RUN: /usr/share/launchpad-buildd/slavebin/slave-prep ['slave-prep'] Forking launchpad-buildd slave process... Kernel version: Linux roseapple 3.2.0-61-generic #93-Ubuntu SMP Fri May 2 21:31:50 UTC 2014 x86_64 Buildd toolchain package versions: launchpad-buildd_125 python-lpbuildd_125 bzr_2.5.1-0ubuntu2 dpkg-dev_1.16.1.2ubuntu7.5. Syncing the system clock with the buildd NTP service... 24 Aug 00:22:23 ntpdate[18048]: adjust time server 10.211.37.1 offset 0.000139 sec RUN: /usr/share/launchpad-buildd/slavebin/unpack-chroot ['unpack-chroot', 'PACKAGEBUILD-6155621', '/home/buildd/filecache-default/f5ea41dcc47e9e1dc171aef481863179130c15c7'] Unpacking chroot for build PACKAGEBUILD-6155621 RUN: /usr/share/launchpad-buildd/slavebin/mount-chroot ['mount-chroot', 'PACKAGEBUILD-6155621'] Mounting chroot for build PACKAGEBUILD-6155621 RUN: /usr/share/launchpad-buildd/slavebin/override-sources-list ['override-sources-list', 'PACKAGEBUILD-6155621', 'deb http://ftpmaster.internal/ubuntu utopic main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu utopic-security main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu utopic-updates main restricted universe multiverse', 'deb http://ftpmaster.internal/ubuntu utopic-proposed main restricted universe multiverse'] Overriding sources.list in build-PACKAGEBUILD-6155621 RUN: /usr/share/launchpad-buildd/slavebin/update-debian-chroot ['update-debian-chroot', 'PACKAGEBUILD-6155621', 'i386'] Updating debian chroot for build PACKAGEBUILD-6155621 Ign http://ftpmaster.internal utopic InRelease Ign http://ftpmaster.internal utopic-security InRelease Ign http://archive-team.internal utopic InRelease Ign http://ftpmaster.internal utopic-updates InRelease Ign http://archive-team.internal utopic Release.gpg Ign http://ftpmaster.internal utopic-proposed InRelease Get:1 http://ftpmaster.internal utopic Release.gpg [933 B] Get:2 http://archive-team.internal utopic Release [723 B] Get:3 http://ftpmaster.internal utopic-security Release.gpg [933 B] Get:4 http://ftpmaster.internal utopic-updates Release.gpg [933 B] Get:5 http://ftpmaster.internal utopic-proposed Release.gpg [933 B] Get:6 http://ftpmaster.internal utopic Release [112 kB] Get:7 http://ftpmaster.internal utopic-security Release [58.5 kB] Get:8 http://archive-team.internal utopic/main i386 Packages Get:9 http://ftpmaster.internal utopic-updates Release [58.5 kB] Ign http://archive-team.internal utopic/main Translation-en Get:10 http://ftpmaster.internal utopic-proposed Release [112 kB] Get:11 http://ftpmaster.internal utopic/main i386 Packages [1327 kB] Get:12 http://ftpmaster.internal utopic/restricted i386 Packages [13.7 kB] Get:13 http://ftpmaster.internal utopic/universe i386 Packages [6184 kB] Get:14 http://ftpmaster.internal utopic/multiverse i386 Packages [132 kB] Get:15 http://ftpmaster.internal utopic/main Translation-en [767 kB] Get:16 http://ftpmaster.internal utopic/multiverse Translation-en [99.5 kB] Get:17 http://ftpmaster.internal utopic/restricted Translation-en [3548 B] Get:18 http://ftpmaster.internal utopic/universe Translation-en [4264 kB] Get:19 http://ftpmaster.internal utopic-security/main i386 Packages [14 B] Get:20 http://ftpmaster.internal utopic-security/restricted i386 Packages [14 B] Get:21 http://ftpmaster.internal utopic-security/universe i386 Packages [14 B] Get:22 http://ftpmaster.internal utopic-security/multiverse i386 Packages [14 B] Get:23 http://ftpmaster.internal utopic-security/main Translation-en [14 B] Get:24 http://ftpmaster.internal utopic-security/multiverse Translation-en [14 B] Get:25 http://ftpmaster.internal utopic-security/restricted Translation-en [14 B] Get:26 http://ftpmaster.internal utopic-security/universe Translation-en [14 B] Get:27 http://ftpmaster.internal utopic-updates/main i386 Packages [14 B] Get:28 http://ftpmaster.internal utopic-updates/restricted i386 Packages [14 B] Get:29 http://ftpmaster.internal utopic-updates/universe i386 Packages [14 B] Get:30 http://ftpmaster.internal utopic-updates/multiverse i386 Packages [14 B] Get:31 http://ftpmaster.internal utopic-updates/main Translation-en [14 B] Get:32 http://ftpmaster.internal utopic-updates/multiverse Translation-en [14 B] Get:33 http://ftpmaster.internal utopic-updates/restricted Translation-en [14 B] Get:34 http://ftpmaster.internal utopic-updates/universe Translation-en [14 B] Get:35 http://ftpmaster.internal utopic-proposed/main i386 Packages [66.0 kB] Get:36 http://ftpmaster.internal utopic-proposed/restricted i386 Packages [14 B] Get:37 http://ftpmaster.internal utopic-proposed/universe i386 Packages [281 kB] Get:38 http://ftpmaster.internal utopic-proposed/multiverse i386 Packages [12.1 kB] Get:39 http://ftpmaster.internal utopic-proposed/main Translation-en [41.0 kB] Get:40 http://ftpmaster.internal utopic-proposed/multiverse Translation-en [8248 B] Get:41 http://ftpmaster.internal utopic-proposed/restricted Translation-en [14 B] Get:42 http://ftpmaster.internal utopic-proposed/universe Translation-en [185 kB] Fetched 13.7 MB in 6s (2015 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-4.8 libgnutls26 libgnutls28 libstdc++-4.8-dev Use 'apt-get autoremove' to remove them. The following NEW packages will be installed: cpp-4.9 g++-4.9 gcc-4.9 libasan1 libcilkrts5 libgcc-4.9-dev libgcrypt20 libgnutls-deb0-28 librtmp1 libsmartcols1 libstdc++-4.9-dev libsystemd-journal0 libubsan0 upstart-bin The following packages will be upgraded: apt apt-transport-https bash binutils bsdutils busybox-initramfs cpp cpp-4.8 dpkg dpkg-dev g++ g++-4.8 gcc gcc-4.8 gcc-4.8-base gcc-4.9-base init-system-helpers initramfs-tools initramfs-tools-bin initscripts iproute2 libapt-pkg4.12 libasan0 libatomic1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcgmanager0 libcurl3-gnutls libdb5.3 libdbus-1-3 libdpkg-perl libdrm2 libgcc-4.8-dev libgcc1 libgcrypt11 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed2 libitm1 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libmpc3 libncurses5 libncursesw5 libnettle4 libpcre3 libplymouth4 libpng12-0 libquadmath0 libreadline6 libssl1.0.0 libstdc++-4.8-dev libstdc++6 libtinfo5 libudev1 libuuid1 linux-libc-dev mount multiarch-support ncurses-base ncurses-bin openssl perl perl-base perl-modules pkg-create-dbgsym plymouth readline-common sysv-rc sysvinit-utils tzdata udev upstart util-linux 81 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. Need to get 89.8 MB of archives. After this operation, 96.8 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ utopic/main bash i386 4.3-9ubuntu1 [592 kB] Get:2 http://ftpmaster.internal/ubuntu/ utopic/main libc-bin i386 2.19-4ubuntu2 [1107 kB] Get:3 http://ftpmaster.internal/ubuntu/ utopic/main libdbus-1-3 i386 1.8.6-1ubuntu1 [157 kB] Get:4 http://ftpmaster.internal/ubuntu/ utopic/main libcgmanager0 i386 0.30-1 [26.1 kB] Get:5 http://ftpmaster.internal/ubuntu/ utopic/main sysvinit-utils i386 2.88dsf-41ubuntu17 [52.4 kB] Get:6 http://ftpmaster.internal/ubuntu/ utopic/main sysv-rc all 2.88dsf-41ubuntu17 [37.7 kB] Get:7 http://ftpmaster.internal/ubuntu/ utopic/main libuuid1 i386 2.25-8ubuntu3 [17.1 kB] Get:8 http://ftpmaster.internal/ubuntu/ utopic/main libblkid1 i386 2.25-8ubuntu3 [116 kB] Get:9 http://ftpmaster.internal/ubuntu/ utopic/main libmount1 i386 2.25-8ubuntu3 [120 kB] Get:10 http://ftpmaster.internal/ubuntu/ utopic/main libsmartcols1 i386 2.25-8ubuntu3 [66.8 kB] Get:11 http://ftpmaster.internal/ubuntu/ utopic/main mount i386 2.25-8ubuntu3 [122 kB] Get:12 http://ftpmaster.internal/ubuntu/ utopic/main initscripts i386 2.88dsf-41ubuntu17 [35.2 kB] Get:13 http://ftpmaster.internal/ubuntu/ utopic/main initramfs-tools all 0.103ubuntu8 [44.7 kB] Get:14 http://ftpmaster.internal/ubuntu/ utopic/main upstart i386 1.13.1-0ubuntu3 [109 kB] Get:15 http://ftpmaster.internal/ubuntu/ utopic/main upstart-bin i386 1.13.1-0ubuntu3 [301 kB] Get:16 http://ftpmaster.internal/ubuntu/ utopic/main tzdata all 2014f-1 [186 kB] Get:17 http://ftpmaster.internal/ubuntu/ utopic/main util-linux i386 2.25-8ubuntu3 [838 kB] Get:18 http://ftpmaster.internal/ubuntu/ utopic/main udev i386 208-8ubuntu1 [819 kB] Get:19 http://ftpmaster.internal/ubuntu/ utopic/main libudev1 i386 208-8ubuntu1 [40.4 kB] Get:20 http://ftpmaster.internal/ubuntu/ utopic/main initramfs-tools-bin i386 0.103ubuntu8 [9152 B] Get:21 http://ftpmaster.internal/ubuntu/ utopic/main busybox-initramfs i386 1:1.22.0-8ubuntu1 [161 kB] Get:22 http://ftpmaster.internal/ubuntu/ utopic/main libc6-dev i386 2.19-4ubuntu2 [1559 kB] Get:23 http://ftpmaster.internal/ubuntu/ utopic/main libc-dev-bin i386 2.19-4ubuntu2 [64.8 kB] Get:24 http://ftpmaster.internal/ubuntu/ utopic/main linux-libc-dev i386 3.16.0-10.15 [763 kB] Get:25 http://ftpmaster.internal/ubuntu/ utopic/main libitm1 i386 4.9.1-8ubuntu1 [32.1 kB] Get:26 http://ftpmaster.internal/ubuntu/ utopic/main libgomp1 i386 4.9.1-8ubuntu1 [41.2 kB] Get:27 http://ftpmaster.internal/ubuntu/ utopic/main gcc-4.9-base i386 4.9.1-8ubuntu1 [15.2 kB] Get:28 http://ftpmaster.internal/ubuntu/ utopic/main libgcc1 i386 1:4.9.1-8ubuntu1 [48.2 kB] Get:29 http://ftpmaster.internal/ubuntu/ utopic/main libquadmath0 i386 4.9.1-8ubuntu1 [195 kB] Get:30 http://ftpmaster.internal/ubuntu/ utopic/main libatomic1 i386 4.9.1-8ubuntu1 [10.0 kB] Get:31 http://ftpmaster.internal/ubuntu/ utopic/main libstdc++6 i386 4.9.1-8ubuntu1 [291 kB] Get:32 http://ftpmaster.internal/ubuntu/ utopic/main libc6 i386 2.19-4ubuntu2 [4018 kB] Get:33 http://ftpmaster.internal/ubuntu/ utopic/main libgpg-error0 i386 1.13-2 [12.1 kB] Get:34 http://ftpmaster.internal/ubuntu/ utopic/main libgcrypt11 i386 1.5.4-2ubuntu1 [258 kB] Get:35 http://ftpmaster.internal/ubuntu/ utopic/main libsystemd-journal0 i386 208-8ubuntu1 [63.4 kB] Get:36 http://ftpmaster.internal/ubuntu/ utopic/main bsdutils i386 1:2.25-8ubuntu3 [48.5 kB] Get:37 http://ftpmaster.internal/ubuntu/ utopic/main dpkg i386 1.17.13ubuntu1 [2049 kB] Get:38 http://ftpmaster.internal/ubuntu/ utopic/main ncurses-bin i386 5.9+20140712-2ubuntu1 [141 kB] Get:39 http://ftpmaster.internal/ubuntu/ utopic-proposed/main perl i386 5.20.0-4 [2175 kB] Get:40 http://ftpmaster.internal/ubuntu/ utopic-proposed/main perl-base i386 5.20.0-4 [1255 kB] Get:41 http://ftpmaster.internal/ubuntu/ utopic-proposed/main perl-modules all 5.20.0-4 [2531 kB] Get:42 http://ftpmaster.internal/ubuntu/ utopic/main libdb5.3 i386 5.3.28-5 [714 kB] Get:43 http://ftpmaster.internal/ubuntu/ utopic/main libapt-pkg4.12 i386 1.0.4ubuntu6 [653 kB] Get:44 http://ftpmaster.internal/ubuntu/ utopic/main apt i386 1.0.4ubuntu6 [972 kB] Get:45 http://ftpmaster.internal/ubuntu/ utopic/main ncurses-base all 5.9+20140712-2ubuntu1 [16.2 kB] Get:46 http://ftpmaster.internal/ubuntu/ utopic/main readline-common all 6.3-8ubuntu1 [51.6 kB] Get:47 http://ftpmaster.internal/ubuntu/ utopic/main libncursesw5 i386 5.9+20140712-2ubuntu1 [130 kB] Get:48 http://ftpmaster.internal/ubuntu/ utopic/main libtinfo5 i386 5.9+20140712-2ubuntu1 [75.6 kB] Get:49 http://ftpmaster.internal/ubuntu/ utopic/main libncurses5 i386 5.9+20140712-2ubuntu1 [102 kB] Get:50 http://ftpmaster.internal/ubuntu/ utopic/main libreadline6 i386 6.3-8ubuntu1 [120 kB] Get:51 http://ftpmaster.internal/ubuntu/ utopic/main libpcre3 i386 1:8.35-3ubuntu1 [219 kB] Get:52 http://ftpmaster.internal/ubuntu/ utopic/main libnettle4 i386 2.7.1-3 [108 kB] Get:53 http://ftpmaster.internal/ubuntu/ utopic/main libhogweed2 i386 2.7.1-3 [125 kB] Get:54 http://ftpmaster.internal/ubuntu/ utopic/main libssl1.0.0 i386 1.0.1f-1ubuntu7 [854 kB] Get:55 http://ftpmaster.internal/ubuntu/ utopic/main libdrm2 i386 2.4.56-1 [24.7 kB] Get:56 http://ftpmaster.internal/ubuntu/ utopic/main init-system-helpers all 1.20ubuntu3 [12.9 kB] Get:57 http://ftpmaster.internal/ubuntu/ utopic/main plymouth i386 0.9.0-0ubuntu3 [110 kB] Get:58 http://ftpmaster.internal/ubuntu/ utopic/main libpng12-0 i386 1.2.51-0ubuntu2 [119 kB] Get:59 http://ftpmaster.internal/ubuntu/ utopic/main libplymouth4 i386 0.9.0-0ubuntu3 [92.9 kB] Get:60 http://ftpmaster.internal/ubuntu/ utopic/main libgnutls-deb0-28 i386 3.2.16-1ubuntu1 [491 kB] Get:61 http://ftpmaster.internal/ubuntu/ utopic/main libk5crypto3 i386 1.12.1+dfsg-7 [81.1 kB] Get:62 http://ftpmaster.internal/ubuntu/ utopic/main libgssapi-krb5-2 i386 1.12.1+dfsg-7 [125 kB] Get:63 http://ftpmaster.internal/ubuntu/ utopic/main libkrb5-3 i386 1.12.1+dfsg-7 [286 kB] Get:64 http://ftpmaster.internal/ubuntu/ utopic/main libkrb5support0 i386 1.12.1+dfsg-7 [31.8 kB] Get:65 http://ftpmaster.internal/ubuntu/ utopic/main libgcrypt20 i386 1.6.1-2ubuntu1 [293 kB] Get:66 http://ftpmaster.internal/ubuntu/ utopic-proposed/main libldap-2.4-2 i386 2.4.31-1+nmu2ubuntu10 [166 kB] Get:67 http://ftpmaster.internal/ubuntu/ utopic/main librtmp1 i386 2.4+20131018.git79459a2-4 [53.6 kB] Get:68 http://ftpmaster.internal/ubuntu/ utopic/main libcurl3-gnutls i386 7.37.1-1ubuntu1 [169 kB] Get:69 http://ftpmaster.internal/ubuntu/ utopic/main libmpc3 i386 1.0.2-1 [38.0 kB] Get:70 http://ftpmaster.internal/ubuntu/ utopic/main g++-4.8 i386 4.8.3-9ubuntu1 [14.6 MB] Get:71 http://ftpmaster.internal/ubuntu/ utopic/main gcc-4.8 i386 4.8.3-9ubuntu1 [4880 kB] Get:72 http://ftpmaster.internal/ubuntu/ utopic/main cpp-4.8 i386 4.8.3-9ubuntu1 [4293 kB] Get:73 http://ftpmaster.internal/ubuntu/ utopic/main binutils i386 2.24.51.20140818-1ubuntu1 [2335 kB] Get:74 http://ftpmaster.internal/ubuntu/ utopic/main libstdc++-4.8-dev i386 4.8.3-9ubuntu1 [1057 kB] Get:75 http://ftpmaster.internal/ubuntu/ utopic/main libgcc-4.8-dev i386 4.8.3-9ubuntu1 [1735 kB] Get:76 http://ftpmaster.internal/ubuntu/ utopic/main libasan0 i386 4.8.3-9ubuntu1 [64.4 kB] Get:77 http://ftpmaster.internal/ubuntu/ utopic/main gcc-4.8-base i386 4.8.3-9ubuntu1 [14.9 kB] Get:78 http://ftpmaster.internal/ubuntu/ utopic/main libasan1 i386 4.9.1-8ubuntu1 [197 kB] Get:79 http://ftpmaster.internal/ubuntu/ utopic/main libcilkrts5 i386 4.9.1-8ubuntu1 [44.9 kB] Get:80 http://ftpmaster.internal/ubuntu/ utopic/main libubsan0 i386 4.9.1-8ubuntu1 [90.4 kB] Get:81 http://ftpmaster.internal/ubuntu/ utopic/main multiarch-support i386 2.19-4ubuntu2 [4552 B] Get:82 http://ftpmaster.internal/ubuntu/ utopic/main iproute2 i386 3.16.0-1 [439 kB] Get:83 http://ftpmaster.internal/ubuntu/ utopic/main apt-transport-https i386 1.0.4ubuntu6 [26.1 kB] Get:84 http://ftpmaster.internal/ubuntu/ utopic/main openssl i386 1.0.1f-1ubuntu7 [502 kB] Get:85 http://ftpmaster.internal/ubuntu/ utopic/main cpp-4.9 i386 4.9.1-8ubuntu1 [5161 kB] Get:86 http://ftpmaster.internal/ubuntu/ utopic/main cpp i386 4:4.9.1-1ubuntu1 [27.6 kB] Get:87 http://ftpmaster.internal/ubuntu/ utopic/main dpkg-dev all 1.17.13ubuntu1 [737 kB] Get:88 http://ftpmaster.internal/ubuntu/ utopic/main libdpkg-perl all 1.17.13ubuntu1 [182 kB] Get:89 http://ftpmaster.internal/ubuntu/ utopic/main libgcc-4.9-dev i386 4.9.1-8ubuntu1 [2063 kB] Get:90 http://ftpmaster.internal/ubuntu/ utopic/main gcc-4.9 i386 4.9.1-8ubuntu1 [5583 kB] Get:91 http://ftpmaster.internal/ubuntu/ utopic/main gcc i386 4:4.9.1-1ubuntu1 [5272 B] Get:92 http://ftpmaster.internal/ubuntu/ utopic/main libstdc++-4.9-dev i386 4.9.1-8ubuntu1 [1133 kB] Get:93 http://ftpmaster.internal/ubuntu/ utopic/main g++-4.9 i386 4.9.1-8ubuntu1 [17.8 MB] Get:94 http://ftpmaster.internal/ubuntu/ utopic/main g++ i386 4:4.9.1-1ubuntu1 [1602 B] Get:95 http://ftpmaster.internal/ubuntu/ utopic/main pkg-create-dbgsym all 0.65 [7666 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 89.8 MB in 4s (18.7 MB/s) (Reading database ... 