs/QualityTransform.shared.o qvs/QualityTransform.shared.d" -c qvs/QualityTransform.cpp -o qvs/QualityTransform.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"qvs/QualityValue.shared.d" -MT"qvs/QualityValue.shared.o qvs/QualityValue.shared.d" -c qvs/QualityValue.cpp -o qvs/QualityValue.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/AlnGroup.shared.d" -MT"saf/AlnGroup.shared.o saf/AlnGroup.shared.d" -c saf/AlnGroup.cpp -o saf/AlnGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/RefInfo.shared.d" -MT"saf/RefInfo.shared.o saf/RefInfo.shared.d" -c saf/RefInfo.cpp -o saf/RefInfo.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/RefGroup.shared.d" -MT"saf/RefGroup.shared.o saf/RefGroup.shared.d" -c saf/RefGroup.cpp -o saf/RefGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"saf/MovieInfo.shared.d" -MT"saf/MovieInfo.shared.o saf/MovieInfo.shared.d" -c saf/MovieInfo.cpp -o saf/MovieInfo.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"utils/BitUtils.shared.d" -MT"utils/BitUtils.shared.o utils/BitUtils.shared.d" -c utils/BitUtils.cpp -o utils/BitUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"utils/SMRTTitle.shared.d" -MT"utils/SMRTTitle.shared.o utils/SMRTTitle.shared.d" -c utils/SMRTTitle.cpp -o utils/SMRTTitle.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"utils/SMRTReadUtils.shared.d" -MT"utils/SMRTReadUtils.shared.o utils/SMRTReadUtils.shared.d" -c utils/SMRTReadUtils.cpp -o utils/SMRTReadUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"loadpulses/MetricField.shared.d" -MT"loadpulses/MetricField.shared.o loadpulses/MetricField.shared.d" -c loadpulses/MetricField.cpp -o loadpulses/MetricField.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"loadpulses/MovieAlnIndexLookupTable.shared.d" -MT"loadpulses/MovieAlnIndexLookupTable.shared.o loadpulses/MovieAlnIndexLookupTable.shared.d" -c loadpulses/MovieAlnIndexLookupTable.cpp -o loadpulses/MovieAlnIndexLookupTable.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"alignment/CmpAlignment.shared.d" -MT"alignment/CmpAlignment.shared.o alignment/CmpAlignment.shared.d" -c alignment/CmpAlignment.cpp -o alignment/CmpAlignment.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"amos/AfgBasWriter.shared.d" -MT"amos/AfgBasWriter.shared.o amos/AfgBasWriter.shared.d" -c amos/AfgBasWriter.cpp -o amos/AfgBasWriter.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/ReferenceSequence.shared.d" -MT"sam/ReferenceSequence.shared.o sam/ReferenceSequence.shared.d" -c sam/ReferenceSequence.cpp -o sam/ReferenceSequence.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/SAMAlignment.shared.d" -MT"sam/SAMAlignment.shared.o sam/SAMAlignment.shared.d" -c sam/SAMAlignment.cpp -o sam/SAMAlignment.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/SAMHeader.shared.d" -MT"sam/SAMHeader.shared.o sam/SAMHeader.shared.d" -c sam/SAMHeader.cpp -o sam/SAMHeader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/ReadGroup.shared.d" -MT"sam/ReadGroup.shared.o sam/ReadGroup.shared.d" -c sam/ReadGroup.cpp -o sam/ReadGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -Imatrix -Ireads -Iqvs -Imetagenome -Isaf -Iutils -Ialignment -fPIC -MF"sam/SAMKeywordValuePair.shared.d" -MT"sam/SAMKeywordValuePair.shared.o sam/SAMKeywordValuePair.shared.d" -c sam/SAMKeywordValuePair.cpp -o sam/SAMKeywordValuePair.shared.o g++ -shared -fPIC -o libpbdata.so -Wl,-soname,libpbdata.so GFFFile.shared.o ChangeListID.shared.o StringUtils.shared.o FASTASequence.shared.o MD5Utils.shared.o FASTAReader.shared.o CommandLineParser.shared.o CCSSequence.shared.o FASTQReader.shared.o ReverseCompressIndex.shared.o PackedDNASequence.shared.o SMRTSequence.shared.o NucConversion.shared.o DNASequence.shared.o FASTQSequence.shared.o reads/RegionTable.shared.o reads/ReadType.shared.o reads/ScanData.shared.o reads/BaseFile.shared.o reads/ZMWGroupEntry.shared.o reads/PulseBaseCommon.shared.o reads/HoleXY.shared.o reads/PulseFile.shared.o metagenome/TitleTable.shared.o qvs/QualityTransform.shared.o qvs/QualityValue.shared.o saf/AlnGroup.shared.o saf/RefInfo.shared.o saf/RefGroup.shared.o saf/MovieInfo.shared.o utils/BitUtils.shared.o utils/SMRTTitle.shared.o utils/SMRTReadUtils.shared.o loadpulses/MetricField.shared.o loadpulses/MovieAlnIndexLookupTable.shared.o alignment/CmpAlignment.shared.o amos/AfgBasWriter.shared.o sam/ReferenceSequence.shared.o sam/SAMAlignment.shared.o sam/SAMHeader.shared.o sam/ReadGroup.shared.o sam/SAMKeywordValuePair.shared.o make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/pbdata' /usr/bin/make -C hdf all make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf' g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAttributable.d" -MT"HDFAttributable.o HDFAttributable.d" -c HDFAttributable.cpp -o HDFAttributable.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFScanDataReader.d" -MT"HDFScanDataReader.o HDFScanDataReader.d" -c HDFScanDataReader.cpp -o HDFScanDataReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFScanDataWriter.d" -MT"HDFScanDataWriter.o HDFScanDataWriter.d" -c HDFScanDataWriter.cpp -o HDFScanDataWriter.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"DatasetCollection.d" -MT"DatasetCollection.o DatasetCollection.d" -c DatasetCollection.cpp -o DatasetCollection.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFRegionTableReader.d" -MT"HDFRegionTableReader.o HDFRegionTableReader.d" -c HDFRegionTableReader.cpp -o HDFRegionTableReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFNewBasReader.d" -MT"HDFNewBasReader.o HDFNewBasReader.d" -c HDFNewBasReader.cpp -o HDFNewBasReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAtom.d" -MT"HDFAtom.o HDFAtom.d" -c HDFAtom.cpp -o HDFAtom.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFCmpExperimentGroup.d" -MT"HDFCmpExperimentGroup.o HDFCmpExperimentGroup.d" -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFPulseDataFile.d" -MT"HDFPulseDataFile.o HDFPulseDataFile.d" -c HDFPulseDataFile.cpp -o HDFPulseDataFile.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFCmpSupportedFields.d" -MT"HDFCmpSupportedFields.o HDFCmpSupportedFields.d" -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFZMWReader.d" -MT"HDFZMWReader.o HDFZMWReader.d" -c HDFZMWReader.cpp -o HDFZMWReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFFile.d" -MT"HDFFile.o HDFFile.d" -c HDFFile.cpp -o HDFFile.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAlnInfoGroup.d" -MT"HDFAlnInfoGroup.o HDFAlnInfoGroup.d" -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFGroup.d" -MT"HDFGroup.o HDFGroup.d" -c HDFGroup.cpp -o HDFGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFUtils.d" -MT"HDFUtils.o HDFUtils.d" -c HDFUtils.cpp -o HDFUtils.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFBasReader.d" -MT"HDFBasReader.o HDFBasReader.d" -c HDFBasReader.cpp -o HDFBasReader.