https://launchpad.net/ubuntu/+source/augustus/3.5.0+dfsg-4build1/+build/27576140 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy02-amd64-120 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 Buildd toolchain package versions: launchpad-buildd_235~645~ubuntu20.04.1 python3-lpbuildd_235~645~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... 19 Dec 15:08:44 ntpdate[1864]: adjust time server 10.131.248.1 offset 0.000187 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576140 --image-type chroot /home/buildd/filecache-default/1fe94ca8758119221c8de2550665a1bb335bd6a9 Creating target for build PACKAGEBUILD-27576140 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576140 Starting target for build PACKAGEBUILD-27576140 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576140 '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-27576140 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576140 Updating target for build PACKAGEBUILD-27576140 Get:1 http://ftpmaster.internal/ubuntu noble InRelease [240 kB] Get:2 http://ftpmaster.internal/ubuntu noble-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu noble-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu noble-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 Packages [1406 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main Translation-en [515 kB] Get:7 http://ftpmaster.internal/ubuntu noble/universe amd64 Packages [15.0 MB] Get:8 http://ftpmaster.internal/ubuntu noble/universe Translation-en [6031 kB] Get:9 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [160 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main Translation-en [44.9 kB] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [1070 kB] Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe Translation-en [325 kB] Fetched 25.1 MB in 3s (8546 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libunistring2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libunistring5 The following packages will be upgraded: apt apt-utils base-files base-passwd bash bash-completion binutils binutils-common binutils-x86-64-linux-gnu bsdextrautils bsdutils coreutils cpp cpp-13 debianutils diffutils dpkg dpkg-dev fakeroot g++ g++-13 gcc gcc-13 gcc-13-base grep init init-system-helpers krb5-locales libapparmor1 libapt-pkg6.0 libargon2-1 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcryptsetup12 libctf-nobfd0 libctf0 libdb5.3 libdebconfclient0 libdpkg-perl libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error-l10n libgpg-error0 libgprofng0 libgssapi-krb5-2 libhwasan0 libidn2-0 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblsan0 liblzma5 libmount1 libncursesw6 libnsl-dev libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libperl5.36 libpng16-16 libproc2-0 libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsframe1 libsmartcols1 libsqlite3-0 libssl3 libstdc++-13-dev libstdc++6 libsystemd-shared libsystemd0 libtinfo6 libtirpc-common libtirpc-dev libtirpc3 libtsan2 libubsan1 libudev1 libuuid1 libxxhash0 libzstd1 linux-libc-dev login lto-disabled-list mawk mount ncurses-base ncurses-bin openssl optipng passwd perl perl-base perl-modules-5.36 pinentry-curses procps readline-common systemd systemd-dev systemd-sysv sysvinit-utils tar ubuntu-keyring util-linux uuid-runtime xz-utils zlib1g 135 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 111 MB of archives. After this operation, 6093 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl-dev amd64 1.3.0-3 [71.2 kB] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.38-3ubuntu1 [2114 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.38-3ubuntu1 [20.3 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-common all 1.3.4+ds-1 [7920 B] Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc-dev amd64 1.3.4+ds-1 [193 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libgssapi-krb5-2 amd64 1.20.1-5build1 [142 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5-3 amd64 1.20.1-5build1 [346 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libk5crypto3 amd64 1.20.1-5build1 [81.3 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libkrb5support0 amd64 1.20.1-5build1 [33.2 kB] Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libssl3 amd64 3.0.10-1ubuntu3 [1910 kB] Get:11 http://ftpmaster.internal/ubuntu noble/main amd64 libtirpc3 amd64 1.3.4+ds-1 [81.4 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libnsl2 amd64 1.3.0-3 [41.3 kB] Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 linux-libc-dev amd64 6.6.0-14.14 [1580 kB] Get:14 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 13.2.0-9ubuntu1 [48.0 kB] Get:15 http://ftpmaster.internal/ubuntu noble/main amd64 libgprofng0 amd64 2.41.50.20231214-1ubuntu1 [858 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libctf0 amd64 2.41.50.20231214-1ubuntu1 [83.2 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libctf-nobfd0 