11914 files and directories currently installed.) Preparing to unpack .../bash_4.3-9ubuntu1_i386.deb ... Unpacking bash (4.3-9ubuntu1) over (4.3-7ubuntu3) ... Setting up bash (4.3-9ubuntu1) ... Installing new version of config file /etc/skel/.bashrc ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 11914 files and directories currently installed.) Preparing to unpack .../libc-bin_2.19-4ubuntu2_i386.deb ... Unpacking libc-bin (2.19-4ubuntu2) over (2.19-4ubuntu1) ... Preparing to unpack .../libc6_2.19-4ubuntu2_i386.deb ... Unpacking libc6:i386 (2.19-4ubuntu2) over (2.19-4ubuntu1) ... Preparing to unpack .../libgcc1_1%3a4.9.1-8ubuntu1_i386.deb ... Unpacking libgcc1:i386 (1:4.9.1-8ubuntu1) over (1:4.9.1-1ubuntu3) ... Preparing to unpack .../gcc-4.9-base_4.9.1-8ubuntu1_i386.deb ... Unpacking gcc-4.9-base:i386 (4.9.1-8ubuntu1) over (4.9.1-1ubuntu3) ... Setting up gcc-4.9-base:i386 (4.9.1-8ubuntu1) ... 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Preparing to unpack .../upstart_1.13.1-0ubuntu3_i386.deb ... Unpacking upstart (1.13.1-0ubuntu3) over (1.13.1-0ubuntu1) ... dpkg: warning: unable to delete old directory '/etc/X11/Xsession.d': Directory not empty dpkg: warning: unable to delete old directory '/etc/X11': Directory not empty Selecting previously unselected package upstart-bin. Preparing to unpack .../upstart-bin_1.13.1-0ubuntu3_i386.deb ... Unpacking upstart-bin (1.13.1-0ubuntu3) ... Preparing to unpack .../tzdata_2014f-1_all.deb ... Unpacking tzdata (2014f-1) over (2014e-1) ... Setting up tzdata (2014f-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Aug 24 00:22:47 UTC 2014. Universal Time is now: Sun Aug 24 00:22:47 UTC 2014. Run 'dpkg-reconfigure tzdata' if you wish to change it. (Reading database ... 11935 files and directories currently installed.) Preparing to unpack .../util-linux_2.25-8ubuntu3_i386.deb ... Unpacking util-linux (2.25-8ubuntu3) over (2.20.1-5.1ubuntu21) ... Setting up util-linux (2.25-8ubuntu3) ... Installing new version of config file /etc/cron.weekly/fstrim ... update-rc.d: warning: default start runlevel arguments (2 3 4 5) do not match hwclock.sh Default-Start values (S) update-rc.d: warning: default stop runlevel arguments (0 1 6) do not match hwclock.sh Default-Stop values (0 6) (Reading database ... 12046 files and directories currently installed.) Preparing to unpack .../udev_208-8ubuntu1_i386.deb ... Unpacking udev (208-8ubuntu1) over (204-14ubuntu2) ... Preparing to unpack .../libudev1_208-8ubuntu1_i386.deb ... Unpacking libudev1:i386 (208-8ubuntu1) over (204-14ubuntu2) ... Preparing to unpack .../initramfs-tools-bin_0.103ubuntu8_i386.deb ... Unpacking initramfs-tools-bin (0.103ubuntu8) over (0.103ubuntu7) ... Preparing to unpack .../busybox-initramfs_1%3a1.22.0-8ubuntu1_i386.deb ... Unpacking busybox-initramfs (1:1.22.0-8ubuntu1) over (1:1.22.0-6ubuntu1) ... Preparing to unpack .../libc6-dev_2.19-4ubuntu2_i386.deb ... 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A chroot environment has been detected, udev not started. update-initramfs: deferring update (trigger activated) update-rc.d: warning: default start runlevel arguments (2 3 4 5) do not match udev Default-Start values (S) update-rc.d: warning: default stop runlevel arguments (0 1 6) do not match udev Default-Stop values (none) update-rc.d: warning: default start runlevel arguments (2 3 4 5) do not match udev-finish Default-Start values (S) update-rc.d: warning: default stop runlevel arguments (0 1 6) do not match udev-finish Default-Stop values (none) update-rc.d: warning: default start runlevel arguments (2 3 4 5) do not match lvm2 Default-Start values (S) update-rc.d: warning: default stop runlevel arguments (0 1 6) do not match lvm2 Default-Stop values (none) Setting up initramfs-tools (0.103ubuntu8) ... update-initramfs: deferring update (trigger activated) Setting up upstart-bin (1.13.1-0ubuntu3) ... Installing new version of config file /etc/X11/Xsession.d/99upstart ... 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Setting up libgcrypt20:i386 (1.6.1-2ubuntu1) ... Setting up libldap-2.4-2:i386 (2.4.31-1+nmu2ubuntu10) ... Setting up librtmp1:i386 (2.4+20131018.git79459a2-4) ... Setting up libcurl3-gnutls:i386 (7.37.1-1ubuntu1) ... Setting up libmpc3:i386 (1.0.2-1) ... Setting up gcc-4.8-base:i386 (4.8.3-9ubuntu1) ... Setting up cpp-4.8 (4.8.3-9ubuntu1) ... Setting up binutils (2.24.51.20140818-1ubuntu1) ... Setting up libasan0:i386 (4.8.3-9ubuntu1) ... Setting up libgcc-4.8-dev:i386 (4.8.3-9ubuntu1) ... Setting up gcc-4.8 (4.8.3-9ubuntu1) ... Setting up libstdc++-4.8-dev:i386 (4.8.3-9ubuntu1) ... Setting up g++-4.8 (4.8.3-9ubuntu1) ... Setting up libasan1:i386 (4.9.1-8ubuntu1) ... Setting up libcilkrts5:i386 (4.9.1-8ubuntu1) ... Setting up libubsan0:i386 (4.9.1-8ubuntu1) ... Setting up iproute2 (3.16.0-1) ... Setting up apt-transport-https (1.0.4ubuntu6) ... Setting up openssl (1.0.1f-1ubuntu7) ... Setting up cpp-4.9 (4.9.1-8ubuntu1) ... Setting up cpp (4:4.9.1-1ubuntu1) ... Setting up libgcc-4.9-dev:i386 (4.9.1-8ubuntu1) ... Setting up gcc-4.9 (4.9.1-8ubuntu1) ... Setting up gcc (4:4.9.1-1ubuntu1) ... Setting up libstdc++-4.9-dev:i386 (4.9.1-8ubuntu1) ... Setting up g++-4.9 (4.9.1-8ubuntu1) ... Setting up g++ (4:4.9.1-1ubuntu1) ... Setting up pkg-create-dbgsym (0.65) ... Setting up perl-modules (5.20.0-4) ... Setting up perl (5.20.0-4) ... Setting up init-system-helpers (1.20ubuntu3) ... Setting up plymouth (0.9.0-0ubuntu3) ... update-initramfs: deferring update (trigger activated) Setting up libdpkg-perl (1.17.13ubuntu1) ... Setting up dpkg-dev (1.17.13ubuntu1) ... Processing triggers for libc-bin (2.19-4ubuntu2) ... Processing triggers for initramfs-tools (0.103ubuntu8) ... RUN: /usr/share/launchpad-buildd/slavebin/sbuild-package ['sbuild-package', 'PACKAGEBUILD-6155621', 'i386', 'utopic-proposed', '--nolog', '--batch', '--archive=ubuntu', '--dist=utopic-proposed', '-A', '--purpose=PRIMARY', '--architecture=i386', '--comp=multiverse', 'gmap_2014-07-04-1.dsc'] Initiating build PACKAGEBUILD-6155621 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 3.2.0-61-generic #93-Ubuntu SMP Fri May 2 21:31:50 UTC 2014 i686 Automatic build of gmap_2014-07-04-1 on roseapple by sbuild/i386 1.170.5 Build started at 20140824-0023 ****************************************************************************** gmap_2014-07-04-1.dsc exists in cwd ** Using build dependencies supplied by package: Build-Depends: debhelper (>= 9), autotools-dev Checking for already installed source dependencies... debhelper: missing autotools-dev: missing Checking for source dependency conflicts... /usr/bin/sudo /usr/bin/apt-get --purge $CHROOT_OPTIONS -q -y install debhelper autotools-dev Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: g++-4.8 libgnutls26 libgnutls28 libstdc++-4.8-dev Use 'apt-get autoremove' to remove them. The following extra packages will be installed: bsdmainutils dh-apparmor file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf Suggested packages: wamerican wordlist whois vacation dh-make apparmor-easyprof gettext-doc groff less www-browser libmail-box-perl Recommended packages: curl wget lynx-cur libasprintf-dev libgettextpo-dev libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl The following NEW packages will be installed: autotools-dev bsdmainutils debhelper dh-apparmor file gettext gettext-base groff-base intltool-debian libasprintf0c2 libcroco3 libglib2.0-0 libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf 0 upgraded, 18 newly installed, 0 to remove and 0 not upgraded. Need to get 6210 kB of archives. After this operation, 23.