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFAlnGroupGroup.d" -MT"HDFAlnGroupGroup.o HDFAlnGroupGroup.d" -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"HDFData.d" -MT"HDFData.o HDFData.d" -c HDFData.cpp -o HDFData.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"BufferedHDFArray.d" -MT"BufferedHDFArray.o BufferedHDFArray.d" -c BufferedHDFArray.cpp -o BufferedHDFArray.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -MF"BufferedHDF2DArray.d" -MT"BufferedHDF2DArray.o BufferedHDF2DArray.d" -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.o ar rc libpbihdf.a HDFAttributable.o HDFScanDataReader.o HDFScanDataWriter.o DatasetCollection.o HDFRegionTableReader.o HDFNewBasReader.o HDFAtom.o HDFCmpExperimentGroup.o HDFPulseDataFile.o HDFCmpSupportedFields.o HDFZMWReader.o HDFFile.o HDFAlnInfoGroup.o HDFGroup.o HDFUtils.o HDFBasReader.o HDFAlnGroupGroup.o HDFData.o BufferedHDFArray.o BufferedHDF2DArray.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAttributable.shared.d" -MT"HDFAttributable.shared.o HDFAttributable.shared.d" -c HDFAttributable.cpp -o HDFAttributable.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFScanDataReader.shared.d" -MT"HDFScanDataReader.shared.o HDFScanDataReader.shared.d" -c HDFScanDataReader.cpp -o HDFScanDataReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFScanDataWriter.shared.d" -MT"HDFScanDataWriter.shared.o HDFScanDataWriter.shared.d" -c HDFScanDataWriter.cpp -o HDFScanDataWriter.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"DatasetCollection.shared.d" -MT"DatasetCollection.shared.o DatasetCollection.shared.d" -c DatasetCollection.cpp -o DatasetCollection.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFRegionTableReader.shared.d" -MT"HDFRegionTableReader.shared.o HDFRegionTableReader.shared.d" -c HDFRegionTableReader.cpp -o HDFRegionTableReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFNewBasReader.shared.d" -MT"HDFNewBasReader.shared.o HDFNewBasReader.shared.d" -c HDFNewBasReader.cpp -o HDFNewBasReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAtom.shared.d" -MT"HDFAtom.shared.o HDFAtom.shared.d" -c HDFAtom.cpp -o HDFAtom.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFCmpExperimentGroup.shared.d" -MT"HDFCmpExperimentGroup.shared.o HDFCmpExperimentGroup.shared.d" -c HDFCmpExperimentGroup.cpp -o HDFCmpExperimentGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFPulseDataFile.shared.d" -MT"HDFPulseDataFile.shared.o HDFPulseDataFile.shared.d" -c HDFPulseDataFile.cpp -o HDFPulseDataFile.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFCmpSupportedFields.shared.d" -MT"HDFCmpSupportedFields.shared.o HDFCmpSupportedFields.shared.d" -c HDFCmpSupportedFields.cpp -o HDFCmpSupportedFields.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFZMWReader.shared.d" -MT"HDFZMWReader.shared.o HDFZMWReader.shared.d" -c HDFZMWReader.cpp -o HDFZMWReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFFile.shared.d" -MT"HDFFile.shared.o HDFFile.shared.d" -c HDFFile.cpp -o HDFFile.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAlnInfoGroup.shared.d" -MT"HDFAlnInfoGroup.shared.o HDFAlnInfoGroup.shared.d" -c HDFAlnInfoGroup.cpp -o HDFAlnInfoGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFGroup.shared.d" -MT"HDFGroup.shared.o HDFGroup.shared.d" -c HDFGroup.cpp -o HDFGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFUtils.shared.d" -MT"HDFUtils.shared.o HDFUtils.shared.d" -c HDFUtils.cpp -o HDFUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFBasReader.shared.d" -MT"HDFBasReader.shared.o HDFBasReader.shared.d" -c HDFBasReader.cpp -o HDFBasReader.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFAlnGroupGroup.shared.d" -MT"HDFAlnGroupGroup.shared.o HDFAlnGroupGroup.shared.d" -c HDFAlnGroupGroup.cpp -o HDFAlnGroupGroup.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"HDFData.shared.d" -MT"HDFData.shared.o HDFData.shared.d" -c HDFData.cpp -o HDFData.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"BufferedHDFArray.shared.d" -MT"BufferedHDFArray.shared.o BufferedHDFArray.shared.d" -c BufferedHDFArray.cpp -o BufferedHDFArray.shared.o g++ -std=c++11 -pedantic -MMD -MP -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../pbdata -I/usr/include/hdf5/serial -fPIC -MF"BufferedHDF2DArray.shared.d" -MT"BufferedHDF2DArray.shared.o BufferedHDF2DArray.shared.d" -c BufferedHDF2DArray.cpp -o BufferedHDF2DArray.shared.o g++ -shared -fPIC -o libpbihdf.so -Wl,-soname,libpbihdf.so HDFAttributable.shared.o HDFScanDataReader.shared.o HDFScanDataWriter.shared.o DatasetCollection.shared.o HDFRegionTableReader.shared.o HDFNewBasReader.shared.o HDFAtom.shared.o HDFCmpExperimentGroup.shared.o HDFPulseDataFile.shared.o HDFCmpSupportedFields.shared.o HDFZMWReader.shared.o HDFFile.shared.o HDFAlnInfoGroup.shared.o HDFGroup.shared.o HDFUtils.shared.o HDFBasReader.shared.o HDFAlnGroupGroup.shared.o HDFData.shared.o BufferedHDFArray.shared.o BufferedHDF2DArray.shared.o ../pbdata/libpbdata.so /usr/lib/powerpc-linux-gnu/hdf5/serial/libhdf5.so make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/hdf' /usr/bin/make -C alignment all make[4]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment' g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/BaseScoreFunction.d" -MT"algorithms/alignment/BaseScoreFunction.o algorithms/alignment/BaseScoreFunction.d" -c algorithms/alignment/BaseScoreFunction.cpp -o algorithms/alignment/BaseScoreFunction.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/AlignmentUtils.d" -MT"algorithms/alignment/AlignmentUtils.o algorithms/alignment/AlignmentUtils.d" -c algorithms/alignment/AlignmentUtils.cpp -o algorithms/alignment/AlignmentUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/ExtendAlign.d" -MT"algorithms/alignment/ExtendAlign.o algorithms/alignment/ExtendAlign.d" -c algorithms/alignment/ExtendAlign.cpp -o algorithms/alignment/ExtendAlign.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/GuidedAlign.d" -MT"algorithms/alignment/GuidedAlign.o algorithms/alignment/GuidedAlign.d" -c algorithms/alignment/GuidedAlign.cpp -o algorithms/alignment/GuidedAlign.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/QualityValueScoreFunction.d" -MT"algorithms/alignment/QualityValueScoreFunction.o algorithms/alignment/QualityValueScoreFunction.d" -c algorithms/alignment/QualityValueScoreFunction.cpp -o algorithms/alignment/QualityValueScoreFunction.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/IDSScoreFunction.d" -MT"algorithms/alignment/IDSScoreFunction.o algorithms/alignment/IDSScoreFunction.d" -c algorithms/alignment/IDSScoreFunction.cpp -o algorithms/alignment/IDSScoreFunction.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/StringToScoreMatrix.d" -MT"algorithms/alignment/StringToScoreMatrix.o algorithms/alignment/StringToScoreMatrix.d" -c algorithms/alignment/StringToScoreMatrix.cpp -o algorithms/alignment/StringToScoreMatrix.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/ScoreMatrices.d" -MT"algorithms/alignment/ScoreMatrices.o algorithms/alignment/ScoreMatrices.d" -c algorithms/alignment/ScoreMatrices.cpp -o algorithms/alignment/ScoreMatrices.