https://launchpad.net/ubuntu/+source/genomethreader/1.7.3+dfsg-10build1/+build/27950568 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos03-amd64-031 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 x86_64 Buildd toolchain package versions: launchpad-buildd_236~650~ubuntu20.04.1 python3-lpbuildd_236~650~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.11 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1.1. Syncing the system clock with the buildd NTP service... 22 Mar 16:18:02 ntpdate[1876]: adjust time server 10.211.37.1 offset -0.001469 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27950568 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27950568 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27950568 Starting target for build PACKAGEBUILD-27950568 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27950568 'deb http://ftpmaster.internal/ubuntu noble main universe' 'deb http://ftpmaster.internal/ubuntu noble-security main universe' 'deb http://ftpmaster.internal/ubuntu noble-updates main universe' 'deb http://ftpmaster.internal/ubuntu noble-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-27950568 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27950568 Updating target for build PACKAGEBUILD-27950568 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1436 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [518 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.3 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6039 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [697 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [239 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4251 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [1553 kB] Fetched 30.6 MB in 5s (5982 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libnettle8* libnpth0* libreadline8* libssl3* libtirpc3* usrmerge* The following NEW packages will be installed: cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64 libgdbm-compat4t64 libgdbm6t64 libnettle8t64 libnpth0t64 libperl5.38t64 libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 perl-modules-5.38 The following packages have been kept back: apt apt-utils optipng The following packages will be upgraded: base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot g++ g++-13 gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libip4tc2 libitm1 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0 liblzma5 libmd0 libmount1 libncursesw6 libnsl-dev libnsl2 libnss-nisplus libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpng16-16 libproc2-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtext-charwidth-perl libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pinentry-curses procps psmisc readline-common sed sensible-utils systemd systemd-dev systemd-sysv sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 157 upgraded, 20 newly installed, 11 to remove and 3 not upgraded. Need to get 117 MB of archives. After this operation, 78.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl-dev amd64 1.3.0-3build2 [70.5 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-common all 1.3.4+ds-1.1 [8018 B] Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1 [193 kB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnss-nisplus amd64 1.3-5 [22.3 kB] Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1 [82.5 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgssapi-krb5-2 amd64 1.20.1-5.1ubuntu1 [142 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5-3 amd64 1.20.1-5.1ubuntu1 [347 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libk5crypto3 amd64 1.20.1-5.1ubuntu1 [81.7 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkrb5support0 amd64 1.20.1-5.1ubuntu1 [33.5 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libacl1 amd64 2.3.2-1 [16.7 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapparmor1 amd64 4.0.0-beta3-0ubuntu2 [49.4 kB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit-common all 1:3.1.2-2.1 [5674 B] Get:16 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcap-ng0 amd64 0.8.4-2build1 [15.1 kB] Get:17 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libaudit1 amd64 1:3.1.2-2.1 [46.8 kB] Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libblkid1 amd64 2.39.3-9ubuntu2 [122 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libcap2 amd64 1:2.66-5ubuntu1 [29.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt1 amd64 1:4.4.36-4 [95.3 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libgcrypt20 amd64 1.10.3-2 [532 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblzma5 amd64 5.6.0-0.2 [157 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libkmod2 amd64 31+20240202-2ubuntu4 [51.5 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libselinux1 amd64 3.5-2ubuntu1 [79.5 kB] Get:29 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmount1 amd64 2.39.3-9ubuntu2 [134 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-modules-5.38 all 5.38.2-3.2 [3110 kB] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [738 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgdbm6t64 amd64 1.23-5.1 [34.4 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgdbm-compat4t64 amd64 1.23-5.1 [6700 B] Get:34 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libperl5.38t64 amd64 5.38.2-3.2 [4871 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl amd64 5.38.2-3.2 [231 kB] Get:36 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 perl-base amd64 5.38.2-3.2 [1823 kB] Get:37 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblocale-gettext-perl amd64 1.07-6ubuntu3 [15.7 kB] Get:38 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-iconv-perl amd64 1.7-8build2 [13.5 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtext-charwidth-perl amd64 0.04-11build2 [9322 B] Get:40 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc6 amd64 2.39-0ubuntu6 [3262 kB] Get:41 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libc-bin amd64 2.39-0ubuntu6 [682 kB] Get:42 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 openssl amd64 3.0.13-0ubuntu2 [1002 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255.4-1ubuntu5 [2067 kB] Get:44 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcryptsetup12 amd64 2:2.7.0-1ubuntu2 [266 kB] Get:45 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libssl3t64 amd64 3.0.13-0ubuntu2 [1936 kB] Get:46 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255.4-1ubuntu5 [103 kB] Get:47 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255.4-1ubuntu5 [11.9 kB] Get:48 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255.4-1ubuntu5 [3470 kB] Get:49 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255.4-1ubuntu5 [428 kB] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules-bin amd64 1.5.3-5ubuntu3 [51.9 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-modules amd64 1.5.3-5ubuntu3 [279 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 bzip2 amd64 1.0.8-5ubuntu1 [34.6 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-1.0 amd64 1.0.8-5ubuntu1 [34.4 kB] Get:54 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3.1ubuntu1 [62.7 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 debconf-i18n all 1.5.86 [205 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 debconf all 1.5.86 [124 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam0g amd64 1.5.3-5ubuntu3 [67.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.5-1ubuntu2 [50.3 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255.4-1ubuntu5 [174 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdevmapper1.02.1 amd64 2:1.02.185-3ubuntu2 [139 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libuuid1 amd64 2.39.3-9ubuntu2 [35.0 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfdisk1 amd64 2.39.3-9ubuntu2 [146 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 mount amd64 2.39.3-9ubuntu2 [118 kB] Get:65 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcom-err2 amd64 1.47.0-2.4~exp1ubuntu2 [22.7 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libkeyutils1 amd64 1.6.3-3 [9386 B] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnsl2 amd64 1.3.0-3build2 [41.3 kB] Get:68 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.8.0-20.20 [1597 kB] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-14-base amd64 14-20240315-1ubuntu1 [47.0 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-s1 amd64 14-20240315-1ubuntu1 [78.1 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu7 [74.2 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.17 [89.8 kB] Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu2 [794 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdutils amd64 1:2.39.3-9ubuntu2 [94.9 kB] Get:75 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 coreutils amd64 9.4-3ubuntu3 [1411 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-4ubuntu1 [299 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.3-1ubuntu1 [996 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libnettle8t64 amd64 3.9.1-2.2 [181 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++6 amd64 14-20240315-1ubuntu1 [795 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0t64 amd64 2.7.13ubuntu1 [985 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.35+dfsg-3 [253 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg amd64 1.22.6ubuntu4 [1283 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 dash amd64 0.5.12-6ubuntu4 [89.8 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-4 [176 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 gzip amd64 1.12-1ubuntu2 [98.8 kB] Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 hostname amd64 3.23+nmu2ubuntu1 [11.0 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-4ubuntu1 [201 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20240113-1ubuntu1 [188 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 sed amd64 4.9-2 [204 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 util-linux amd64 2.39.3-9ubuntu2 [1127 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdebconfclient0 amd64 0.271ubuntu2 [11.3 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20240113-1ubuntu1 [25.4 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-6ubuntu2 [34.1 kB] Get:99 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 logsave amd64 1.47.0-2.4~exp1ubuntu2 [22.4 kB] Get:100 