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu/ utopic/main libmagic1 i386 1:5.19-1ubuntu1 [201 kB] Get:2 http://ftpmaster.internal/ubuntu/ utopic/main libasprintf0c2 i386 0.18.3.2-1ubuntu1 [6360 B] Get:3 http://ftpmaster.internal/ubuntu/ utopic/main libglib2.0-0 i386 2.41.3-1 [1146 kB] Get:4 http://ftpmaster.internal/ubuntu/ utopic/main libpipeline1 i386 1.3.0-1 [23.5 kB] Get:5 http://ftpmaster.internal/ubuntu/ utopic/main libxml2 i386 2.9.1+dfsg1-4 [609 kB] Get:6 http://ftpmaster.internal/ubuntu/ utopic/main groff-base i386 1.22.2-6 [1034 kB] Get:7 http://ftpmaster.internal/ubuntu/ utopic/main bsdmainutils i386 9.0.5ubuntu1 [197 kB] Get:8 http://ftpmaster.internal/ubuntu/ utopic/main man-db i386 2.6.7.1-1 [851 kB] Get:9 http://ftpmaster.internal/ubuntu/ utopic/main libcroco3 i386 0.6.8-3 [89.2 kB] Get:10 http://ftpmaster.internal/ubuntu/ utopic/main libunistring0 i386 0.9.3-5ubuntu3 [272 kB] Get:11 http://ftpmaster.internal/ubuntu/ utopic/main file i386 1:5.19-1ubuntu1 [19.7 kB] Get:12 http://ftpmaster.internal/ubuntu/ utopic/main gettext-base i386 0.18.3.2-1ubuntu1 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu/ utopic/main autotools-dev all 20140510.1 [39.7 kB] Get:14 http://ftpmaster.internal/ubuntu/ utopic/main gettext i386 0.18.3.2-1ubuntu1 [816 kB] Get:15 http://ftpmaster.internal/ubuntu/ utopic/main intltool-debian all 0.35.0+20060710.1 [31.6 kB] Get:16 http://ftpmaster.internal/ubuntu/ utopic/main po-debconf all 1.0.16+nmu3 [207 kB] Get:17 http://ftpmaster.internal/ubuntu/ utopic-proposed/main dh-apparmor all 2.8.96~2541-0ubuntu3.1 [12.0 kB] Get:18 http://ftpmaster.internal/ubuntu/ utopic/main debhelper all 9.20140613ubuntu2 [607 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 6210 kB in 0s (16.4 MB/s) Selecting previously unselected package libmagic1:i386. (Reading database ... 12405 files and directories currently installed.) Preparing to unpack .../libmagic1_1%3a5.19-1ubuntu1_i386.deb ... Unpacking libmagic1:i386 (1:5.19-1ubuntu1) ... Selecting previously unselected package libasprintf0c2:i386. Preparing to unpack .../libasprintf0c2_0.18.3.2-1ubuntu1_i386.deb ... Unpacking libasprintf0c2:i386 (0.18.3.2-1ubuntu1) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../libglib2.0-0_2.41.3-1_i386.deb ... Unpacking libglib2.0-0:i386 (2.41.3-1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../libpipeline1_1.3.0-1_i386.deb ... Unpacking libpipeline1:i386 (1.3.0-1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../libxml2_2.9.1+dfsg1-4_i386.deb ... Unpacking libxml2:i386 (2.9.1+dfsg1-4) ... Selecting previously unselected package groff-base. Preparing to unpack .../groff-base_1.22.2-6_i386.deb ... Unpacking groff-base (1.22.2-6) ... 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Setting up libasprintf0c2:i386 (0.18.3.2-1ubuntu1) ... Setting up libglib2.0-0:i386 (2.41.3-1) ... No schema files found: doing nothing. Setting up libpipeline1:i386 (1.3.0-1) ... Setting up libxml2:i386 (2.9.1+dfsg1-4) ... Setting up groff-base (1.22.2-6) ... Setting up bsdmainutils (9.0.5ubuntu1) ... 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 man-db (2.6.7.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libcroco3:i386 (0.6.8-3) ... Setting up libunistring0:i386 (0.9.3-5ubuntu3) ... Setting up file (1:5.19-1ubuntu1) ... Setting up gettext-base (0.18.3.2-1ubuntu1) ... Setting up autotools-dev (20140510.1) ... Setting up gettext (0.18.3.2-1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.1) ... Setting up po-debconf (1.0.16+nmu3) ... Setting up dh-apparmor (2.8.96~2541-0ubuntu3.1) ... Setting up debhelper (9.20140613ubuntu2) ... Processing triggers for libc-bin (2.19-4ubuntu2) ... Checking correctness of source dependencies... Toolchain package versions: libc6-dev_2.19-4ubuntu2 make_4.0-8 dpkg-dev_1.17.13ubuntu1 gcc-4.9_4.9.1-8ubuntu1 g++-4.9_4.9.1-8ubuntu1 binutils_2.24.51.20140818-1ubuntu1 libstdc++-4.9-dev_4.9.1-8ubuntu1 libstdc++6_4.9.1-8ubuntu1 ------------------------------------------------------------------------------ dpkg-source: warning: -sn is not a valid option for Dpkg::Source::Package::V3::Quilt gpgv: Signature made Fri Jul 4 09:33:55 2014 UTC using RSA key ID 1B5228B0 gpgv: Can't check signature: public key not found dpkg-source: warning: failed to verify signature on ./gmap_2014-07-04-1.dsc dpkg-source: info: extracting gmap in gmap-2014-07-04 dpkg-source: info: unpacking gmap_2014-07-04.orig.tar.gz dpkg-source: info: unpacking gmap_2014-07-04-1.debian.tar.xz dpkg-source: info: applying install-data-local dpkg-buildpackage: source package gmap dpkg-buildpackage: source version 2014-07-04-1 dpkg-buildpackage: source distribution unstable dpkg-source --before-build gmap-2014-07-04 dpkg-buildpackage: host architecture i386 /usr/bin/fakeroot debian/rules clean dh clean --with autotools_dev dh_testdir dh_auto_clean dh_autotools-dev_restoreconfig dh_clean debian/rules build dh build --with autotools_dev dh_testdir dh_autotools-dev_updateconfig debian/rules override_dh_auto_configure make[1]: Entering directory '/build/buildd/gmap-2014-07-04' dh_auto_configure -- --enable-shared --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap configure: WARNING: unrecognized options: --disable-maintainer-mode checking package version... 2014-07-04 checking CONFIG_SITE... ./config.site loading script ./config.site checking CFLAGS... -g -O2 -fstack-protector-strong -Wformat -Werror=format-security checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking target system type... i686-pc-linux-gnu checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking dependency style of gcc... none checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc and cc understand -c and -o together... yes checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for ANSI C header files... (cached) yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking stddef.h usability... yes checking stddef.h presence... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 4 checking size of unsigned long long... 8 checking size of off_t... 8 checking for working alloca.h... yes checking for alloca... yes checking for _LARGEFILE_SOURCE value needed for large files... no checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... yes checking for sigaction... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for popcnt feature... not specified so enabled by default checking for __builtin_popcount... yes checking for __builtin_clz... yes checking for __builtin_ctz... yes checking for bsr instruction in assembly... yes checking whether sse2 is enabled... not specified so enabled by default checking compiler is defective and requires an immediate in sse2 shift commands... yes checking whether sse4.1 is enabled... not specified so enabled by default checking whether simd is enabled... not specified so enabled by default checking for x86 cpuid 0x00000001 output... 106a5:7100800:9ce3bd:bfebfbff checking whether mmx is enabled and supported... yes checking whether sse is enabled and supported... yes checking whether sse2 is enabled and supported... yes checking whether sse3 is enabled and supported... yes checking whether ssse3 is enabled and supported... yes checking whether sse4.1 is enabled and supported... yes checking whether sse4.2 is enabled and supported... yes checking whether avx is enabled and supported by processor... no checking whether popcnt is enabled and supported... yes checking for x86 cpuid 0x80000001 output... 0:0:1:28100000 checking whether lzcnt is enabled and supported... no checking for x86 cpuid 0x00000007 output... 0:0:0:0 checking whether avx2 is enabled and supported... no checking whether bmi1 is enabled and supported... no checking whether bmi2 is enabled and supported... no checking whether C compiler accepts -mmmx... yes checking whether C compiler accepts -msse... yes checking whether C compiler accepts -msse2... yes checking whether C compiler accepts -msse3... yes checking whether C compiler accepts -mssse3... yes checking whether C compiler accepts -msse4.1... yes checking whether C compiler accepts -msse4.2... yes checking for immintrin.h header file... no configure: WARNING: Your processor supports _popcnt instructions but your compiler cannot find immintrin.h. Will try another method. checking gmapdb... /var/cache/gmap checking MAX_READLENGTH... 