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/KBandAlign.d" -MT"algorithms/alignment/KBandAlign.o algorithms/alignment/KBandAlign.d" -c algorithms/alignment/KBandAlign.cpp -o algorithms/alignment/KBandAlign.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/sdp/SparseDynamicProgramming.d" -MT"algorithms/alignment/sdp/SparseDynamicProgramming.o algorithms/alignment/sdp/SparseDynamicProgramming.d" -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o algorithms/alignment/sdp/SparseDynamicProgramming.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/alignment/sdp/SDPFragment.d" -MT"algorithms/alignment/sdp/SDPFragment.o algorithms/alignment/sdp/SDPFragment.d" -c algorithms/alignment/sdp/SDPFragment.cpp -o algorithms/alignment/sdp/SDPFragment.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/Coordinate.d" -MT"algorithms/anchoring/Coordinate.o algorithms/anchoring/Coordinate.d" -c algorithms/anchoring/Coordinate.cpp -o algorithms/anchoring/Coordinate.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/ClusterProbability.d" -MT"algorithms/anchoring/ClusterProbability.o algorithms/anchoring/ClusterProbability.d" -c algorithms/anchoring/ClusterProbability.cpp -o algorithms/anchoring/ClusterProbability.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/FindMaxInterval.d" -MT"algorithms/anchoring/FindMaxInterval.o algorithms/anchoring/FindMaxInterval.d" -c algorithms/anchoring/FindMaxInterval.cpp -o algorithms/anchoring/FindMaxInterval.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/anchoring/BWTSearch.d" -MT"algorithms/anchoring/BWTSearch.o algorithms/anchoring/BWTSearch.d" -c algorithms/anchoring/BWTSearch.cpp -o algorithms/anchoring/BWTSearch.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/LightweightSuffixArray.d" -MT"algorithms/sorting/LightweightSuffixArray.o algorithms/sorting/LightweightSuffixArray.d" -c algorithms/sorting/LightweightSuffixArray.cpp -o algorithms/sorting/LightweightSuffixArray.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/qsufsort.d" -MT"algorithms/sorting/qsufsort.o algorithms/sorting/qsufsort.d" -c algorithms/sorting/qsufsort.cpp -o algorithms/sorting/qsufsort.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/DifferenceCovers.d" -MT"algorithms/sorting/DifferenceCovers.o algorithms/sorting/DifferenceCovers.d" -c algorithms/sorting/DifferenceCovers.cpp -o algorithms/sorting/DifferenceCovers.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"algorithms/sorting/MultikeyQuicksort.d" -MT"algorithms/sorting/MultikeyQuicksort.o algorithms/sorting/MultikeyQuicksort.d" -c algorithms/sorting/MultikeyQuicksort.cpp -o algorithms/sorting/MultikeyQuicksort.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentContext.d" -MT"datastructures/alignment/AlignmentContext.o datastructures/alignment/AlignmentContext.d" -c datastructures/alignment/AlignmentContext.cpp -o datastructures/alignment/AlignmentContext.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentCandidate.d" -MT"datastructures/alignment/AlignmentCandidate.o datastructures/alignment/AlignmentCandidate.d" -c datastructures/alignment/AlignmentCandidate.cpp -o datastructures/alignment/AlignmentCandidate.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/CmpFile.d" -MT"datastructures/alignment/CmpFile.o datastructures/alignment/CmpFile.d" -c datastructures/alignment/CmpFile.cpp -o datastructures/alignment/CmpFile.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentStats.d" -MT"datastructures/alignment/AlignmentStats.o datastructures/alignment/AlignmentStats.d" -c datastructures/alignment/AlignmentStats.cpp -o datastructures/alignment/AlignmentStats.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/FilterCriteria.d" -MT"datastructures/alignment/FilterCriteria.o datastructures/alignment/FilterCriteria.d" -c datastructures/alignment/FilterCriteria.cpp -o datastructures/alignment/FilterCriteria.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/Alignment.d" -MT"datastructures/alignment/Alignment.o datastructures/alignment/Alignment.d" -c datastructures/alignment/Alignment.cpp -o datastructures/alignment/Alignment.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/SAMToAlignmentCandidateAdapter.d" -MT"datastructures/alignment/SAMToAlignmentCandidateAdapter.o datastructures/alignment/SAMToAlignmentCandidateAdapter.d" -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o datastructures/alignment/SAMToAlignmentCandidateAdapter.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignment/AlignmentMap.d" -MT"datastructures/alignment/AlignmentMap.o datastructures/alignment/AlignmentMap.d" -c datastructures/alignment/AlignmentMap.cpp -o datastructures/alignment/AlignmentMap.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignmentset/SAMSupplementalQVList.d" -MT"datastructures/alignmentset/SAMSupplementalQVList.o datastructures/alignmentset/SAMSupplementalQVList.d" -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o datastructures/alignmentset/SAMSupplementalQVList.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/alignmentset/SAMQVConversion.d" -MT"datastructures/alignmentset/SAMQVConversion.o datastructures/alignmentset/SAMQVConversion.d" -c datastructures/alignmentset/SAMQVConversion.cpp -o datastructures/alignmentset/SAMQVConversion.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/AnchorParameters.d" -MT"datastructures/anchoring/AnchorParameters.o datastructures/anchoring/AnchorParameters.d" -c datastructures/anchoring/AnchorParameters.cpp -o datastructures/anchoring/AnchorParameters.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/MatchPos.d" -MT"datastructures/anchoring/MatchPos.o datastructures/anchoring/MatchPos.d" -c datastructures/anchoring/MatchPos.cpp -o datastructures/anchoring/MatchPos.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/WeightedInterval.d" -MT"datastructures/anchoring/WeightedInterval.o datastructures/anchoring/WeightedInterval.d" -c datastructures/anchoring/WeightedInterval.cpp -o datastructures/anchoring/WeightedInterval.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"datastructures/anchoring/ClusterList.d" -MT"datastructures/anchoring/ClusterList.o datastructures/anchoring/ClusterList.d" -c datastructures/anchoring/ClusterList.cpp -o datastructures/anchoring/ClusterList.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"qvs/QualityValueProfile.d" -MT"qvs/QualityValueProfile.o qvs/QualityValueProfile.d" -c qvs/QualityValueProfile.cpp -o qvs/QualityValueProfile.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/pdfs.d" -MT"statistics/pdfs.o statistics/pdfs.d" -c statistics/pdfs.cpp -o statistics/pdfs.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/LookupAnchorDistribution.d" -MT"statistics/LookupAnchorDistribution.o statistics/LookupAnchorDistribution.d" -c statistics/LookupAnchorDistribution.cpp -o statistics/LookupAnchorDistribution.