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libext2fs2t64 amd64 1.47.0-2.4~exp1ubuntu2 [221 kB] Get:101 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 e2fsprogs amd64 1.47.0-2.4~exp1ubuntu2 [601 kB] Get:102 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg amd64 2.4.4-2ubuntu15 [565 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libreadline8t64 amd64 8.2-3.1 [153 kB] Get:104 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgconf amd64 2.4.4-2ubuntu15 [103 kB] Get:105 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpg-agent amd64 2.4.4-2ubuntu15 [227 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libnpth0t64 amd64 1.6-3.1 [8316 B] Get:107 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 readline-common all 8.2-3.1 [56.4 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20240113-1ubuntu1 [148 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20240113-1ubuntu1 [108 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:111 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsmartcols1 amd64 2.39.3-9ubuntu2 [64.4 kB] Get:112 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 uuid-runtime amd64 2.39.3-9ubuntu2 [33.0 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libattr1 amd64 1:2.5.2-1 [11.4 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libmd0 amd64 1.1.0-2 [27.1 kB] Get:115 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpam-runtime all 1.5.3-5ubuntu3 [40.8 kB] Get:116 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage-common all 3.5-1build4 [10.1 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:118 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsemanage2 amd64 3.5-1build4 [93.1 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-4ubuntu1 [844 kB] Get:120 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gpgv amd64 2.4.4-2ubuntu15 [157 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.6-1 [24.7 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.7-2 [66.0 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:124 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13 amd64 13.2.0-19ubuntu1 [14.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13 amd64 13.2.0-19ubuntu1 [477 kB] Get:126 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13 amd64 13.2.0-19ubuntu1 [1032 B] Get:127 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-19ubuntu1 [11.2 MB] Get:128 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcc1-0 amd64 14-20240315-1ubuntu1 [47.7 kB] Get:129 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgprofng0 amd64 2.42-4ubuntu1 [851 kB] Get:130 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libctf0 amd64 2.42-4ubuntu1 [94.6 kB] Get:131 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libctf-nobfd0 amd64 2.42-4ubuntu1 [97.1 kB] Get:132 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsframe1 amd64 2.42-4ubuntu1 [14.8 kB] Get:133 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 binutils-x86-64-linux-gnu amd64 2.42-4ubuntu1 [2470 kB] Get:134 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbinutils amd64 2.42-4ubuntu1 [573 kB] Get:135 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 binutils amd64 2.42-4ubuntu1 [18.0 kB] Get:136 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 binutils-common amd64 2.42-4ubuntu1 [239 kB] Get:137 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libstdc++-13-dev amd64 13.2.0-19ubuntu1 [2342 kB] Get:138 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgomp1 amd64 14-20240315-1ubuntu1 [147 kB] Get:139 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libitm1 amd64 14-20240315-1ubuntu1 [28.9 kB] Get:140 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libatomic1 amd64 14-20240315-1ubuntu1 [10.4 kB] Get:141 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libasan8 amd64 14-20240315-1ubuntu1 [3026 kB] Get:142 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 liblsan0 amd64 14-20240315-1ubuntu1 [1310 kB] Get:143 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libgcc-13-dev amd64 13.2.0-19ubuntu1 [2687 kB] Get:144 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libtsan2 amd64 14-20240315-1ubuntu1 [2732 kB] Get:145 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libubsan1 amd64 14-20240315-1ubuntu1 [1172 kB] Get:146 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libhwasan0 amd64 14-20240315-1ubuntu1 [1629 kB] Get:147 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libquadmath0 amd64 14-20240315-1ubuntu1 [155 kB] Get:148 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-19ubuntu1 [21.8 MB] Get:149 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-19ubuntu1 [12.5 MB] Get:150 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 gcc-13-base amd64 13.2.0-19ubuntu1 [47.7 kB] Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-4ubuntu1 [59.2 kB] Get:152 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libss2 amd64 1.47.0-2.4~exp1ubuntu2 [17.0 kB] Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20240123-1 [127 kB] Get:154 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-4ubuntu1 [708 kB] Get:155 http://ftpmaster.internal/ubuntu noble/main amd64 sensible-utils all 0.0.22 [22.5 kB] Get:156 http://ftpmaster.internal/ubuntu noble/main amd64 ca-certificates all 20240203 [159 kB] Get:157 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 krb5-locales all 1.20.1-5.1ubuntu1 [13.9 kB] Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 libip4tc2 amd64 1.8.10-3ubuntu1 [23.3 kB] Get:159 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsqlite3-0 amd64 3.45.1-1ubuntu1 [701 kB] Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 tzdata all 2024a-1ubuntu1 [273 kB] Get:161 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:162 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 bsdextrautils amd64 2.39.3-9ubuntu2 [73.6 kB] Get:163 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.43-1 [186 kB] Get:164 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 psmisc amd64 23.7-1 [179 kB] Get:165 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 xz-utils amd64 5.6.0-0.2 [272 kB] Get:166 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] Get:167 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] Get:168 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] Get:169 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] Get:172 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dpkg-dev all 1.22.6ubuntu4 [1074 kB] Get:173 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdpkg-perl all 1.22.6ubuntu4 [268 kB] Get:174 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 47 [12.4 kB] Get:175 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.33-1 [32.4 kB] Get:176 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.33-1 [67.2 kB] Get:177 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 pinentry-curses amd64 1.2.1-3ubuntu4 [35.2 kB] Preconfiguring packages ... 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Setting up g++-13 (13.2.0-19ubuntu1) ... Setting up g++ (4:13.2.0-7ubuntu1) ... Processing triggers for libc-bin (2.39-0ubuntu6) ... Processing triggers for debianutils (5.17) ... (Reading database ... 15762 files and directories currently installed.) Purging configuration files for libssl3:amd64 (3.0.10-1ubuntu2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27950568 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27950568 --arch=amd64 --dist=noble-proposed --nolog -A genomethreader_1.7.3+dfsg-10build1.dsc Initiating build PACKAGEBUILD-27950568 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on bos03-amd64-031.buildd +==============================================================================+ | genomethreader 1.7.3+dfsg-10build1 (amd64) Fri, 22 Mar 2024 16:19:09 +0000 | +==============================================================================+ Package: genomethreader Version: 1.7.3+dfsg-10build1 Source Version: 1.7.3+dfsg-10build1 Distribution: noble-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-27950568/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/genomethreader-Jl6tYD/resolver-2Ci9bA' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- genomethreader_1.7.3+dfsg-10build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/genomethreader-Jl6tYD/genomethreader-1.7.3+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/genomethreader-Jl6tYD' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, libvmatch-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, liblua5.1-0-dev, libtre-dev, asciidoctor, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, libvmatch-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, liblua5.1-0-dev, libtre-dev, asciidoctor, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [428 B] Get:5 copy:/<>/apt_archive ./ Packages [509 B] Fetched 1894 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: apt-utils bash-completion debconf-i18n krb5-locales libgpg-error-l10n libgpm2 libgssapi-krb5-2 libip4tc2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev libtirpc3t64 libunistring2 perl-modules-5.36 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono genometools genometools-common gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev libcairo2 libdatrie1 libdebhelper-perl libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgenometools0-dev libgenometools0t64 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libicu74 liblua5.1-0 liblua5.1-0-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpipeline1 libpixman-1-0 libpng16-16t64 libreadline-dev libruby libruby3.2 libsub-override-perl libthai-data libthai0 libtool libtre-dev libtre5 libuchardet0 libvmatch-dev libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 libyaml-0-2 lua-filesystem lua-lpeg lua-md5 m4 man-db po-debconf rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 rubygems-integration zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff low-memory-monitor ncurses-doc readline-doc libtool-doc gfortran | fortran95-compiler gcj-jdk tre-agrep m4-doc apparmor less www-browser libmail-box-perl ri ruby-dev bundler Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs pkg-config libtool-bin libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following packages will be REMOVED: libpng16-16* The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono genometools genometools-common gettext gettext-base groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev libcairo2 libdatrie1 libdebhelper-perl libdw1t64 libedit2 libelf1t64 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0 libgenometools0-dev libgenometools0t64 libglib2.0-0t64 libgraphite2-3 libharfbuzz0b libicu74 liblua5.1-0 liblua5.1-0-dev libmagic-mgc libmagic1t64 libncurses-dev libncurses6 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpipeline1 libpixman-1-0 libpng16-16t64 libreadline-dev libruby libruby3.2 libsub-override-perl libthai-data libthai0 libtool libtre-dev libtre5 libuchardet0 libvmatch-dev libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxrender1 libyaml-0-2 lua-filesystem lua-lpeg lua-md5 m4 man-db po-debconf rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.2 rubygems-integration sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 95 newly installed, 1 to remove and 3 not upgraded. Need to get 37.8 MB of archives. After this operation, 139 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [726 B] Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpng16-16t64 amd64 1.6.43-3 [187 kB] Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbsd0 amd64 0.12.1-1 [41.