300 checking for zlib support... enabled checking zlib.h usability... no checking zlib.h presence... no checking for zlib.h... no checking for gzopen in -lz... no checking for gzeof in -lz... no checking for gzgetc in -lz... no checking for gzgets in -lz... no checking for gzclose in -lz... no checking if zlib package is complete... no -- some components failed test checking for bzlib support... enabled checking bzlib.h usability... no checking bzlib.h presence... no checking for bzlib.h... no checking for BZ2_bzReadOpen in -lbz2... no checking for BZ2_bzRead in -lbz2... no checking for BZ2_bzReadClose in -lbz2... no checking if bzlib package is complete... no -- some components failed test checking for goby library... disabled configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_compress.pl config.status: creating util/gmap_uncompress.pl config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_reassemble.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode configure: WARNING: WARNING: Your C compiler does not know how to handle a particular form of the SSE2 shift commands, and must be somewhat old (probably gcc 4.1 or gcc 4.2). The configure script has therefore substituted alternate C code that your compiler can handle. However, for optimal performance, you may want to obtain a more recent C compiler and build the code with that. make[1]: Leaving directory '/build/buildd/gmap-2014-07-04' dh_auto_build make[1]: Entering directory '/build/buildd/gmap-2014-07-04' Making all in src make[2]: Entering directory '/build/buildd/gmap-2014-07-04/src' make all-am make[3]: Entering directory '/build/buildd/gmap-2014-07-04/src' gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-except.o `test -f 'except.c' || echo './'`except.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-assert.o `test -f 'assert.c' || echo './'`assert.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-mem.o `test -f 'mem.c' || echo './'`mem.c mem.c: In function 'Mem_alloc': mem.c:287:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to alloc %lu bytes\n",nbytes); ^ mem.c: In function 'Mem_alloc_keep': mem.c:360:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to alloc %lu bytes\n",nbytes); ^ mem.c: In function 'Mem_alloc_in': mem.c:424:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to alloc %lu bytes\n",nbytes); ^ mem.c: In function 'Mem_alloc_out': mem.c:488:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to alloc %lu bytes\n",nbytes); ^ mem.c: In function 'Mem_calloc': mem.c:528:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:528:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c:586:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:586:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c: In function 'Mem_calloc_keep': mem.c:619:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:619:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c:669:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:669:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c: In function 'Mem_calloc_in': mem.c:700:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:700:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c:743:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:743:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c: In function 'Mem_calloc_out': mem.c:773:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:773:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c:816:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to calloc %lu x %lu bytes\n",count,nbytes); ^ mem.c:816:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c: In function 'Mem_calloc_no_exception': mem.c:848:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to allocate %lu x %lu bytes\n",count,nbytes); ^ mem.c:848:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] mem.c: In function 'Mem_resize': mem.c:1132:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Failed attempt to realloc %lu bytes\n",nbytes); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-intlist.o `test -f 'intlist.c' || echo './'`intlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-list.o `test -f 'list.c' || echo './'`list.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-littleendian.o `test -f 'littleendian.c' || echo './'`littleendian.c littleendian.c: In function 'Littleendian_write_char': littleendian.c:14:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,1); ^ littleendian.c: In function 'Littleendian_write_uint': littleendian.c:27:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c: In function 'Littleendian_write_uint8': littleendian.c:44:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ littleendian.c: In function 'Littleendian_write_uint8_as_uint': littleendian.c:57:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ littleendian.c:63:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bigendian.o `test -f 'bigendian.c' || echo './'`bigendian.c bigendian.c: In function 'Bigendian_write_uint': bigendian.c:285:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,4); ^ bigendian.c: In function 'Bigendian_fileio_read_uint': bigendian.c:445:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,4); ^ bigendian.c: In function 'Bigendian_write_uint8': bigendian.c:527:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] write(fd,buf,8); ^ bigendian.c: In function 'Bigendian_fileio_read_uint8': bigendian.c:781:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(fd,buf,8); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-univinterval.o `test -f 'univinterval.c' || echo './'`univinterval.c univinterval.c: In function 'Univinterval_print': univinterval.c:71:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu %lu %d",this->low,this->high,this->type); ^ univinterval.c:71:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-interval.o `test -f 'interval.c' || echo './'`interval.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-uintlist.o `test -f 'uintlist.c' || echo './'`uintlist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stopwatch.o `test -f 'stopwatch.c' || echo './'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-access.o `test -f 'access.c' || echo './'`access.c access.c: In function 'Access_mmap_offset': access.c:509:8: warning: format '%ju' expects argument of type 'uintmax_t', but argument 5 has type 'size_t' [-Wformat=] fd,offset,length,errno,strerror(errno)); ^ access.c: In function 'Access_mmap_rw': access.c:579:8: warning: format '%ju' expects argument of type 'uintmax_t', but argument 3 has type 'size_t' [-Wformat=] *len,length,errno,strerror(errno)); ^ access.c: In function 'Access_mmap_offset_rw': access.c:642:8: warning: format '%ju' expects argument of type 'uintmax_t', but argument 4 has type 'size_t' [-Wformat=] offset,length,errno,strerror(errno)); ^ access.c: In function 'Access_mmap_and_preload': access.c:727:8: warning: format '%ju' expects argument of type 'uintmax_t', but argument 3 has type 'size_t' [-Wformat=] *len,length,errno,strerror(errno)); ^ access.c: In function 'Access_allocated': access.c:319:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),FREAD_BATCH,fp); ^ access.c:324:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(unsigned char),(*len)/eltsize - i,fp); ^ access.c:330:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),FREAD_BATCH,fp); ^ access.c:335:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT4),(*len)/eltsize - i,fp); ^ access.c:341:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),FREAD_BATCH,fp); ^ access.c:346:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(p,sizeof(UINT8),(*len)/eltsize - i,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-iit-read-univ.o `test -f 'iit-read-univ.c' || echo './'`iit-read-univ.c iit-read-univ.c: In function 'Univ_IIT_dump': iit-read-univ.c:509:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf(" %lu..