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/cdfs.d" -MT"statistics/cdfs.o statistics/cdfs.d" -c statistics/cdfs.cpp -o statistics/cdfs.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"statistics/StatUtils.d" -MT"statistics/StatUtils.o statistics/StatUtils.d" -c statistics/StatUtils.cpp -o statistics/StatUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"tuples/BaseTuple.d" -MT"tuples/BaseTuple.o tuples/BaseTuple.d" -c tuples/BaseTuple.cpp -o tuples/BaseTuple.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"tuples/DNATuple.d" -MT"tuples/DNATuple.o tuples/DNATuple.d" -c tuples/DNATuple.cpp -o tuples/DNATuple.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"tuples/TupleMetrics.d" -MT"tuples/TupleMetrics.o tuples/TupleMetrics.d" -c tuples/TupleMetrics.cpp -o tuples/TupleMetrics.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/RegionUtils.d" -MT"utils/RegionUtils.o utils/RegionUtils.d" -c utils/RegionUtils.cpp -o utils/RegionUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/FileOfFileNames.d" -MT"utils/FileOfFileNames.o utils/FileOfFileNames.d" -c utils/FileOfFileNames.cpp -o utils/FileOfFileNames.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/LogUtils.d" -MT"utils/LogUtils.o utils/LogUtils.d" -c utils/LogUtils.cpp -o utils/LogUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/TimeUtils.d" -MT"utils/TimeUtils.o utils/TimeUtils.d" -c utils/TimeUtils.cpp -o utils/TimeUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/PhredUtils.d" -MT"utils/PhredUtils.o utils/PhredUtils.d" -c utils/PhredUtils.cpp -o utils/PhredUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/RangeUtils.d" -MT"utils/RangeUtils.o utils/RangeUtils.d" -c utils/RangeUtils.cpp -o utils/RangeUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"utils/FileUtils.d" -MT"utils/FileUtils.o utils/FileUtils.d" -c utils/FileUtils.cpp -o utils/FileUtils.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/ReaderAgglomerate.d" -MT"files/ReaderAgglomerate.o files/ReaderAgglomerate.d" -c files/ReaderAgglomerate.cpp -o files/ReaderAgglomerate.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/FragmentCCSIterator.d" -MT"files/FragmentCCSIterator.o files/FragmentCCSIterator.d" -c files/FragmentCCSIterator.cpp -o files/FragmentCCSIterator.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/CCSIterator.d" -MT"files/CCSIterator.o files/CCSIterator.d" -c files/CCSIterator.cpp -o files/CCSIterator.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"files/BaseSequenceIO.d" -MT"files/BaseSequenceIO.o files/BaseSequenceIO.d" -c files/BaseSequenceIO.cpp -o files/BaseSequenceIO.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/CompareSequencesPrinter.d" -MT"format/CompareSequencesPrinter.o format/CompareSequencesPrinter.d" -c format/CompareSequencesPrinter.cpp -o format/CompareSequencesPrinter.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/SAMHeaderPrinter.d" -MT"format/SAMHeaderPrinter.o format/SAMHeaderPrinter.d" -c format/SAMHeaderPrinter.cpp -o format/SAMHeaderPrinter.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/SAMPrinter.d" -MT"format/SAMPrinter.o format/SAMPrinter.d" -c format/SAMPrinter.cpp -o format/SAMPrinter.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/SummaryPrinter.d" -MT"format/SummaryPrinter.o format/SummaryPrinter.d" -c format/SummaryPrinter.cpp -o format/SummaryPrinter.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"format/IntervalPrinter.d" -MT"format/IntervalPrinter.o format/IntervalPrinter.d" -c format/IntervalPrinter.cpp -o format/IntervalPrinter.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/ContextSet.d" -MT"simulator/ContextSet.o simulator/ContextSet.d" -c simulator/ContextSet.cpp -o simulator/ContextSet.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/ContextSample.d" -MT"simulator/ContextSample.o simulator/ContextSample.d" -c simulator/ContextSample.cpp -o simulator/ContextSample.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/QualitySample.d" -MT"simulator/QualitySample.o simulator/QualitySample.d" -c simulator/QualitySample.cpp -o simulator/QualitySample.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"simulator/LengthHistogram.d" -MT"simulator/LengthHistogram.o simulator/LengthHistogram.d" -c simulator/LengthHistogram.cpp -o simulator/LengthHistogram.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -MF"MappingMetrics.d" -MT"MappingMetrics.o MappingMetrics.d" -c MappingMetrics.cpp -o MappingMetrics.o ar rc libblasr.a algorithms/alignment/BaseScoreFunction.o algorithms/alignment/AlignmentUtils.o algorithms/alignment/ExtendAlign.o algorithms/alignment/GuidedAlign.o algorithms/alignment/QualityValueScoreFunction.o algorithms/alignment/IDSScoreFunction.o algorithms/alignment/StringToScoreMatrix.o algorithms/alignment/ScoreMatrices.o algorithms/alignment/KBandAlign.o algorithms/alignment/sdp/SparseDynamicProgramming.o algorithms/alignment/sdp/SDPFragment.o algorithms/anchoring/Coordinate.o algorithms/anchoring/ClusterProbability.o algorithms/anchoring/FindMaxInterval.o algorithms/anchoring/BWTSearch.o algorithms/sorting/LightweightSuffixArray.o algorithms/sorting/qsufsort.o algorithms/sorting/DifferenceCovers.o algorithms/sorting/MultikeyQuicksort.o datastructures/alignment/AlignmentContext.o datastructures/alignment/AlignmentCandidate.o datastructures/alignment/CmpFile.o datastructures/alignment/AlignmentStats.o datastructures/alignment/FilterCriteria.o datastructures/alignment/Alignment.o datastructures/alignment/SAMToAlignmentCandidateAdapter.o datastructures/alignment/AlignmentMap.o datastructures/alignmentset/SAMSupplementalQVList.o datastructures/alignmentset/SAMQVConversion.o datastructures/anchoring/AnchorParameters.o datastructures/anchoring/MatchPos.o datastructures/anchoring/WeightedInterval.o datastructures/anchoring/ClusterList.o qvs/QualityValueProfile.o statistics/pdfs.o statistics/LookupAnchorDistribution.o statistics/cdfs.o statistics/StatUtils.o tuples/BaseTuple.o tuples/DNATuple.o tuples/TupleMetrics.o utils/RegionUtils.o utils/FileOfFileNames.o utils/LogUtils.o utils/TimeUtils.o utils/PhredUtils.o utils/RangeUtils.o utils/FileUtils.o files/ReaderAgglomerate.o files/FragmentCCSIterator.o files/CCSIterator.o files/BaseSequenceIO.o format/CompareSequencesPrinter.o format/SAMHeaderPrinter.o format/SAMPrinter.o format/SummaryPrinter.o format/IntervalPrinter.o simulator/ContextSet.o simulator/ContextSample.o simulator/QualitySample.o simulator/LengthHistogram.o MappingMetrics.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/BaseScoreFunction.shared.d" -MT"algorithms/alignment/BaseScoreFunction.shared.o algorithms/alignment/BaseScoreFunction.shared.d" -c algorithms/alignment/BaseScoreFunction.cpp -o algorithms/alignment/BaseScoreFunction.