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libexpat1 amd64 2.6.1-2 [86.9 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libfribidi0 amd64 1.0.13-3 [26.1 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libicu74 amd64 74.2-1ubuntu1 [10.9 MB] Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.3ubuntu2 [762 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libyaml-0-2 amd64 0.2.5-1 [52.8 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmagic-mgc amd64 1:5.45-3 [307 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmagic1t64 amd64 1:5.45-3 [87.2 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 file amd64 1:5.45-3 [22.0 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-14ubuntu1 [38.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.8-1 [75.3 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 groff-base amd64 1.23.0-3build1 [1020 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libedit2 amd64 3.1-20230828-1 [95.8 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses6 amd64 6.4+20240113-1ubuntu1 [112 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libxau6 amd64 1:1.0.9-1build5 [7634 B] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu5 [10.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb1 amd64 1.15-1 [48.0 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-data all 2:1.8.7-1 [115 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libx11-6 amd64 2:1.8.7-1 [642 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libxext6 amd64 2:1.3.4-1build1 [31.8 kB] Get:24 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 man-db amd64 2.12.0-3build4 [1230 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 rubygems-integration all 1.18 [5336 B] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 rake all 13.0.6-3 [61.6 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-net-telnet all 0.2.0-1 [13.3 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-webrick all 1.8.1-1 [52.3 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] Get:30 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libruby amd64 1:3.2~ubuntu1 [4694 B] Get:31 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ruby-sdbm amd64 1.0.0-5build4 [16.2 kB] Get:32 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libruby3.2 amd64 3.2.3-1build2 [5339 kB] Get:33 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ruby3.2 amd64 3.2.3-1build2 [50.7 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-rubygems all 3.4.20-1 [238 kB] Get:35 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 ruby amd64 1:3.2~ubuntu1 [3466 B] Get:36 http://ftpmaster.internal/ubuntu noble/universe amd64 ruby-asciidoctor all 2.0.20-1 [174 kB] Get:37 http://ftpmaster.internal/ubuntu noble/universe amd64 asciidoctor all 2.0.20-1 [44.2 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3ubuntu1 [558 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14ubuntu1 [422 kB] Get:43 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:50 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libelf1t64 amd64 0.190-1.1build2 [57.5 kB] Get:51 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libdw1t64 amd64 0.190-1.1build2 [261 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:53 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 dwz amd64 0.15-1build5 [115 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14ubuntu1 [864 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:57 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 debhelper all 13.14.1ubuntu5 [869 kB] Get:58 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libbrotli1 amd64 1.1.0-2build1 [331 kB] Get:59 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfreetype6 amd64 2.13.2+dfsg-1build2 [402 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 fontconfig-config amd64 2.15.0-1.1ubuntu1 [37.3 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libfontconfig1 amd64 2.15.0-1.1ubuntu1 [139 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 fontconfig amd64 2.15.0-1.1ubuntu1 [180 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5ubuntu1 [33.6 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libcairo2 amd64 1.18.0-1ubuntu1 [566 kB] Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libexpat1-dev amd64 2.6.1-2 [139 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libglib2.0-0t64 amd64 2.79.3-3ubuntu5 [1540 kB] Get:74 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 liblua5.1-0 amd64 5.1.5-9build1 [120 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libharfbuzz0b amd64 8.3.0-2build1 [469 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpango-1.0-0 amd64 1.52.1+ds-1 [231 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpangoft2-1.0-0 amd64 1.52.1+ds-1 [42.5 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpangocairo-1.0-0 amd64 1.52.1+ds-1 [28.8 kB] Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 libtre5 amd64 0.8.0-7 [50.1 kB] Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 lua-md5 amd64 1.2+git+1+8d87fee-2 [14.0 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 genometools-common all 1.6.5+ds-2.1build1 [195 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libgenometools0t64 amd64 1.6.5+ds-2.1build1 [540 kB] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20240113-1ubuntu1 [384 kB] Get:87 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libreadline-dev amd64 8.2-3.1 [167 kB] Get:88 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 liblua5.1-0-dev amd64 5.1.5-9build1 [138 kB] Get:89 http://ftpmaster.internal/ubuntu noble/universe amd64 libtre-dev amd64 0.8.0-7 [37.2 kB] Get:90 http://ftpmaster.internal/ubuntu noble/universe amd64 libvmatch-dev amd64 2.3.1+dfsg-9 [730 kB] Get:91 http://ftpmaster.internal/ubuntu noble/universe amd64 lua-filesystem amd64 1.8.0-3 [13.0 kB] Get:92 http://ftpmaster.internal/ubuntu noble/universe amd64 lua-lpeg amd64 1.0.2-2 [38.6 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1ubuntu1 [894 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 genometools amd64 1.6.5+ds-2.1build1 [1949 kB] Get:95 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libgenometools0-dev amd64 1.6.5+ds-2.1build1 [87.6 kB] Preconfiguring packages ... Fetched 37.8 MB in 2s (16.7 MB/s) dpkg: libpng16-16:amd64: dependency problems, but removing anyway as you requested: optipng depends on libpng16-16 (>= 1.6.2-1). (Reading database ... 15762 files and directories currently installed.) Removing libpng16-16:amd64 (1.6.43-1) ... Selecting previously unselected package libpng16-16t64:amd64. (Reading database ... 15752 files and directories currently installed.) Preparing to unpack .../00-libpng16-16t64_1.6.43-3_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.43-3) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.12.1-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.1-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../02-libexpat1_2.6.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.6.1-2) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../03-libfribidi0_1.0.13-3_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.13-3) ... 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Setting up libncurses6:amd64 (6.4+20240113-1ubuntu1) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libfribidi0:amd64 (1.0.13-3) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-3) ... Setting up autopoint (0.21-14ubuntu1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up libicu74:amd64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1ubuntu1) ... Setting up dwz (0.15-1build5) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up liblua5.1-0:amd64 (5.1.5-9build1) ... Setting up debugedit (1:5.0-5) ... Setting up libsub-override-perl (0.10-1) ... Setting up libthai-data (0.1.29-2) ... Setting up libbsd0:amd64 (0.12.1-1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3ubuntu2) ... Setting up libbz2-dev:amd64 (1.0.8-5ubuntu1) ... Setting up automake (1:1.16.5-1.3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libtre-dev (0.8.0-7) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up libncurses-dev:amd64 (6.4+20240113-1ubuntu1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-14ubuntu1) ... Setting up libtool (2.4.7-7) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.15.0-1.1ubuntu1) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libreadline-dev:amd64 (8.2-3.1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1build2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3build1) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2build1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1ubuntu1) ... Setting up fontconfig (2.15.0-1.1ubuntu1) ... Regenerating fonts cache... done. Setting up liblua5.1-0-dev:amd64 (5.1.5-9build1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpango-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up man-db (2.12.0-3build4) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer. Setting up libcairo2:amd64 (1.18.0-1ubuntu1) ... Setting up libpangoft2-1.0-0:amd64 (1.52.1+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.1+ds-1) ... Setting up debhelper (13.14.1ubuntu5) ... Setting up genometools-common (1.6.5+ds-2.1build1) ... Setting up libgenometools0t64 (1.6.5+ds-2.1build1) ... Setting