%lu",startpos,endpos); ^ iit-read-univ.c:509:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_table': iit-read-univ.c:547:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos,endpos); ^ iit-read-univ.c:547:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:549:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1,endpos+1); ^ iit-read-univ.c:549:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'Univ_IIT_dump_contigs': iit-read-univ.c:706:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:706:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:712:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",endpos+1U,startpos+1U); ^ iit-read-univ.c:712:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c:715:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'Univcoord_T' [-Wformat=] printf("%lu..%lu\t",startpos+1U,endpos+1U); ^ iit-read-univ.c:715:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] iit-read-univ.c: In function 'read_words_debug': iit-read-univ.c:1089:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"label_length: %lu\n",new->label_length); ^ iit-read-univ.c:1111:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"annot_length: %lu\n",new->annot_length); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_tree_univ': littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:885:2: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:887:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].a),fp); ^ littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:888:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].b),fp); ^ littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:889:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].leftindex),fp); ^ littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:890:2: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->nodes[i].rightindex),fp); ^ iit-read-univ.c: In function 'read_intervals_univ': littleendian.h:25:27: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:932:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].low),fp); ^ littleendian.h:25:27: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read-univ.c:933:7: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&(new->intervals[i].high),fp); ^ littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:934:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:939:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:941:7: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&uint4,fp); ^ littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read-univ.c:943:7: note: in expansion of macro 'FREAD_INT' FREAD_INT(&(new->intervals[i].type),fp); ^ iit-read-univ.c: In function 'read_words': littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1003:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read-univ.c: In function 'read_annotations': iit-read-univ.c:1225:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read-univ.c:1229:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1233:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read-univ.c:1237:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read-univ.c:1241:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read-univ.c:11:0: iit-read-univ.c: In function 'read_words_debug': littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read-univ.c:1085:3: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-iit-read.o `test -f 'iit-read.c' || echo './'`iit-read.c iit-read.c: In function 'read_tree': iit-read.c:1548:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' [-Wformat=] fprintf(stderr,"IIT file %s appears to be truncated. items_read = %lu\n",filename,items_read); ^ iit-read.c: In function 'read_words_debug': iit-read.c:1981:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"label_length: %lu\n",new->label_length); ^ iit-read.c:2011:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"annot_length: %lu\n",new->annot_length); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_read_divint': littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2313:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&version,fp); ^ iit-read.c: In function 'IIT_read': littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2571:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_tree': iit-read.c:1624:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); ^ iit-read.c:1625:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); ^ iit-read.c:1626:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); ^ iit-read.c:1627:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); ^ iit-read.c:1628:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); ^ iit-read.c: In function 'read_intervals': iit-read.c:1709:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); ^ iit-read.c:1710:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); ^ iit-read.c:1712:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); ^ iit-read.c:1716:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'read_words': littleendian.h:25:27: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1821:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1827:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ iit-read.c: In function 'read_annotations': iit-read.c:2208:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2212:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->values,new->value_length*sizeof(char)); ^ iit-read.c:2217:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); ^ iit-read.c:2223:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2228:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2239:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->labels,new->label_length*sizeof(char)); ^ iit-read.c:2245:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); ^ iit-read.c:2250:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); ^ iit-read.c:2261:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(new->fd,new->annotations,new->annot_length*sizeof(char)); ^ In file included from iit-read.c:12:0: iit-read.c: In function 'IIT_debug': littleendian.h:20:25: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) ^ iit-read.c:2982:5: note: in expansion of macro 'FREAD_INT' FREAD_INT(&new->version,fp); ^ iit-read.c: In function 'read_words_debug': littleendian.h:25:27: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) ^ iit-read.c:1965:5: note: in expansion of macro 'FREAD_UINT8' FREAD_UINT8(&length8,fp); ^ littleendian.h:21:26: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) ^ iit-read.c:1970:5: note: in expansion of macro 'FREAD_UINT' FREAD_UINT(&length,fp); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-md5.o `test -f 'md5.c' || echo './'`md5.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bzip2.o `test -f 'bzip2.c' || echo './'`bzip2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-sequence.o `test -f 'sequence.c' || echo './'`sequence.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-reader.o `test -f 'reader.c' || echo './'`reader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genomicpos.o `test -f 'genomicpos.c' || echo './'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-compress.o `test -f 'compress.c' || echo './'`compress.