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/AlignmentUtils.shared.d" -MT"algorithms/alignment/AlignmentUtils.shared.o algorithms/alignment/AlignmentUtils.shared.d" -c algorithms/alignment/AlignmentUtils.cpp -o algorithms/alignment/AlignmentUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/ExtendAlign.shared.d" -MT"algorithms/alignment/ExtendAlign.shared.o algorithms/alignment/ExtendAlign.shared.d" -c algorithms/alignment/ExtendAlign.cpp -o algorithms/alignment/ExtendAlign.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/GuidedAlign.shared.d" -MT"algorithms/alignment/GuidedAlign.shared.o algorithms/alignment/GuidedAlign.shared.d" -c algorithms/alignment/GuidedAlign.cpp -o algorithms/alignment/GuidedAlign.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/QualityValueScoreFunction.shared.d" -MT"algorithms/alignment/QualityValueScoreFunction.shared.o algorithms/alignment/QualityValueScoreFunction.shared.d" -c algorithms/alignment/QualityValueScoreFunction.cpp -o algorithms/alignment/QualityValueScoreFunction.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/IDSScoreFunction.shared.d" -MT"algorithms/alignment/IDSScoreFunction.shared.o algorithms/alignment/IDSScoreFunction.shared.d" -c algorithms/alignment/IDSScoreFunction.cpp -o algorithms/alignment/IDSScoreFunction.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/StringToScoreMatrix.shared.d" -MT"algorithms/alignment/StringToScoreMatrix.shared.o algorithms/alignment/StringToScoreMatrix.shared.d" -c algorithms/alignment/StringToScoreMatrix.cpp -o algorithms/alignment/StringToScoreMatrix.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/ScoreMatrices.shared.d" -MT"algorithms/alignment/ScoreMatrices.shared.o algorithms/alignment/ScoreMatrices.shared.d" -c algorithms/alignment/ScoreMatrices.cpp -o algorithms/alignment/ScoreMatrices.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/KBandAlign.shared.d" -MT"algorithms/alignment/KBandAlign.shared.o algorithms/alignment/KBandAlign.shared.d" -c algorithms/alignment/KBandAlign.cpp -o algorithms/alignment/KBandAlign.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/sdp/SparseDynamicProgramming.shared.d" -MT"algorithms/alignment/sdp/SparseDynamicProgramming.shared.o algorithms/alignment/sdp/SparseDynamicProgramming.shared.d" -c algorithms/alignment/sdp/SparseDynamicProgramming.cpp -o algorithms/alignment/sdp/SparseDynamicProgramming.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/alignment/sdp/SDPFragment.shared.d" -MT"algorithms/alignment/sdp/SDPFragment.shared.o algorithms/alignment/sdp/SDPFragment.shared.d" -c algorithms/alignment/sdp/SDPFragment.cpp -o algorithms/alignment/sdp/SDPFragment.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/Coordinate.shared.d" -MT"algorithms/anchoring/Coordinate.shared.o algorithms/anchoring/Coordinate.shared.d" -c algorithms/anchoring/Coordinate.cpp -o algorithms/anchoring/Coordinate.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/ClusterProbability.shared.d" -MT"algorithms/anchoring/ClusterProbability.shared.o algorithms/anchoring/ClusterProbability.shared.d" -c algorithms/anchoring/ClusterProbability.cpp -o algorithms/anchoring/ClusterProbability.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/FindMaxInterval.shared.d" -MT"algorithms/anchoring/FindMaxInterval.shared.o algorithms/anchoring/FindMaxInterval.shared.d" -c algorithms/anchoring/FindMaxInterval.cpp -o algorithms/anchoring/FindMaxInterval.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/anchoring/BWTSearch.shared.d" -MT"algorithms/anchoring/BWTSearch.shared.o algorithms/anchoring/BWTSearch.shared.d" -c algorithms/anchoring/BWTSearch.cpp -o algorithms/anchoring/BWTSearch.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/LightweightSuffixArray.shared.d" -MT"algorithms/sorting/LightweightSuffixArray.shared.o algorithms/sorting/LightweightSuffixArray.shared.d" -c algorithms/sorting/LightweightSuffixArray.cpp -o algorithms/sorting/LightweightSuffixArray.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/qsufsort.shared.d" -MT"algorithms/sorting/qsufsort.shared.o algorithms/sorting/qsufsort.shared.d" -c algorithms/sorting/qsufsort.cpp -o algorithms/sorting/qsufsort.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/DifferenceCovers.shared.d" -MT"algorithms/sorting/DifferenceCovers.shared.o algorithms/sorting/DifferenceCovers.shared.d" -c algorithms/sorting/DifferenceCovers.cpp -o algorithms/sorting/DifferenceCovers.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"algorithms/sorting/MultikeyQuicksort.shared.d" -MT"algorithms/sorting/MultikeyQuicksort.shared.o algorithms/sorting/MultikeyQuicksort.shared.d" -c algorithms/sorting/MultikeyQuicksort.cpp -o algorithms/sorting/MultikeyQuicksort.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentContext.shared.d" -MT"datastructures/alignment/AlignmentContext.shared.o datastructures/alignment/AlignmentContext.shared.d" -c datastructures/alignment/AlignmentContext.cpp -o datastructures/alignment/AlignmentContext.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentCandidate.shared.d" -MT"datastructures/alignment/AlignmentCandidate.shared.o datastructures/alignment/AlignmentCandidate.shared.d" -c datastructures/alignment/AlignmentCandidate.cpp -o datastructures/alignment/AlignmentCandidate.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/CmpFile.shared.d" -MT"datastructures/alignment/CmpFile.shared.o datastructures/alignment/CmpFile.shared.d" -c datastructures/alignment/CmpFile.cpp -o datastructures/alignment/CmpFile.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentStats.shared.d" -MT"datastructures/alignment/AlignmentStats.shared.o datastructures/alignment/AlignmentStats.shared.d" -c datastructures/alignment/AlignmentStats.cpp -o datastructures/alignment/AlignmentStats.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/FilterCriteria.shared.d" -MT"datastructures/alignment/FilterCriteria.shared.o datastructures/alignment/FilterCriteria.shared.d" -c datastructures/alignment/FilterCriteria.cpp -o datastructures/alignment/FilterCriteria.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/Alignment.shared.d" -MT"datastructures/alignment/Alignment.shared.o datastructures/alignment/Alignment.shared.d" -c datastructures/alignment/Alignment.cpp -o datastructures/alignment/Alignment.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.d" -MT"datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.o datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.d" -c datastructures/alignment/SAMToAlignmentCandidateAdapter.cpp -o datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignment/AlignmentMap.shared.d" -MT"datastructures/alignment/AlignmentMap.shared.o datastructures/alignment/AlignmentMap.shared.d" -c datastructures/alignment/AlignmentMap.cpp -o datastructures/alignment/AlignmentMap.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignmentset/SAMSupplementalQVList.shared.d" -MT"datastructures/alignmentset/SAMSupplementalQVList.shared.o datastructures/alignmentset/SAMSupplementalQVList.shared.d" -c datastructures/alignmentset/SAMSupplementalQVList.cpp -o datastructures/alignmentset/SAMSupplementalQVList.