up genometools (1.6.5+ds-2.1build1) ... Setting up libgenometools0-dev (1.6.5+ds-2.1build1) ... Setting up libruby:amd64 (1:3.2~ubuntu1) ... Setting up ruby-sdbm:amd64 (1.0.0-5build4) ... Setting up libruby3.2:amd64 (3.2.3-1build2) ... Setting up ruby3.2 (3.2.3-1build2) ... Setting up ruby (1:3.2~ubuntu1) ... Setting up ruby-asciidoctor (2.0.20-1) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.20-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up ruby-rubygems (3.4.20-1) ... Processing triggers for libc-bin (2.39-0ubuntu6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:55:07 UTC 2024 amd64 (x86_64) Toolchain package versions: binutils_2.42-4ubuntu1 dpkg-dev_1.22.6ubuntu4 g++-13_13.2.0-19ubuntu1 gcc-13_13.2.0-19ubuntu1 libc6-dev_2.39-0ubuntu6 libstdc++-13-dev_13.2.0-19ubuntu1 libstdc++6_14-20240315-1ubuntu1 linux-libc-dev_6.8.0-20.20 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.3 apt-utils_2.7.3 asciidoctor_2.0.20-1 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu1 autotools-dev_20220109.1 base-files_13ubuntu7 base-passwd_3.6.3 bash_5.2.21-2ubuntu2 bash-completion_1:2.11-8 binutils_2.42-4ubuntu1 binutils-common_2.42-4ubuntu1 binutils-x86-64-linux-gnu_2.42-4ubuntu1 bsdextrautils_2.39.3-9ubuntu2 bsdutils_1:2.39.3-9ubuntu2 build-essential_12.10ubuntu1 bzip2_1.0.8-5ubuntu1 ca-certificates_20240203 coreutils_9.4-3ubuntu3 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-19ubuntu1 cpp-13-x86-64-linux-gnu_13.2.0-19ubuntu1 cpp-x86-64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu4 debconf_1.5.86 debconf-i18n_1.5.86 debhelper_13.14.1ubuntu5 debianutils_5.17 debugedit_1:5.0-5 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.6ubuntu4 dpkg-dev_1.22.6ubuntu4 dwz_0.15-1build5 e2fsprogs_1.47.0-2.4~exp1ubuntu2 fakeroot_1.33-1 file_1:5.45-3 findutils_4.9.0-5 fontconfig_2.15.0-1.1ubuntu1 fontconfig-config_2.15.0-1.1ubuntu1 fonts-dejavu-core_2.37-8 fonts-dejavu-mono_2.37-8 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-19ubuntu1 g++-13-x86-64-linux-gnu_13.2.0-19ubuntu1 g++-x86-64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-19ubuntu1 gcc-13-base_13.2.0-19ubuntu1 gcc-13-x86-64-linux-gnu_13.2.0-19ubuntu1 gcc-14-base_14-20240315-1ubuntu1 gcc-x86-64-linux-gnu_4:13.2.0-7ubuntu1 genometools_1.6.5+ds-2.1build1 genometools-common_1.6.5+ds-2.1build1 gettext_0.21-14ubuntu1 gettext-base_0.21-14ubuntu1 gpg_2.4.4-2ubuntu15 gpg-agent_2.4.4-2ubuntu15 gpgconf_2.4.4-2ubuntu15 gpgv_2.4.4-2ubuntu15 grep_3.11-4 groff-base_1.23.0-3build1 gzip_1.12-1ubuntu2 hostname_3.23+nmu2ubuntu1 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-5.1ubuntu1 libacl1_2.3.2-1 libapparmor1_4.0.0-beta3-0ubuntu2 libapt-pkg6.0t64_2.7.13ubuntu1 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4 libasan8_14-20240315-1ubuntu1 libassuan0_2.5.6-1 libatomic1_14-20240315-1ubuntu1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4ubuntu1 libblkid1_2.39.3-9ubuntu2 libbrotli1_1.1.0-2build1 libbsd0_0.12.1-1 libbz2-1.0_1.0.8-5ubuntu1 libbz2-dev_1.0.8-5ubuntu1 libc-bin_2.39-0ubuntu6 libc-dev-bin_2.39-0ubuntu6 libc6_2.39-0ubuntu6 libc6-dev_2.39-0ubuntu6 libcairo2_1.18.0-1ubuntu1 libcap-ng0_0.8.4-2build1 libcap2_1:2.66-5ubuntu1 libcc1-0_14-20240315-1ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libcryptsetup12_2:2.7.0-1ubuntu2 libctf-nobfd0_2.42-4ubuntu1 libctf0_2.42-4ubuntu1 libdatrie1_0.2.13-3 libdb5.3t64_5.3.28+dfsg2-6 libdebconfclient0_0.271ubuntu2 libdebhelper-perl_13.14.1ubuntu5 libdevmapper1.02.1_2:1.02.185-3ubuntu2 libdpkg-perl_1.22.6ubuntu4 libdw1t64_0.190-1.1build2 libedit2_3.1-20230828-1 libelf1t64_0.190-1.1build2 libexpat1_2.6.1-2 libexpat1-dev_2.6.1-2 libext2fs2t64_1.47.0-2.4~exp1ubuntu2 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu2 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.13.1-1 libfontconfig1_2.15.0-1.1ubuntu1 libfreetype6_2.13.2+dfsg-1build2 libfribidi0_1.0.13-3 libgcc-13-dev_13.2.0-19ubuntu1 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ruby-asciidoctor_2.0.20-1 ruby-net-telnet_0.2.0-1 ruby-rubygems_3.4.20-1 ruby-sdbm_1.0.0-5build4 ruby-webrick_1.8.1-1 ruby-xmlrpc_0.3.2-2 ruby3.2_3.2.3-1build2 rubygems-integration_1.18 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 systemd_255.4-1ubuntu5 systemd-dev_255.4-1ubuntu5 systemd-sysv_255.4-1ubuntu5 sysvinit-utils_3.08-6ubuntu2 tar_1.35+dfsg-3 tzdata_2024a-1ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu2 uuid-runtime_2.39.3-9ubuntu2 xz-utils_5.6.0-0.2 zlib1g_1:1.3.dfsg-3.1ubuntu1 zlib1g-dev_1:1.3.dfsg-3.1ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: genomethreader Binary: genomethreader Architecture: any Version: 1.7.3+dfsg-10build1 Maintainer: Ubuntu Developers Uploaders: Sascha Steinbiss Homepage: https://genomethreader.org Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/genomethreader Vcs-Git: https://salsa.debian.org/med-team/genomethreader.git Testsuite: autopkgtest Testsuite-Triggers: genometools, ruby Build-Depends: debhelper-compat (= 13), genometools, libgenometools0-dev, libvmatch-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, liblua5.1-0-dev, libtre-dev, asciidoctor Package-List: genomethreader deb science optional arch=any Checksums-Sha1: 84e7de5ac11ef4305a5e40eddb1c07383c464964 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz 5edfc64c95d917cfbe52fb2d2dc5db29aefae9b3 14272 genomethreader_1.7.3+dfsg-10build1.debian.tar.xz Checksums-Sha256: d19808894b1c86312b51f1aeb6e11f5ba0dfc8dcf237bf08fc0615d26b0cf051 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz bb65982bc773a38954019f91f50d4230e1f506dda2cc373fa1eb43bf920aff6a 14272 genomethreader_1.7.3+dfsg-10build1.debian.tar.xz Files: 62eb8a06280490f22b646147f0e0f444 39993616 genomethreader_1.7.3+dfsg.orig.tar.xz 36d1140fda28143a6de4185b1f20e44b 14272 genomethreader_1.7.3+dfsg-10build1.debian.tar.xz Original-Maintainer: Debian Med Packaging Team -----BEGIN PGP SIGNATURE----- iQJHBAEBCgAxFiEET7WIqEwt3nmnTHeHb6RY3R2wP3EFAmX9rSATHGp1bGlhbmtA dWJ1bnR1LmNvbQAKCRBvpFjdHbA/cfsAEACmb1wfEC//cCxcxe2rEebGJeir78n6 IWzWdurGsYeSFtEQrZSTA6m4z/pFr7B7zSccISLD8m8rDsNZHA/6Q0Too4lUo06z ZvkMoXroVNE1M18YliIRiryVUPz5ve/EEUY3bXYxtbx9n0p49T14UXDeGpAQzhED fWThK4E8QqI4mbmOlwqJZm7XMaV1PfUoybnWu439PjX8rapEeXRBXiO6s7NbqG9y HGzBLrPPLLGiG6Ie5oxC7cWIDYrvJHbBXERFqfL7gshIXyzIzsxQ+jZUIlPA2T6R hqQGk91ak4t5NBo+ZO52Py1XTp8w0BoR4j2qC3byy6yHJtZAKl83KLGuVVE1IBDn AiembTtXS/jgOBu3RD3P0IysvNwjiGE4GqlIouvXkOMXwYwFcDLPaU/fgoJim55s 8jBOWz46JoGU9kE+PVbXXOjiEgh+4BeZbgi+Or/CyT69B9tvsb4+oGPSG7EaVUMG tUY73UE2GYA678+VZnGjJuB4YTUU5rsRXbquT4MFF1YQxNV9acAJ0d6YpTCLAyet dDa+h5561XV7SeR/vYtLQbwRHy7X/b4dK95z8Botd2UeTGdiZbV5r3F+GaRVSebN sNQf9y7EBzzS5InTL9gytNdrOSlfsIs3wA3UPHTowqvLOclLOlXDqxRgUBOv1TFA ZBQftPWS2AHBTg== =9rv5 -----END PGP SIGNATURE----- gpgv: Signature made Fri Mar 22 16:09:04 2024 UTC gpgv: using RSA key 4FB588A84C2DDE79A74C77876FA458DD1DB03F71 gpgv: issuer "juliank@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./genomethreader_1.7.3+dfsg-10build1.dsc: no acceptable signature found dpkg-source: info: extracting genomethreader in /<> dpkg-source: info: unpacking genomethreader_1.7.3+dfsg.orig.tar.xz dpkg-source: info: unpacking genomethreader_1.7.3+dfsg-10build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-ftbfs-with-ruby-3.2.patch dpkg-source: info: applying debian-gt-libs.patch dpkg-source: info: applying gt-path-fix.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying search-paths.patch dpkg-source: info: applying m32-m64-ignore.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying disable-fastdp-tests.patch dpkg-source: info: applying extend-clean.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-27950568 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27950568 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27950568 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package genomethreader dpkg-buildpackage: info: source version 1.7.3+dfsg-10build1 dpkg-buildpackage: info: source distribution noble dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_clean make licensemanager=no opt=yes 64bit=yes cleanup make[2]: Entering directory '/<>' rm -rf obj lib rm -rf testsuite/stest_testsuite testsuite/stest_stest_tests rm -rf bin find gthdata -name '*.des' | xargs rm -f find gthdata -name '*.esq' | xargs rm -f find gthdata -name '*.md5' | xargs rm -f find gthdata -name '*.ois' | xargs rm -f find gthdata -name '*.sds' | xargs rm -f find gthdata -name '*.suf' | xargs rm -f find gthdata -name '*.bck' | xargs rm -f find gthdata -name '*.llv' | xargs rm -f find gthdata -name '*.bwt' | xargs rm -f find gthdata -name '*.tis' | xargs rm -f find gthdata -name '*.ssp' | xargs rm -f find gthdata -name '*.lcp' | xargs rm -f find gthdata -name '*.sti1' | xargs rm -f find testdata -name '*.des' | xargs rm -f find testdata -name '*.esq' | xargs rm -f find testdata -name '*.md5' | xargs rm -f find testdata -name '*.ois' | xargs rm -f find testdata -name '*.sds' | xargs rm -f find testdata -name '*.suf' | xargs rm -f find testdata -name '*.bck' | xargs rm -f find testdata -name '*.llv' | xargs rm -f find testdata -name '*.bwt' | xargs rm -f find testdata -name '*.tis' | xargs rm -f find testdata -name '*.ssp' | xargs rm -f find testdata -name '*.lcp' | xargs rm -f find testdata -name '*.sti1' | xargs rm -f find testdata -name '*.al1' | xargs rm -f find testdata -name '*.prj' | xargs rm -f find testdata -name '*.polya*' | xargs rm -f make[2]: Leaving directory '/<>' rm -rf bin/bssm debian/bssm bin/gthdata debian/gthdata rm -rf /<>/debian/man rm -f debian/*substvars make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' make licensemanager=no opt=yes 64bit=yes make[2]: Entering directory '/<>' [create obj/gth_config.h] [compile findfile.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfile.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/findfile.o [compile gt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_align_dna.o [compile gt_gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_gthgetseq.o [compile gthmkvtree.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmkvtree.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthmkvtree.o [compile gthpolyafunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gthpolyafunc.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpolyafunc.o [compile gthpre.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpre.o [compile gthversionfunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/gthversionfunc.