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-compress-write.o `test -f 'compress-write.c' || echo './'`compress-write.c compress-write.c: In function 'fill_buffer': compress-write.c:73:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] printf("Parsing error; saw non-ACGT flag plus %c at position %lu\n",Buffer[i],position+i); ^ compress-write.c: In function 'write_compressed_one': compress-write.c:252:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ compress-write.c: In function 'put_compressed_one': compress-write.c:300:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] Buffer[i],position+i); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gbuffer.o `test -f 'gbuffer.c' || echo './'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome.o `test -f 'genome.c' || echo './'`genome.c genome.c: In function 'Genome_fill_buffer_simple': genome.c:10488:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10488:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10611:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"left %lu + length %u < left %lu\n",left,length,left); ^ genome.c:10611:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome.c: In function 'fill_buffer': genome.c:10381:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'genomecomp_read_current': genome.c:379:3: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,buffer,4); ^ genome.c: In function 'Genome_fill_buffer_simple': genome.c:10516:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,length); ^ genome.c: In function 'Genome_fill_buffer_simple_alt': genome.c:10636:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(genomealt->fd,gbuffer1,length); ^ genome.c: In function 'Genome_get_char': genome.c:10805:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer1,/*length*/1); ^ genome.c: In function 'Genome_ntcounts': genome.c:11106:7: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(this->fd,gbuffer,length); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-popcount.o `test -f 'popcount.c' || echo './'`popcount.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome128_hr.o `test -f 'genome128_hr.c' || echo './'`genome128_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome_sites.o `test -f 'genome_sites.c' || echo './'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-genome-write.o `test -f 'genome-write.c' || echo './'`genome-write.c genome-write.c: In function 'genome_write_file': genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:253:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:256:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_writeraw_file': genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:430:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:433:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'fill_circular_chromosomes': genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Chromosome %s is circular. Copying %lu..%lu to %lu..%lu\n",chr,orig_startpos+1U,orig_endpos+1U,alias_startpos+1U,alias_endpos+1U); ^ genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'Univcoord_T' [-Wformat=] genome-write.c:595:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'genome_write_memory': genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition,endposition,fileroot); ^ genome-write.c:643:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Univcoord_T' [-Wformat=] accession,startposition+1U,endposition+1U,fileroot); ^ genome-write.c:646:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'Univcoord_T' [-Wformat=] genome-write.c: In function 'Genome_write_comp32': genome-write.c:787:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Univcoord_T' [-Wformat=] fprintf(stderr,"Genome length is %lu nt\n",genomelength); ^ genome-write.c:826:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' [-Wformat=] fprintf(stderr,"Trying to allocate %lu*%lu bytes of memory...",nuint4,sizeof(Genomecomp_T)); ^ genome-write.c:826:5: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=] gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bitpack64-read.o `test -f 'bitpack64-read.c' || echo './'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo './'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-indexdb.o `test -f 'indexdb.c' || echo './'`indexdb.c indexdb.c: In function 'Indexdb_get_filenames_bitpack': indexdb.c:758:5: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'int' [-Wformat=] idx_filesuffix,filename,q-p,BASE_KMER_SAMPLING); ^ indexdb.c: In function 'Indexdb_new_genome': indexdb.c:1179:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Positionsptr_T' [-Wformat=] filenames->positions_low_filename,end0*sizeof(UINT4),filesize); ^ indexdb.c:1179:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'off_t' [-Wformat=] indexdb.c:1309:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'Positionsptr_T' [-Wformat=] filenames->positions_low_filename,end0*sizeof(UINT4),filesize); ^ indexdb.c:1309:3: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'off_t' [-Wformat=] indexdb.c: In function 'positions_move_absolute_1': indexdb.c:1524:6: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'off_t' [-Wformat=] ptr,sizeof(unsigned char),offset); ^ indexdb.c:1524:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=] indexdb.c:1524:6: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'off_t' [-Wformat=] indexdb.c: In function 'positions_move_absolute_4': indexdb.c:1537:6: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'off_t' [-Wformat=] ptr,sizeof(UINT4),offset); ^ indexdb.c:1537:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=] indexdb.c:1537:6: warning: format '%ld' expects argument of type 'long int', but argument 5 has type 'off_t' [-Wformat=] indexdb.c: In function 'Indexdb_offsets_from_bitpack': indexdb.c:1747:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'Oligospace_T' [-Wformat=] ); ^ indexdb.c: In function 'positions_read_multiple': indexdb.c:1647:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-indexdb_hr.o `test -f 'indexdb_hr.c' || echo './'`indexdb_hr.c indexdb_hr.c: In function 'positions_move_absolute': indexdb_hr.c:594:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=] ptr,sizeof(Univcoord_T),(long unsigned int) offset); ^ indexdb_hr.c: In function 'positions_read_multiple': indexdb_hr.c:624:5: warning: ignoring return value of 'read', declared with attribute warn_unused_result [-Wunused-result] read(positions_fd,buffer,4); ^ gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-oligo.o `test -f 'oligo.c' || echo './'`oligo.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-block.o `test -f 'block.c' || echo './'`block.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-chrom.o `test -f 'chrom.c' || echo './'`chrom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-segmentpos.o `test -f 'segmentpos.c' || echo './'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-chrnum.o `test -f 'chrnum.c' || echo './'`chrnum.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-uinttable.o `test -f 'uinttable.c' || echo './'`uinttable.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gregion.o `test -f 'gregion.c' || echo './'`gregion.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-match.o `test -f 'match.c' || echo './'`match.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-matchpool.o `test -f 'matchpool.c' || echo './'`matchpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-diagnostic.o `test -f 'diagnostic.c' || echo './'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stage1.o `test -f 'stage1.c' || echo './'`stage1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-diag.o `test -f 'diag.c' || echo './'`diag.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-diagpool.o `test -f 'diagpool.c' || echo './'`diagpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-cmet.o `test -f 'cmet.c' || echo './'`cmet.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-atoi.o `test -f 'atoi.c' || echo './'`atoi.