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/alignmentset/SAMQVConversion.shared.d" -MT"datastructures/alignmentset/SAMQVConversion.shared.o datastructures/alignmentset/SAMQVConversion.shared.d" -c datastructures/alignmentset/SAMQVConversion.cpp -o datastructures/alignmentset/SAMQVConversion.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/AnchorParameters.shared.d" -MT"datastructures/anchoring/AnchorParameters.shared.o datastructures/anchoring/AnchorParameters.shared.d" -c datastructures/anchoring/AnchorParameters.cpp -o datastructures/anchoring/AnchorParameters.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/MatchPos.shared.d" -MT"datastructures/anchoring/MatchPos.shared.o datastructures/anchoring/MatchPos.shared.d" -c datastructures/anchoring/MatchPos.cpp -o datastructures/anchoring/MatchPos.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/WeightedInterval.shared.d" -MT"datastructures/anchoring/WeightedInterval.shared.o datastructures/anchoring/WeightedInterval.shared.d" -c datastructures/anchoring/WeightedInterval.cpp -o datastructures/anchoring/WeightedInterval.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"datastructures/anchoring/ClusterList.shared.d" -MT"datastructures/anchoring/ClusterList.shared.o datastructures/anchoring/ClusterList.shared.d" -c datastructures/anchoring/ClusterList.cpp -o datastructures/anchoring/ClusterList.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"qvs/QualityValueProfile.shared.d" -MT"qvs/QualityValueProfile.shared.o qvs/QualityValueProfile.shared.d" -c qvs/QualityValueProfile.cpp -o qvs/QualityValueProfile.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/pdfs.shared.d" -MT"statistics/pdfs.shared.o statistics/pdfs.shared.d" -c statistics/pdfs.cpp -o statistics/pdfs.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/LookupAnchorDistribution.shared.d" -MT"statistics/LookupAnchorDistribution.shared.o statistics/LookupAnchorDistribution.shared.d" -c statistics/LookupAnchorDistribution.cpp -o statistics/LookupAnchorDistribution.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/cdfs.shared.d" -MT"statistics/cdfs.shared.o statistics/cdfs.shared.d" -c statistics/cdfs.cpp -o statistics/cdfs.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"statistics/StatUtils.shared.d" -MT"statistics/StatUtils.shared.o statistics/StatUtils.shared.d" -c statistics/StatUtils.cpp -o statistics/StatUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"tuples/BaseTuple.shared.d" -MT"tuples/BaseTuple.shared.o tuples/BaseTuple.shared.d" -c tuples/BaseTuple.cpp -o tuples/BaseTuple.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"tuples/DNATuple.shared.d" -MT"tuples/DNATuple.shared.o tuples/DNATuple.shared.d" -c tuples/DNATuple.cpp -o tuples/DNATuple.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"tuples/TupleMetrics.shared.d" -MT"tuples/TupleMetrics.shared.o tuples/TupleMetrics.shared.d" -c tuples/TupleMetrics.cpp -o tuples/TupleMetrics.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/RegionUtils.shared.d" -MT"utils/RegionUtils.shared.o utils/RegionUtils.shared.d" -c utils/RegionUtils.cpp -o utils/RegionUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/FileOfFileNames.shared.d" -MT"utils/FileOfFileNames.shared.o utils/FileOfFileNames.shared.d" -c utils/FileOfFileNames.cpp -o utils/FileOfFileNames.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/LogUtils.shared.d" -MT"utils/LogUtils.shared.o utils/LogUtils.shared.d" -c utils/LogUtils.cpp -o utils/LogUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/TimeUtils.shared.d" -MT"utils/TimeUtils.shared.o utils/TimeUtils.shared.d" -c utils/TimeUtils.cpp -o utils/TimeUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/PhredUtils.shared.d" -MT"utils/PhredUtils.shared.o utils/PhredUtils.shared.d" -c utils/PhredUtils.cpp -o utils/PhredUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/RangeUtils.shared.d" -MT"utils/RangeUtils.shared.o utils/RangeUtils.shared.d" -c utils/RangeUtils.cpp -o utils/RangeUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"utils/FileUtils.shared.d" -MT"utils/FileUtils.shared.o utils/FileUtils.shared.d" -c utils/FileUtils.cpp -o utils/FileUtils.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/ReaderAgglomerate.shared.d" -MT"files/ReaderAgglomerate.shared.o files/ReaderAgglomerate.shared.d" -c files/ReaderAgglomerate.cpp -o files/ReaderAgglomerate.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/FragmentCCSIterator.shared.d" -MT"files/FragmentCCSIterator.shared.o files/FragmentCCSIterator.shared.d" -c files/FragmentCCSIterator.cpp -o files/FragmentCCSIterator.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/CCSIterator.shared.d" -MT"files/CCSIterator.shared.o files/CCSIterator.shared.d" -c files/CCSIterator.cpp -o files/CCSIterator.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"files/BaseSequenceIO.shared.d" -MT"files/BaseSequenceIO.shared.o files/BaseSequenceIO.shared.d" -c files/BaseSequenceIO.cpp -o files/BaseSequenceIO.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/CompareSequencesPrinter.shared.d" -MT"format/CompareSequencesPrinter.shared.o format/CompareSequencesPrinter.shared.d" -c format/CompareSequencesPrinter.cpp -o format/CompareSequencesPrinter.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/SAMHeaderPrinter.shared.d" -MT"format/SAMHeaderPrinter.shared.o format/SAMHeaderPrinter.shared.d" -c format/SAMHeaderPrinter.cpp -o format/SAMHeaderPrinter.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/SAMPrinter.shared.d" -MT"format/SAMPrinter.shared.o format/SAMPrinter.shared.d" -c format/SAMPrinter.cpp -o format/SAMPrinter.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/SummaryPrinter.shared.d" -MT"format/SummaryPrinter.shared.o format/SummaryPrinter.shared.d" -c format/SummaryPrinter.cpp -o format/SummaryPrinter.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"format/IntervalPrinter.shared.d" -MT"format/IntervalPrinter.shared.o format/IntervalPrinter.shared.d" -c format/IntervalPrinter.cpp -o format/IntervalPrinter.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/ContextSet.shared.d" -MT"simulator/ContextSet.shared.o simulator/ContextSet.shared.d" -c simulator/ContextSet.cpp -o simulator/ContextSet.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/ContextSample.shared.d" -MT"simulator/ContextSample.shared.o simulator/ContextSample.shared.d" -c simulator/ContextSample.cpp -o simulator/ContextSample.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/QualitySample.shared.d" -MT"simulator/QualitySample.shared.o simulator/QualitySample.shared.d" -c simulator/QualitySample.cpp -o simulator/QualitySample.