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthversionfunc.o [compile gthvmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvmatch.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthvmatch.o [compile jt.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt.o [compile jt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_align_dna.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_dna.o [compile jt_align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader/jt_align_protein.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_protein.o [compile seq_con_multiseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader/seq_con_multiseq.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/seq_con_multiseq.o [compile ags.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/ags.c -o obj/src/gth/ags.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags.c -o obj/src/gth/ags.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/ags.o [compile ags_build.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/ags_build.c -o obj/src/gth/ags_build.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/ags_build.c -o obj/src/gth/ags_build.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/ags_build.o [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/align_dna.c -o obj/src/gth/align_dna.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_dna.c -o obj/src/gth/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/align_dna.o [compile align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/align_protein.c -o obj/src/gth/align_protein.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/align_protein.c -o obj/src/gth/align_protein.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/align_protein.o [compile backtrace_path.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/backtrace_path.c -o obj/src/gth/backtrace_path.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/backtrace_path.o [compile bssm_helper.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_helper.c -o obj/src/gth/bssm_helper.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_helper.o [compile bssm_param.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param.c -o obj/src/gth/bssm_param.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_param.o [compile bssm_param_rmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_param_rmsd.c -o obj/src/gth/bssm_param_rmsd.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_param_rmsd.o [compile bssm_seq_processor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_seq_processor.c -o obj/src/gth/bssm_seq_processor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_seq_processor.o [compile bssm_train_stream.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_stream.c -o obj/src/gth/bssm_train_stream.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_train_stream.o [compile bssm_train_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/bssm_train_visitor.c -o obj/src/gth/bssm_train_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/bssm_train_visitor.o [compile call_info.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/call_info.c -o obj/src/gth/call_info.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/call_info.c -o obj/src/gth/call_info.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/call_info.o [compile chain_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chain_collection.c -o obj/src/gth/chain_collection.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/chain_collection.o [compile chaining.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/chaining.c -o obj/src/gth/chaining.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/chaining.c -o obj/src/gth/chaining.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/chaining.o [compile compute_scores.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/compute_scores.c -o obj/src/gth/compute_scores.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/compute_scores.o [compile desc_cache.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/desc_cache.c -o obj/src/gth/desc_cache.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/desc_cache.o [compile dp_options_core.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_core.c -o obj/src/gth/dp_options_core.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_core.o [compile dp_options_est.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_est.c -o obj/src/gth/dp_options_est.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_est.o [compile dp_options_postpro.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_options_postpro.c -o obj/src/gth/dp_options_postpro.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_options_postpro.o [compile dp_param.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/dp_param.c -o obj/src/gth/dp_param.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_param.c -o obj/src/gth/dp_param.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_param.o [compile dp_scores_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/dp_scores_protein.c -o obj/src/gth/dp_scores_protein.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/dp_scores_protein.o [compile editoperation.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/editoperation.c -o obj/src/gth/editoperation.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/editoperation.c -o obj/src/gth/editoperation.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/editoperation.o [compile gff3_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_pgl_visitor.c -o obj/src/gth/gff3_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gff3_pgl_visitor.o [compile gff3_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gff3_sa_visitor.c -o obj/src/gth/gff3_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gff3_sa_visitor.o [compile gt_gth.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gth.c -o obj/src/gth/gt_gth.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gth.o [compile gt_gthbssmbuild.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmbuild.c -o obj/src/gth/gt_gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmbuild.o [compile gt_gthbssmfileinfo.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmfileinfo.c -o obj/src/gth/gt_gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmfileinfo.o [compile gt_gthbssmprint.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmprint.c -o obj/src/gth/gt_gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmprint.o [compile gt_gthbssmrmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmrmsd.c -o obj/src/gth/gt_gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmrmsd.o [compile gt_gthbssmtrain.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthbssmtrain.c -o obj/src/gth/gt_gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthbssmtrain.o [compile gt_gthconsensus.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthconsensus.c -o obj/src/gth/gt_gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthconsensus.o [compile gt_gthfilestat.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthfilestat.c -o obj/src/gth/gt_gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthfilestat.o [compile gt_gthmkbssmfiles.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthmkbssmfiles.c -o obj/src/gth/gt_gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthmkbssmfiles.o [compile gt_gthsplit.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gt_gthsplit.c -o obj/src/gth/gt_gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gt_gthsplit.o [compile gthalignment.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthalignment.c -o obj/src/gth/gthalignment.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthalignment.o [compile gthchain.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthchain.c -o obj/src/gth/gthchain.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthchain.c -o obj/src/gth/gthchain.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthchain.o [compile gthcluster.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcluster.c -o obj/src/gth/gthcluster.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcluster.o [compile gthcutoffsminimal.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsminimal.c -o obj/src/gth/gthcutoffsminimal.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsminimal.o [compile gthcutoffsrelaxed.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsrelaxed.c -o obj/src/gth/gthcutoffsrelaxed.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsrelaxed.o [compile gthcutoffsstrict.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthcutoffsstrict.c -o obj/src/gth/gthcutoffsstrict.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthcutoffsstrict.o [compile gthmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthmatch.c -o obj/src/gth/gthmatch.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthmatch.o [compile gthorf.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthorf.c -o obj/src/gth/gthorf.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthorf.c -o obj/src/gth/gthorf.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthorf.o [compile gthoutput.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthoutput.c -o obj/src/gth/gthoutput.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthoutput.o [compile gthsadistri.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsadistri.c -o obj/src/gth/gthsadistri.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsadistri.o [compile gthsortags.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsortags.c -o obj/src/gth/gthsortags.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsortags.o [compile gthsplicesitescr.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthsplicesitescr.c -o obj/src/gth/gthsplicesitescr.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthsplicesitescr.o [compile gthtrans.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtrans.c -o obj/src/gth/gthtrans.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthtrans.o [compile gthtravalign.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthtravalign.c -o obj/src/gth/gthtravalign.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthtravalign.o [compile gthverbosefunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefunc.c -o obj/src/gth/gthverbosefunc.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthverbosefunc.o [compile gthverbosefuncvm.