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-orderstat.o `test -f 'orderstat.c' || echo './'`orderstat.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo './'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-intron.o `test -f 'intron.c' || echo './'`intron.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-maxent.o `test -f 'maxent.c' || echo './'`maxent.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-maxent_hr.o `test -f 'maxent_hr.c' || echo './'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-pair.o `test -f 'pair.c' || echo './'`pair.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-pairpool.o `test -f 'pairpool.c' || echo './'`pairpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-cellpool.o `test -f 'cellpool.c' || echo './'`cellpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stage2.o `test -f 'stage2.c' || echo './'`stage2.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-doublelist.o `test -f 'doublelist.c' || echo './'`doublelist.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-smooth.o `test -f 'smooth.c' || echo './'`smooth.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-splicestringpool.o `test -f 'splicestringpool.c' || echo './'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-splicetrie_build.o `test -f 'splicetrie_build.c' || echo './'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-splicetrie.o `test -f 'splicetrie.c' || echo './'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-boyer-moore.o `test -f 'boyer-moore.c' || echo './'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog.o `test -f 'dynprog.c' || echo './'`dynprog.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_simd.o `test -f 'dynprog_simd.c' || echo './'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_single.o `test -f 'dynprog_single.c' || echo './'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_genome.o `test -f 'dynprog_genome.c' || echo './'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo './'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-dynprog_end.o `test -f 'dynprog_end.c' || echo './'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-translation.o `test -f 'translation.c' || echo './'`translation.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-pbinom.o `test -f 'pbinom.c' || echo './'`pbinom.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-changepoint.o `test -f 'changepoint.c' || echo './'`changepoint.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-stage3.o `test -f 'stage3.c' || echo './'`stage3.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-request.o `test -f 'request.c' || echo './'`request.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-result.o `test -f 'result.c' || echo './'`result.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-inbuffer.o `test -f 'inbuffer.c' || echo './'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-samheader.o `test -f 'samheader.c' || echo './'`samheader.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-outbuffer.o `test -f 'outbuffer.c' || echo './'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-chimera.o `test -f 'chimera.c' || echo './'`chimera.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-datadir.o `test -f 'datadir.c' || echo './'`datadir.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-getopt.o `test -f 'getopt.c' || echo './'`getopt.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-getopt1.o `test -f 'getopt1.c' || echo './'`getopt1.c gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o gmap-gmap.o `test -f 'gmap.c' || echo './'`gmap.c gmap.c: In function 'print_program_version': gmap.c:654:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=] sizeof(off_t),sizeof(size_t),sizeof(unsigned int),sizeof(long int)); ^ gmap.c:654:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=] gmap.c:654:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=] gmap.c:654:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 6 has type 'unsigned int' [-Wformat=] /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lm libtool: link: gcc -pthread -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -DTARGET=\"i686-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -o gmap gmap-except.o gmap-assert.o gmap-mem.o gmap-intlist.o gmap-list.o gmap-littleendian.o gmap-bigendian.o gmap-univinterval.o gmap-interval.o gmap-uintlist.o gmap-stopwatch.o gmap-access.o gmap-iit-read-univ.o gmap-iit-read.o gmap-md5.o gmap-bzip2.o gmap-sequence.o gmap-reader.o gmap-genomicpos.o gmap-compress.o gmap-compress-write.o gmap-gbuffer.o gmap-genome.o gmap-popcount.o gmap-genome128_hr.o gmap-genome_sites.o gmap-genome-write.o gmap-bitpack64-read.o gmap-bitpack64-readtwo.o gmap-indexdb.o gmap-indexdb_hr.o gmap-oligo.o gmap-block.o gmap-chrom.o gmap-segmentpos.o gmap-chrnum.o gmap-uinttable.o gmap-gregion.o gmap-match.o gmap-matchpool.o gmap-diagnostic.o gmap-stage1.o gmap-diag.o gmap-diagpool.o gmap-cmet.o gmap-atoi.o gmap-orderstat.o gmap-oligoindex_hr.o gmap-intron.o gmap-maxent.o gmap-maxent_hr.o gmap-pair.o gmap-pairpool.o gmap-cellpool.o gmap-stage2.o gmap-doublelist.o gmap-smooth.o gmap-splicestringpool.o gmap-splicetrie_build.o gmap-splicetrie.o gmap-boyer-moore.o gmap-dynprog.o gmap-dynprog_simd.o gmap-dynprog_single.o gmap-dynprog_genome.o gmap-dynprog_cdna.o gmap-dynprog_end.o gmap-translation.o gmap-pbinom.o gmap-changepoint.o gmap-stage3.o gmap-request.o gmap-result.o gmap-inbuffer.o gmap-samheader.o gmap-outbuffer.o gmap-chimera.o gmap-datadir.o gmap-getopt.o gmap-getopt1.o gmap-gmap.o -lm -pthread gmap-genome128_hr.o: In function `count_trailing_zeroes': /build/buildd/gmap-2014-07-04/src/genome128_hr.c:18369: undefined reference to `_mm_extract_epi64' /build/buildd/gmap-2014-07-04/src/genome128_hr.c:18372: undefined reference to `_mm_extract_epi64' gmap-genome128_hr.o: In function `count_leading_zeroes': /build/buildd/gmap-2014-07-04/src/genome128_hr.c:18322: undefined reference to `_mm_extract_epi64' /build/buildd/gmap-2014-07-04/src/genome128_hr.c:18325: undefined reference to `_mm_extract_epi64' gmap-genome128_hr.o: In function `count_mismatches_limit_snps': /build/buildd/gmap-2014-07-04/src/genome128_hr.c:19739: undefined reference to `_mm_extract_epi64' gmap-genome128_hr.o:/build/buildd/gmap-2014-07-04/src/genome128_hr.c:19739: more undefined references to `_mm_extract_epi64' follow collect2: error: ld returned 1 exit status Makefile:1212: recipe for target 'gmap' failed make[3]: *** [gmap] Error 1 make[3]: Leaving directory '/build/buildd/gmap-2014-07-04/src' Makefile:1124: recipe for target 'all' failed make[2]: *** [all] Error 2 make[2]: Leaving directory '/build/buildd/gmap-2014-07-04/src' Makefile:280: recipe for target 'all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory '/build/buildd/gmap-2014-07-04' dh_auto_build: make -j1 returned exit code 2 debian/rules:7: recipe for target 'build' failed make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 ****************************************************************************** Build finished at 20140824-0024 FAILED [dpkg-buildpackage died] ****************************************************************************** Finished at 20140824-0024 Build needed 00:00:56, 40144k disk space RUN: /usr/share/launchpad-buildd/slavebin/scan-for-processes ['scan-for-processes', 'PACKAGEBUILD-6155621'] Scanning for processes to kill in build /home/buildd/build-PACKAGEBUILD-6155621/chroot-autobuild... RUN: /usr/share/launchpad-buildd/slavebin/umount-chroot ['umount-chroot', 'PACKAGEBUILD-6155621'] Unmounting chroot for build PACKAGEBUILD-6155621... RUN: /usr/share/launchpad-buildd/slavebin/remove-build ['remove-build', 'PACKAGEBUILD-6155621'] Removing build PACKAGEBUILD-6155621