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"simulator/LengthHistogram.shared.d" -MT"simulator/LengthHistogram.shared.o simulator/LengthHistogram.shared.d" -c simulator/LengthHistogram.cpp -o simulator/LengthHistogram.shared.o g++ -std=c++11 -pedantic -MMD -MP -Wno-long-long -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I. -I../pbdata -I../hdf -I/usr/include/hdf5/serial -fPIC -MF"MappingMetrics.shared.d" -MT"MappingMetrics.shared.o MappingMetrics.shared.d" -c MappingMetrics.cpp -o MappingMetrics.shared.o g++ -shared -fPIC -o libblasr.so -Wl,-soname,libblasr.so algorithms/alignment/BaseScoreFunction.shared.o algorithms/alignment/AlignmentUtils.shared.o algorithms/alignment/ExtendAlign.shared.o algorithms/alignment/GuidedAlign.shared.o algorithms/alignment/QualityValueScoreFunction.shared.o algorithms/alignment/IDSScoreFunction.shared.o algorithms/alignment/StringToScoreMatrix.shared.o algorithms/alignment/ScoreMatrices.shared.o algorithms/alignment/KBandAlign.shared.o algorithms/alignment/sdp/SparseDynamicProgramming.shared.o algorithms/alignment/sdp/SDPFragment.shared.o algorithms/anchoring/Coordinate.shared.o algorithms/anchoring/ClusterProbability.shared.o algorithms/anchoring/FindMaxInterval.shared.o algorithms/anchoring/BWTSearch.shared.o algorithms/sorting/LightweightSuffixArray.shared.o algorithms/sorting/qsufsort.shared.o algorithms/sorting/DifferenceCovers.shared.o algorithms/sorting/MultikeyQuicksort.shared.o datastructures/alignment/AlignmentContext.shared.o datastructures/alignment/AlignmentCandidate.shared.o datastructures/alignment/CmpFile.shared.o datastructures/alignment/AlignmentStats.shared.o datastructures/alignment/FilterCriteria.shared.o datastructures/alignment/Alignment.shared.o datastructures/alignment/SAMToAlignmentCandidateAdapter.shared.o datastructures/alignment/AlignmentMap.shared.o datastructures/alignmentset/SAMSupplementalQVList.shared.o datastructures/alignmentset/SAMQVConversion.shared.o datastructures/anchoring/AnchorParameters.shared.o datastructures/anchoring/MatchPos.shared.o datastructures/anchoring/WeightedInterval.shared.o datastructures/anchoring/ClusterList.shared.o qvs/QualityValueProfile.shared.o statistics/pdfs.shared.o statistics/LookupAnchorDistribution.shared.o statistics/cdfs.shared.o statistics/StatUtils.shared.o tuples/BaseTuple.shared.o tuples/DNATuple.shared.o tuples/TupleMetrics.shared.o utils/RegionUtils.shared.o utils/FileOfFileNames.shared.o utils/LogUtils.shared.o utils/TimeUtils.shared.o utils/PhredUtils.shared.o utils/RangeUtils.shared.o utils/FileUtils.shared.o files/ReaderAgglomerate.shared.o files/FragmentCCSIterator.shared.o files/CCSIterator.shared.o files/BaseSequenceIO.shared.o format/CompareSequencesPrinter.shared.o format/SAMHeaderPrinter.shared.o format/SAMPrinter.shared.o format/SummaryPrinter.shared.o format/IntervalPrinter.shared.o simulator/ContextSet.shared.o simulator/ContextSample.shared.o simulator/QualitySample.shared.o simulator/LengthHistogram.shared.o MappingMetrics.shared.o ../pbdata/libpbdata.so /usr/lib/powerpc-linux-gnu/hdf5/serial/libhdf5.so make[4]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp/alignment' make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/libcpp' make[2]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' /usr/bin/make make[2]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' g++ -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -c -o Blasr.o Blasr.cpp g++ -o blasr -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -MF"blasr.d" Blasr.o -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl LD_LIBRARY_PATH=/usr/lib/powerpc-linux-gnu/hdf5/serial:./libcpp/alignment:./libcpp/hdf:./libcpp/pbdata /usr/bin/make -C utils make[3]: Entering directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils' g++ -o loadPulses LoadPulses.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"loadPulses.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o pls2fasta PulseToFasta.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"pls2fasta.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o samtoh5 SamToCmpH5.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"samtoh5.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o samtom4 SamToM4.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"samtom4.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o samFilter SamFilter.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"samFilter.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o toAfg ToAfg.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"toAfg.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o sawriter SAWriter.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"sawriter.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl g++ -o sdpMatcher SDPMatcher.cpp -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -fno-builtin-malloc -fno-builtin-calloc -fno-builtin-realloc -fno-builtin-free -fno-omit-frame-pointer -std=c++0x -pedantic -Wall -Wuninitialized -Wno-div-by-zero -MMD -MP -w -fpermissive -D_FORTIFY_SOURCE=2 -I./libcpp/alignment -I./libcpp/pbdata -I./libcpp/hdf -I/usr/include/hdf5/serial -I../libcpp/alignment -I../libcpp/pbdata -I../libcpp/hdf -I/usr/include/hdf5/serial -MF"sdpMatcher.d" -Wl,-Bsymbolic-functions -Wl,-z,relro -static -L./libcpp/alignment -L./libcpp/pbdata -L./libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -static -L../libcpp/alignment -L../libcpp/pbdata -L../libcpp/hdf -L/usr/lib/powerpc-linux-gnu/hdf5/serial -Wl,-Bstatic -lpbihdf -Wl,-Bstatic -lblasr -Wl,-Bstatic -lpbdata -Wl,-Bstatic -lpbihdf -Wl,-Bdynamic -lhdf5_cpp -lhdf5 -Wl,-Bdynamic -lz -Wl,-Bdynamic -lpthread -Wl,-Bdynamic -ldl make[3]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8/utils' make[2]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' make[1]: Leaving directory '/«BUILDDIR»/blasr-0~20150724+git3ca7fe8' fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a dh_auto_install -a dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_strip -a 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 powerpc: blasr dh_strip debug symbol extraction: packages to act on: blasr dh_strip debug symbol extraction: ignored packages: Using buildid for compat level >= 9 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 /usr/bin/pkg_create_dbgsym: deferring build of .ddeb to dh_gencontrol dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a 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 powerpc: blasr dh_gencontrol debug symbol wrapper: packages to act on: blasr dh_gencontrol debug symbol wrapper: ignored packages: dh_gencontrol debug symbol wrapper: processing package blasr (pkgdir debian/blasr, ddeb package dir debian/blasr-dbgsym) dh_gencontrol debug symbol wrapper: building blasr-dbgsym_0~20150724+git3ca7fe8-1build2_powerpc.ddeb dpkg-deb: building package 'blasr-dbgsym' in '../blasr-dbgsym_0~20150724+git3ca7fe8-1build2_powerpc.ddeb'. dh_gencontrol debug symbol wrapper: dpkg-distaddfile blasr-dbgsym_0~20150724+git3ca7fe8-1build2_powerpc.ddeb science extra dpkg-distaddfile: warning: File::FcntlLock not available; using flock which is not NFS-safe dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 