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthverbosefuncvm.c -o obj/src/gth/gthverbosefuncvm.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthverbosefuncvm.o [compile gthxml.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/gthxml.c -o obj/src/gth/gthxml.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/gthxml.c -o obj/src/gth/gthxml.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/gthxml.o [compile indent.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/indent.c -o obj/src/gth/indent.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/indent.c -o obj/src/gth/indent.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/indent.o [compile input.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/input.c -o obj/src/gth/input.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/input.c -o obj/src/gth/input.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/input.o [compile intermediate.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/intermediate.c -o obj/src/gth/intermediate.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/intermediate.c -o obj/src/gth/intermediate.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/intermediate.o [compile md5_cache.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/md5_cache.c -o obj/src/gth/md5_cache.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/md5_cache.o [compile parse_options.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/parse_options.c -o obj/src/gth/parse_options.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/parse_options.c -o obj/src/gth/parse_options.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/parse_options.o [compile path_matrix.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_matrix.c -o obj/src/gth/path_matrix.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/path_matrix.o [compile path_walker.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/path_walker.c -o obj/src/gth/path_walker.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/path_walker.c -o obj/src/gth/path_walker.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/path_walker.o [compile pgl.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/pgl.c -o obj/src/gth/pgl.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl.c -o obj/src/gth/pgl.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl.o [compile pgl_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_collection.c -o obj/src/gth/pgl_collection.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl_collection.o [compile pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/pgl_visitor.c -o obj/src/gth/pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/pgl_visitor.o [compile proc_sa_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/proc_sa_collection.c -o obj/src/gth/proc_sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/proc_sa_collection.o [compile region_factory.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/region_factory.c -o obj/src/gth/region_factory.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/region_factory.c -o obj/src/gth/region_factory.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/region_factory.o [compile run_header.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/run_header.c -o obj/src/gth/run_header.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/run_header.c -o obj/src/gth/run_header.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/run_header.o [compile sa.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/sa.c -o obj/src/gth/sa.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa.c -o obj/src/gth/sa.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa.o [compile sa_cmp.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_cmp.c -o obj/src/gth/sa_cmp.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_cmp.o [compile sa_collection.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_collection.c -o obj/src/gth/sa_collection.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_collection.o [compile sa_filter.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_filter.c -o obj/src/gth/sa_filter.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_filter.o [compile sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/sa_visitor.c -o obj/src/gth/sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/sa_visitor.o [compile seq_con.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/seq_con.c -o obj/src/gth/seq_con.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/seq_con.c -o obj/src/gth/seq_con.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/seq_con.o [compile similarity_filter.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/similarity_filter.c -o obj/src/gth/similarity_filter.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/similarity_filter.o [compile splice_site_model.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/splice_site_model.c -o obj/src/gth/splice_site_model.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/splice_site_model.o [compile spliced_seq.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/spliced_seq.c -o obj/src/gth/spliced_seq.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/spliced_seq.o [compile stat.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/stat.c -o obj/src/gth/stat.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/stat.c -o obj/src/gth/stat.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/stat.o [compile time.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/time.c -o obj/src/gth/time.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/time.c -o obj/src/gth/time.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/time.o [compile txt_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_pgl_visitor.c -o obj/src/gth/txt_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/txt_pgl_visitor.o [compile txt_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/txt_sa_visitor.c -o obj/src/gth/txt_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/txt_sa_visitor.o [compile xml_final_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_final_sa_visitor.c -o obj/src/gth/xml_final_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_final_sa_visitor.o [compile xml_inter_sa_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_inter_sa_visitor.c -o obj/src/gth/xml_inter_sa_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_inter_sa_visitor.o [compile xml_pgl_visitor.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth/xml_pgl_visitor.c -o obj/src/gth/xml_pgl_visitor.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth/xml_pgl_visitor.o [link libgenomethreader.a] ar: `u' modifier ignored since `D' is the default (see `U') ar: creating lib/libgenomethreader.a [compile gth.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gth.c -o obj/src/gth.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gth.c -o obj/src/gth.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gth.o [link gth] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gth.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gth [compile gthconsensus.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthconsensus.c -o obj/src/gthconsensus.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthconsensus.c -o obj/src/gthconsensus.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthconsensus.o [link gthconsensus] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthconsensus.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthconsensus [compile gthbssmfileinfo.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmfileinfo.c -o obj/src/gthbssmfileinfo.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmfileinfo.o [link gthbssmfileinfo] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmfileinfo.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmfileinfo [compile gthbssmbuild.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmbuild.c -o obj/src/gthbssmbuild.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmbuild.o [link gthbssmbuild] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmbuild.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmbuild [compile gthbssmprint.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthbssmprint.c -o obj/src/gthbssmprint.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmprint.c -o obj/src/gthbssmprint.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmprint.o [link gthbssmprint] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmprint.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmprint [compile gthbssmrmsd.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmrmsd.c -o obj/src/gthbssmrmsd.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmrmsd.o [link gthbssmrmsd] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmrmsd.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmrmsd [compile gthbssmtrain.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthbssmtrain.c -o obj/src/gthbssmtrain.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthbssmtrain.o [link gthbssmtrain] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthbssmtrain.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthbssmtrain [compile gthfilestat.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthfilestat.c -o obj/src/gthfilestat.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthfilestat.c -o obj/src/gthfilestat.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthfilestat.o [link gthfilestat] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthfilestat.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthfilestat [compile gthmkbssmfiles.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthmkbssmfiles.c -o obj/src/gthmkbssmfiles.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthmkbssmfiles.o [link gthmkbssmfiles] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthmkbssmfiles.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthmkbssmfiles [compile gthsplit.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthsplit.c -o obj/src/gthsplit.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthsplit.c -o obj/src/gthsplit.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthsplit.o [link gthsplit] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthsplit.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthsplit [compile gthunit.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthunit.c -o obj/src/gthunit.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthunit.c -o obj/src/gthunit.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthunit.o [link gthunit] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthunit.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthunit [compile gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/gthgetseq.c -o obj/src/gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/gthgetseq.c -o obj/src/gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/gthgetseq.o [link gthgetseq] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/gthgetseq.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/gthgetseq [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3 -c src/align_dna.c -o obj/src/align_dna.o -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fdebug-prefix-map=/<>=/usr/src/genomethreader-1.7.3+dfsg-10build1 -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=misleading-indentation -Werror -O3 cc -c src/align_dna.c -o obj/src/align_dna.d -Wdate-time -D_FORTIFY_SOURCE=3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DWITHLCP -DUNISTD_H="" -DEXPAT_H="" -DRNV_VERSION=\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/<>/src -I/<>/obj -U_FORTIFY_SOURCE -I/<>/../vstree/src/include -I/<>/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/align_dna.o [link align_dna] cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -Llib obj/src/align_dna.o lib/libgenomethreader.a /usr/lib/libvmatch.a /usr/lib/libvmengine.a /usr/lib/libmkvtree.a /usr/lib/libkurtz.a /usr/lib/libkurtz-basic.a -lm -lgenometools -lbz2 -lz -lexpat -ltre -llua5.1 -ldl -lpthread -o bin/align_dna make[2]: Leaving directory '/<>' make licensemanager=no opt=yes 64bit=yes train make[2]: Entering directory '/<>' [train arabidopsis.bssm] [train rice.bssm] [train maize.bssm] [train medicago.bssm] [write old BSSMs] [copy gthdata stuff to bin] make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' make licensemanager=no 64bit=yes test make[2]: Entering directory '/<>' cd testsuite && env -i GTH_MEM_BOOKKEEPING=on MAKE=make PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" \ BSSMDIR=/<>/bin/bssm GTHDATADIR=/<>/gthdata/gth \ CCACHE_DISABLE=yes HOME=/sbuild-nonexistent GTHTESTDATADIR= \ ruby -I. testsuite.rb \ -testdata /<>/testdata -bin /<>/bin -cur /<> \ -gtruby /<>/gtruby 1: gth : ok 2: gth -help : ok 3: gth -help+ : ok 4: gth -version : ok 5: gth regression test (assertion in gthsafilter) : ok 6: gth regression test (-gff3out -intermediate) : ok 7: gth regression test (-gff3out -intermediate -fastdp) : ok 8: gth regression test (-gff3out -skipalignmentout) : ok 9: gth regression test (-gff3out -skipalignmentout -fastdp) : ok 10: gth regression test (-gff3out -intermediate -o) : ok 11: gth regression test (-gff3out -skipalignmentout -o) : ok 12: gthconsensus regression test (-gff3out -intermediate) : ok 13: gthconsensus regression test (-gff3out -skipalignmentout) : ok 14: gthconsensus regression test (-gff3out -intermediate -o) : ok 15: gthconsensus regression test (-gff3out -skipalignmentout -o): ok 16: gth regression test (-exondistri) : ok 17: gth regression test (-introndistri) : ok 18: gth regression test (-refseqcovdistri) : ok 19: gth regression test (all distributions) : ok 20: gth regression test (-skipindexcheck) : ok 21: gth regression test (index reconstruction) : ok 22: gth regression test (-createindicesonly & -noautoindex) : ok 23: gth regression test (coverage assertion) : ok 24: gth -gff3out -intermediate (long intron files) : ok 25: gth -gff3out -skipalignmentout (long intron files) : ok 26: gth -gff3out -frompos (correct positions in sequence region): ok 27: gth -gff3out -intermediate (correct reverse positions) : ok 28: gth arabidopsis : ok 29: gth illegal character in protein file : ok 30: align_dna : ok 31: gth -gff3descranges (single exon) : ok 32: gthconsensus -help : ok 33: gthconsensus -help+ : ok 34: gthconsensus empty_file : ok 35: gthconsensus empty_file.gz : ok 36: gthconsensus empty_file.bz2 : ok 37: gthbssmfileinfo (arabidopsis) : ok 38: gthbssmfileinfo (human) : ok 39: gthbssmprint (arabidopsis) : ok 40: gthbssmprint (human) : ok 41: gthbssmrmsd (arabidopsis) : ok 42: gthbssmtrain (examples from manual) : ok 43: gthbssmtrain (file, no introns) : ok 44: gthbssmtrain (file, introns) : ok 45: gthbssmtrain (stdin, no introns) : ok 46: gthbssmtrain (stdin, introns) : ok 47: gthbssmtrain (short intron) : ok 48: gthunit : ok 49: fastdp 01 : ok 50: fastdp (U89959) : ok 51: fastdp (U89959, introncutout) : ok make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mv bin/bssm debian/bssm mv bin/gthdata debian/gthdata dh_auto_install make[1]: Leaving directory '/<>' dh_install dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man asciidoctor -a docdate='' -b manpage /<>/debian/man_src/*.adoc cp /<>/debian/man_src/*.? /<>/debian/man dh_installman -- make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/genomethreader/usr/bin/gthbssmfileinfo: Unknown DWARF DW_FORM_0x1f20 a035c002598e5063240425b94ae9902882923ef3 debugedit: debian/genomethreader/usr/bin/gthbssmtrain: Unknown DWARF DW_FORM_0x1f20 fea98ab5ff99f22a3f5b1e4827d66ee88ba9d7ea debugedit: debian/genomethreader/usr/bin/gthbssmprint: Unknown DWARF DW_FORM_0x1f20 e7fd02eabe521c80e03de5f826e42aa2cf36f058 debugedit: debian/genomethreader/usr/bin/gthbssmbuild: Unknown DWARF DW_FORM_0x1f20 1a1025da22ff327cf466214f63aaa2b3ee870efb debugedit: debian/genomethreader/usr/bin/gthsplit: Unknown DWARF DW_FORM_0x1f20 ea28bbed8cf0d6b8fc975b174f0923dbbdc591ef debugedit: debian/genomethreader/usr/bin/gthgetseq: Unknown DWARF DW_FORM_0x1f20 27f70b981fde120642df38d6cc077a1d3576748e debugedit: debian/genomethreader/usr/bin/gthbssmrmsd: Unknown DWARF DW_FORM_0x1f20 42c6632dca690fce760ea9fe8b24b87f59034b6f debugedit: debian/genomethreader/usr/bin/gthconsensus: Unknown DWARF DW_FORM_0x1f21 ae8a6c6a79dca4413b9a91904c42fdcaa1c01ba0 debugedit: debian/genomethreader/usr/bin/gth: Unknown DWARF DW_FORM_0x1f20 338c5798cedd444f1b1b9570aa89b1df8472c0eb debugedit: debian/genomethreader/usr/bin/align_dna: Unknown DWARF DW_FORM_0x1f20 74ec71b5b6ae113ef55fefbeb9b66e49805e255d debugedit: debian/genomethreader/usr/bin/gthmkbssmfiles: Unknown DWARF DW_FORM_0x1f20 0dc5a34630a0363e24003d9a33b41858a548418f debugedit: debian/genomethreader/usr/bin/gthfilestat: Unknown DWARF DW_FORM_0x1f20 83451c8e5e6a05daad89bb4ba16b7c99b5f9ddf1 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol make[1]: Entering directory '/<>' echo "libvmatch-dev:Version=2.3.1+dfsg-9" >> debian/genomethreader.substvars dh_gencontrol make[1]: Leaving directory '/<>' dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing genomethreader-dbgsym (in debian/.debhelper/genomethreader/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing genomethreader (in debian/genomethreader); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/.debhelper/genomethreader/dbgsym-root/DEBIAN/control, package genomethreader-dbgsym, directory debian/.debhelper/genomethreader/dbgsym-root dpkg-deb: building package 'genomethreader-dbgsym' in 'debian/.debhelper/scratch-space/build-genomethreader/genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.deb'. pkgstripfiles: processing control file: debian/genomethreader/DEBIAN/control, package genomethreader, directory debian/genomethreader pkgstripfiles: Truncating usr/share/doc/genomethreader/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package genomethreader ... pkgstripfiles: No PNG files. dpkg-deb: building package 'genomethreader' in '../genomethreader_1.7.3+dfsg-10build1_amd64.deb'. Renaming genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.deb to genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../genomethreader_1.7.3+dfsg-10build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../genomethreader_1.7.3+dfsg-10build1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-03-22T16:20:52Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ genomethreader_1.7.3+dfsg-10build1_amd64.changes: ------------------------------------------------- Format: 1.8 Date: Fri, 22 Mar 2024 17:09:02 +0100 Source: genomethreader Binary: genomethreader Built-For-Profiles: noudeb Architecture: amd64 Version: 1.7.3+dfsg-10build1 Distribution: noble-proposed Urgency: high Maintainer: Launchpad Build Daemon Changed-By: Julian Andres Klode Description: genomethreader - software tool to compute gene structure predictions Changes: genomethreader (1.7.3+dfsg-10build1) noble; urgency=high . * No change rebuild against libgenometools0t64. Checksums-Sha1: e0408058e944889bc51c536eb872f84b9ff9cf87 1372912 genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb 80279344a3732d2395564a9cbf53a3d160ae1069 8105 genomethreader_1.7.3+dfsg-10build1_amd64.buildinfo f525f0de6ab152c4d27fa8aaef92567e0e62219e 1969172 genomethreader_1.7.3+dfsg-10build1_amd64.deb Checksums-Sha256: 615f12ab7a3f5e378416464a2bd6832d8bde6fea47969c8b6aa332b823d93a65 1372912 genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb c05a08f3e58a58f57d0212dfaa0398750e7dc7d817e974f296c5ee4775a455b7 8105 genomethreader_1.7.3+dfsg-10build1_amd64.buildinfo 77e8b546513399049af7022af044fb4b30e0a495235a23e817156d5807964a2f 1969172 genomethreader_1.7.3+dfsg-10build1_amd64.deb Files: 29389095e95c17bb5d9de32fb64f6c8b 1372912 debug optional genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb 707af92586630ccc4e834483a276c1aa 8105 science optional genomethreader_1.7.3+dfsg-10build1_amd64.buildinfo 64cb74ad02bebbd7adf30e0ab273b0b6 1969172 science optional genomethreader_1.7.3+dfsg-10build1_amd64.deb Original-Maintainer: Debian Med Packaging Team /<>/genomethreader_1.7.3+dfsg-10build1_amd64.changes.new could not be renamed to /<>/genomethreader_1.7.3+dfsg-10build1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: genomethreader Binary: genomethreader genomethreader-dbgsym Architecture: amd64 Version: 1.7.3+dfsg-10build1 Checksums-Md5: 29389095e95c17bb5d9de32fb64f6c8b 1372912 genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb 64cb74ad02bebbd7adf30e0ab273b0b6 1969172 genomethreader_1.7.3+dfsg-10build1_amd64.deb Checksums-Sha1: e0408058e944889bc51c536eb872f84b9ff9cf87 1372912 genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb f525f0de6ab152c4d27fa8aaef92567e0e62219e 1969172 genomethreader_1.7.3+dfsg-10build1_amd64.deb Checksums-Sha256: 615f12ab7a3f5e378416464a2bd6832d8bde6fea47969c8b6aa332b823d93a65 1372912 