125 pkgstriptranslations: processing blasr (in debian/blasr); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/blasr/DEBIAN/control, package blasr, directory debian/blasr DEBUG: wait blasr 1:blasr DEBUG: clear blasr 1:blasr DEBUG: done blasr pkgstripfiles: Running PNG optimization (using 8 cpus) for package blasr ... pkgstripfiles: No PNG files. dpkg-deb: building package 'blasr' in '../blasr_0~20150724+git3ca7fe8-1build2_powerpc.deb'. dpkg-genchanges -B -mLaunchpad Build Daemon >../blasr_0~20150724+git3ca7fe8-1build2_powerpc.changes dpkg-genchanges: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build blasr-0~20150724+git3ca7fe8 dpkg-buildpackage: binary-only upload (no source included) ──────────────────────────────────────────────────────────────────────────────── Build finished at 20151215-0320 Finished ──────── I: Built successfully ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build Chroot │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Changes │ └──────────────────────────────────────────────────────────────────────────────┘ blasr_0~20150724+git3ca7fe8-1build2_powerpc.changes: ──────────────────────────────────────────────────── Format: 1.8 Date: Tue, 15 Dec 2015 08:12:29 +0000 Source: blasr Binary: blasr Architecture: powerpc Version: 0~20150724+git3ca7fe8-1build2 Distribution: xenial Urgency: high Maintainer: Launchpad Build Daemon Changed-By: Dimitri John Ledkov Description: blasr - mapping single-molecule sequencing reads Changes: blasr (0~20150724+git3ca7fe8-1build2) xenial; urgency=high . * No change rebuild for libhdf5-cpp-11. Checksums-Sha1: f1ff053a3561f3c65df2b50e0aad5381d788475d 9412792 blasr-dbgsym_0~20150724+git3ca7fe8-1build2_powerpc.ddeb e2eafd10588e2191a6a8cc6198d1f4ed83624268 1365688 blasr_0~20150724+git3ca7fe8-1build2_powerpc.deb Checksums-Sha256: a64af4a0c18b137fcd637ce1f1ac26b0d1a4020a64c63ce4f22b1b8bfcf6af0e 9412792 blasr-dbgsym_0~20150724+git3ca7fe8-1build2_powerpc.ddeb ba51db3eda45c30471b725eef8e8141fa6000ded28c46aac6f5cee56c260ff27 1365688 blasr_0~20150724+git3ca7fe8-1build2_powerpc.deb Files: 1e8725a88a77875f50fe002f3b796cc6 9412792 science extra blasr-dbgsym_0~20150724+git3ca7fe8-1build2_powerpc.ddeb 382c27ca8c7288318d8fb5a99d397e8a 1365688 science optional blasr_0~20150724+git3ca7fe8-1build2_powerpc.deb ┌──────────────────────────────────────────────────────────────────────────────┐ │ Package contents │ └──────────────────────────────────────────────────────────────────────────────┘ blasr_0~20150724+git3ca7fe8-1build2_powerpc.deb ─────────────────────────────────────────────── new debian package, version 2.0. size 1365688 bytes: control archive=1363 bytes. 770 bytes, 15 lines control 1457 bytes, 24 lines md5sums Package: blasr Version: 0~20150724+git3ca7fe8-1build2 Architecture: powerpc Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6281 Depends: libc6 (>= 2.17), libhdf5-10, libhdf5-cpp-11 (>= 1.8.16), libstdc++6 (>= 5.2) Section: science Priority: optional Homepage: https://github.com/PacificBiosciences/blasr Description: mapping single-molecule sequencing reads Basic local alignment with successive refinement (BLASR) is a method for mapping single-molecule sequencing reads against a reference genome. Such reads are thousands of bases long, with divergence between them and the genome being dominated by insertion and deletion error. drwxr-xr-x root/root 0 2015-12-15 03:20 ./ drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/ drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/bin/ -rwxr-xr-x root/root 2895276 2015-12-15 03:20 ./usr/bin/blasr -rwxr-xr-x root/root 731668 2015-12-15 03:20 ./usr/bin/loadPulses -rwxr-xr-x root/root 600516 2015-12-15 03:20 ./usr/bin/pls2fasta -rwxr-xr-x root/root 403740 2015-12-15 03:20 ./usr/bin/samFilter -rwxr-xr-x root/root 535172 2015-12-15 03:20 ./usr/bin/samtoh5 -rwxr-xr-x root/root 272576 2015-12-15 03:20 ./usr/bin/samtom4 -rwxr-xr-x root/root 206744 2015-12-15 03:20 ./usr/bin/sawriter -rwxr-xr-x root/root 207544 2015-12-15 03:20 ./usr/bin/sdpMatcher -rwxr-xr-x root/root 534932 2015-12-15 03:20 ./usr/bin/toAfg drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/share/ drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/share/doc/blasr/ -rw-r--r-- root/root 1617 2015-07-27 00:52 ./usr/share/doc/blasr/LICENSES.txt -rw-r--r-- root/root 2596 2015-07-27 00:52 ./usr/share/doc/blasr/MANUAL.md -rw-r--r-- root/root 1136 2015-07-27 00:52 ./usr/share/doc/blasr/README.md -rw-r--r-- root/root 111 2015-07-31 03:51 ./usr/share/doc/blasr/TODO.Debian -rw-r--r-- root/root 375 2015-12-15 03:12 ./usr/share/doc/blasr/changelog.Debian.gz -rw-r--r-- root/root 4613 2015-07-31 03:51 ./usr/share/doc/blasr/copyright drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/share/man/ drwxr-xr-x root/root 0 2015-12-15 03:20 ./usr/share/man/man1/ -rw-r--r-- root/root 5732 2015-12-15 03:20 ./usr/share/man/man1/blasr.1.gz -rw-r--r-- root/root 936 2015-12-15 03:20 ./usr/share/man/man1/loadPulses.1.gz -rw-r--r-- root/root 925 2015-12-15 03:20 ./usr/share/man/man1/pls2fasta.1.gz -rw-r--r-- root/root 1397 2015-12-15 03:20 ./usr/share/man/man1/samFilter.1.gz -rw-r--r-- root/root 925 2015-12-15 03:20 ./usr/share/man/man1/samtoh5.1.gz -rw-r--r-- root/root 401 2015-12-15 03:20 ./usr/share/man/man1/samtom4.1.gz -rw-r--r-- root/root 841 2015-12-15 03:20 ./usr/share/man/man1/sawriter.1.gz -rw-r--r-- root/root 440 2015-12-15 03:20 ./usr/share/man/man1/sdpMatcher.1.gz -rw-r--r-- root/root 311 2015-12-15 03:20 ./usr/share/man/man1/toAfg.1.gz ┌──────────────────────────────────────────────────────────────────────────────┐ │ Post Build │ └──────────────────────────────────────────────────────────────────────────────┘ ┌──────────────────────────────────────────────────────────────────────────────┐ │ Cleanup │ └──────────────────────────────────────────────────────────────────────────────┘ Not removing build depends: as requested Keeping session: ┌──────────────────────────────────────────────────────────────────────────────┐ │ Summary │ └──────────────────────────────────────────────────────────────────────────────┘ Build Architecture: powerpc Build-Space: 197636 Build-Time: 303 Distribution: xenial Host Architecture: powerpc Install-Time: 24 Job: blasr_0~20150724+git3ca7fe8-1build2.dsc Machine Architecture: powerpc Package: blasr Package-Time: 329 Source-Version: 0~20150724+git3ca7fe8-1build2 Space: 197636 Status: successful Version: 0~20150724+git3ca7fe8-1build2 ──────────────────────────────────────────────────────────────────────────────── Finished at 20151215-0320 Build needed 00:05:29, 197636k disc space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-8441450'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-8441450/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-8441450'] Unmounting chroot for build PACKAGEBUILD-8441450... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-8441450'] Removing build PACKAGEBUILD-8441450