genomethreader-dbgsym_1.7.3+dfsg-10build1_amd64.ddeb 77e8b546513399049af7022af044fb4b30e0a495235a23e817156d5807964a2f 1969172 genomethreader_1.7.3+dfsg-10build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Fri, 22 Mar 2024 16:20:51 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.20-1), autoconf (= 2.71-3), automake (= 1:1.16.5-1.3ubuntu1), autopoint (= 0.21-14ubuntu1), autotools-dev (= 20220109.1), base-files (= 13ubuntu7), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu2), binutils (= 2.42-4ubuntu1), binutils-common (= 2.42-4ubuntu1), binutils-x86-64-linux-gnu (= 2.42-4ubuntu1), bsdextrautils (= 2.39.3-9ubuntu2), bsdutils (= 1:2.39.3-9ubuntu2), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5ubuntu1), ca-certificates (= 20240203), coreutils (= 9.4-3ubuntu3), cpp (= 4:13.2.0-7ubuntu1), 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libdatrie1 (= 0.2.13-3), libdb5.3t64 (= 5.3.28+dfsg2-6), libdebconfclient0 (= 0.271ubuntu2), libdebhelper-perl (= 13.14.1ubuntu5), libdpkg-perl (= 1.22.6ubuntu4), libdw1t64 (= 0.190-1.1build2), libedit2 (= 3.1-20230828-1), libelf1t64 (= 0.190-1.1build2), libexpat1 (= 2.6.1-2), libexpat1-dev (= 2.6.1-2), libffi8 (= 3.4.6-1), libfile-stripnondeterminism-perl (= 1.13.1-1), libfontconfig1 (= 2.15.0-1.1ubuntu1), libfreetype6 (= 2.13.2+dfsg-1build2), libfribidi0 (= 1.0.13-3), libgcc-13-dev (= 13.2.0-19ubuntu1), libgcc-s1 (= 14-20240315-1ubuntu1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4t64 (= 1.23-5.1), libgdbm6t64 (= 1.23-5.1), libgenometools0-dev (= 1.6.5+ds-2.1build1), libgenometools0t64 (= 1.6.5+ds-2.1build1), libglib2.0-0t64 (= 2.79.3-3ubuntu5), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgomp1 (= 14-20240315-1ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.42-4ubuntu1), libgraphite2-3 (= 1.3.14-2), libharfbuzz0b (= 8.3.0-2build1), libhwasan0 (= 14-20240315-1ubuntu1), libicu74 (= 74.2-1ubuntu1), libisl23 (= 0.26-3), libitm1 (= 14-20240315-1ubuntu1), libjansson4 (= 2.14-2), liblsan0 (= 14-20240315-1ubuntu1), liblua5.1-0 (= 5.1.5-9build1), liblua5.1-0-dev (= 5.1.5-9build1), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.6.0-0.2), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-9ubuntu2), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libncurses-dev (= 6.4+20240113-1ubuntu1), libncurses6 (= 6.4+20240113-1ubuntu1), libncursesw6 (= 6.4+20240113-1ubuntu1), libpam-modules (= 1.5.3-5ubuntu3), libpam-modules-bin (= 1.5.3-5ubuntu3), libpam-runtime (= 1.5.3-5ubuntu3), libpam0g (= 1.5.3-5ubuntu3), libpango-1.0-0 (= 1.52.1+ds-1), libpangocairo-1.0-0 (= 1.52.1+ds-1), libpangoft2-1.0-0 (= 1.52.1+ds-1), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.38t64 (= 5.38.2-3.2), libpipeline1 (= 1.5.7-1), libpixman-1-0 (= 0.42.2-1), libpng16-16t64 (= 1.6.43-3), libquadmath0 (= 14-20240315-1ubuntu1), libreadline-dev (= 8.2-3.1), libreadline8t64 (= 8.2-3.1), libruby (= 1:3.2~ubuntu1), libruby3.2 (= 3.2.3-1build2), libseccomp2 (= 2.5.5-1ubuntu2), libselinux1 (= 3.5-2ubuntu1), libsframe1 (= 2.42-4ubuntu1), libsmartcols1 (= 2.39.3-9ubuntu2), libsqlite3-0 (= 3.45.1-1ubuntu1), libssl3t64 (= 3.0.13-0ubuntu2), libstdc++-13-dev (= 13.2.0-19ubuntu1), libstdc++6 (= 14-20240315-1ubuntu1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1ubuntu5), libthai-data (= 0.1.29-2), libthai0 (= 0.1.29-2), libtinfo6 (= 6.4+20240113-1ubuntu1), libtool (= 2.4.7-7), libtre-dev (= 0.8.0-7), libtre5 (= 0.8.0-7), libtsan2 (= 14-20240315-1ubuntu1), libubsan1 (= 14-20240315-1ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255.4-1ubuntu5), libunistring5 (= 1.1-2), libuuid1 (= 2.39.3-9ubuntu2), libvmatch-dev (= 2.3.1+dfsg-9), libx11-6 (= 2:1.8.7-1), libx11-data (= 2:1.8.7-1), libxau6 (= 1:1.0.9-1build5), libxcb-render0 (= 1.15-1), libxcb-shm0 (= 1.15-1), libxcb1 (= 1.15-1), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxml2 (= 2.9.14+dfsg-1.3ubuntu2), libxrender1 (= 1:0.9.10-1.1), libyaml-0-2 (= 0.2.5-1), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.0-20.20), login (= 1:4.13+dfsg1-4ubuntu1), lto-disabled-list (= 47), lua-filesystem (= 1.8.0-3), lua-lpeg (= 1.0.2-2), lua-md5 (= 1.2+git+1+8d87fee-2), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-3build4), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.4+20240113-1ubuntu1), ncurses-bin (= 6.4+20240113-1ubuntu1), openssl (= 3.0.13-0ubuntu2), patch (= 2.7.6-7build2), perl (= 5.38.2-3.2), perl-base (= 5.38.2-3.2), perl-modules-5.38 (= 5.38.2-3.2), po-debconf (= 1.0.21+nmu1), rake (= 13.0.6-3), readline-common (= 8.2-3.1), rpcsvc-proto (= 1.4.2-0ubuntu6), ruby (= 1:3.2~ubuntu1), ruby-asciidoctor (= 2.0.20-1), ruby-net-telnet (= 0.2.0-1), ruby-rubygems (= 3.4.20-1), ruby-sdbm (= 1.0.0-5build4), ruby-webrick (= 1.8.1-1), ruby-xmlrpc (= 0.3.2-2), ruby3.2 (= 3.2.3-1build2), rubygems-integration (= 1.18), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-6ubuntu2), tar (= 1.35+dfsg-3), util-linux (= 2.39.3-9ubuntu2), xz-utils (= 5.6.0-0.2), zlib1g (= 1:1.3.dfsg-3.1ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3.1ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1711123742" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ genomethreader_1.7.3+dfsg-10build1_amd64.deb -------------------------------------------- new Debian package, version 2.0. size 1969172 bytes: control archive=1945 bytes. 973 bytes, 18 lines control 3015 bytes, 44 lines md5sums Package: genomethreader Version: 1.7.3+dfsg-10build1 Architecture: amd64 Maintainer: Ubuntu Developers Installed-Size: 10987 Depends: libc6 (>= 2.38), libexpat1 (>= 2.0.1), libgenometools0t64 (>= 1.6.5+ds), liblua5.1-0, zlib1g (>= 1:1.2.3.3) Built-Using: vmatch (= 2.3.1+dfsg-9) Section: science Priority: optional Homepage: https://genomethreader.org Description: software tool to compute gene structure predictions GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2024-03-22 16:09 ./ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/bin/ -rwxr-xr-x root/root 704600 2024-03-22 16:09 ./usr/bin/align_dna -rwxr-xr-x root/root 913592 2024-03-22 16:09 ./usr/bin/gth -rwxr-xr-x root/root 27016 2024-03-22 16:09 ./usr/bin/gthbssmbuild -rwxr-xr-x root/root 22896 2024-03-22 16:09 ./usr/bin/gthbssmfileinfo -rwxr-xr-x root/root 22896 2024-03-22 16:09 ./usr/bin/gthbssmprint -rwxr-xr-x root/root 22896 2024-03-22 16:09 ./usr/bin/gthbssmrmsd -rwxr-xr-x root/root 59704 2024-03-22 16:09 ./usr/bin/gthbssmtrain -rwxr-xr-x root/root 766040 2024-03-22 16:09 ./usr/bin/gthconsensus -rwxr-xr-x root/root 647256 2024-03-22 16:09 ./usr/bin/gthfilestat -rwxr-xr-x root/root 614488 2024-03-22 16:09 ./usr/bin/gthgetseq -rwxr-xr-x root/root 1583496 2024-03-22 16:09 ./usr/bin/gthmkbssmfiles -rwxr-xr-x root/root 639064 2024-03-22 16:09 ./usr/bin/gthsplit drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/lib/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/lib/genomethreader/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/ -rw-r--r-- root/root 551095 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/arabidopsis.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/arabidopsis.old.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/aspergillus.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/chicken.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/drosophila.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/fission_yeast.bssm -rw-r--r-- root/root 105131 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/human.bssm -rw-r--r-- root/root 551095 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/maize.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/maize.old.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/medicago.bssm -rw-r--r-- root/root 105131 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/mouse.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/nematode.bssm -rw-r--r-- root/root 367401 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/rat.bssm -rw-r--r-- root/root 551095 2024-03-22 16:09 ./usr/lib/genomethreader/bssm/rice.bssm drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/doc/genomethreader/ -rw-r--r-- root/root 991 2024-03-22 16:09 ./usr/share/doc/genomethreader/changelog.Debian.gz -rw-r--r-- root/root 3466 2024-02-24 19:05 ./usr/share/doc/genomethreader/copyright drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/genomethreader/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/genomethreader/gthdata/ -rw-r--r-- root/root 2122 2024-03-22 16:09 ./usr/share/genomethreader/gthdata/BLOSUM62 -rw-r--r-- root/root 39 2024-03-22 16:09 ./usr/share/genomethreader/gthdata/TransDNAX -rw-r--r-- root/root 146 2024-03-22 16:09 ./usr/share/genomethreader/gthdata/TransProt11 -rw-r--r-- root/root 290 2024-03-22 16:09 ./usr/share/genomethreader/gthdata/polyatail.dna drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/man/ drwxr-xr-x root/root 0 2024-03-22 16:09 ./usr/share/man/man1/ -rw-r--r-- root/root 508 2024-03-22 16:09 ./usr/share/man/man1/align_dna.1.gz -rw-r--r-- root/root 3183 2024-03-22 16:09 ./usr/share/man/man1/gth.1.gz -rw-r--r-- root/root 630 2024-03-22 16:09 ./usr/share/man/man1/gthbssmbuild.1.gz -rw-r--r-- root/root 476 2024-03-22 16:09 ./usr/share/man/man1/gthbssmfileinfo.1.gz -rw-r--r-- root/root 462 2024-03-22 16:09 ./usr/share/man/man1/gthbssmprint.1.gz -rw-r--r-- root/root 483 2024-03-22 16:09 ./usr/share/man/man1/gthbssmrmsd.1.gz -rw-r--r-- root/root 1235 2024-03-22 16:09 ./usr/share/man/man1/gthbssmtrain.1.gz -rw-r--r-- root/root 944 2024-03-22 16:09 ./usr/share/man/man1/gthconsensus.1.gz -rw-r--r-- root/root 622 2024-03-22 16:09 ./usr/share/man/man1/gthfilestat.1.gz -rw-r--r-- root/root 728 2024-03-22 16:09 ./usr/share/man/man1/gthgetseq.1.gz -rw-r--r-- root/root 459 2024-03-22 16:09 ./usr/share/man/man1/gthmkbssmfiles.1.gz -rw-r--r-- root/root 729 2024-03-22 16:09 ./usr/share/man/man1/gthsplit.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 159388 Build-Time: 89 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 12 Job: genomethreader_1.7.3+dfsg-10build1.dsc Machine Architecture: amd64 Package: genomethreader Package-Time: 103 Source-Version: 1.7.3+dfsg-10build1 Space: 159388 Status: successful Version: 1.7.3+dfsg-10build1 -------------------------------------------------------------------------------- Finished at 2024-03-22T16:20:52Z Build needed 00:01:43, 159388k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27950568 Scanning for processes to kill in build PACKAGEBUILD-27950568