amd64 2.41.50.20231214-1ubuntu1 [86.3 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-x86-64-linux-gnu amd64 2.41.50.20231214-1ubuntu1 [2510 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 libbinutils amd64 2.41.50.20231214-1ubuntu1 [539 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 binutils-common amd64 2.41.50.20231214-1ubuntu1 [258 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 binutils amd64 2.41.50.20231214-1ubuntu1 [7696 B] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-base amd64 13.2.0-9ubuntu1 [45.2 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-s1 amd64 13.2.0-9ubuntu1 [63.1 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 13.2.0-9ubuntu1 [142 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 13.2.0-9ubuntu1 [29.5 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 13.2.0-9ubuntu1 [10.5 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 13.2.0-9ubuntu1 [2835 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 13.2.0-9ubuntu1 [1203 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 13.2.0-9ubuntu1 [2606 kB] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 13.2.0-9ubuntu1 [1105 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 13.2.0-9ubuntu1 [1262 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 13.2.0-9ubuntu1 [153 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-9ubuntu1 [12.2 MB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-9ubuntu1 [2336 kB] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-9ubuntu1 [2687 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-9ubuntu1 [21.5 MB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-9ubuntu1 [10.7 MB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++6 amd64 13.2.0-9ubuntu1 [771 kB] Get:39 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g amd64 1:1.3.dfsg-3ubuntu1 [63.3 kB] Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 libsframe1 amd64 2.41.50.20231214-1ubuntu1 [13.8 kB] Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [297 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.38-3ubuntu1 [3248 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 base-files amd64 13ubuntu5 [73.6 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 debianutils amd64 5.14 [89.0 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 bash amd64 5.2.21-2ubuntu1 [795 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 bsdutils amd64 1:2.39.2-6ubuntu1 [93.9 kB] Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 coreutils amd64 9.4-2ubuntu1 [1395 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 diffutils amd64 1:3.10-1 [176 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma5 amd64 5.4.5-0.1 [128 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 libapparmor1 amd64 4.0.0~alpha2-0ubuntu7 [48.2 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit-common all 1:3.1.2-1 [5512 B] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libcap-ng0 amd64 0.8.3-3 [15.3 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libaudit1 amd64 1:3.1.2-1 [46.7 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libblkid1 amd64 2.39.2-6ubuntu1 [122 kB] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libkmod2 amd64 30+20230601-2ubuntu1 [51.4 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 libpcre2-8-0 amd64 10.42-4ubuntu1 [228 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 libselinux1 amd64 3.5-1build2 [78.5 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libmount1 amd64 2.39.2-6ubuntu1 [132 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libpam0g amd64 1.5.2-9.1ubuntu1 [65.1 kB] Get:60 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libseccomp2 amd64 2.5.4-2ubuntu1 [49.3 kB] Get:61 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-sysv amd64 255-1ubuntu1 [11.7 kB] Get:62 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd-dev all 255-1ubuntu1 [98.5 kB] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 systemd amd64 255-1ubuntu1 [3484 kB] Get:64 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd-shared amd64 255-1ubuntu1 [2062 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libargon2-1 amd64 0~20190702+dfsg-4 [21.4 kB] Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libuuid1 amd64 2.39.2-6ubuntu1 [34.1 kB] Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libcryptsetup12 amd64 2:2.6.1-5ubuntu1 [242 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libfdisk1 amd64 2.39.2-6ubuntu1 [145 kB] Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 mount amd64 2.39.2-6ubuntu1 [118 kB] Get:70 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libsystemd0 amd64 255-1ubuntu1 [427 kB] Get:71 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libudev1 amd64 255-1ubuntu1 [169 kB] Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libxxhash0 amd64 0.8.2-2 [25.5 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libapt-pkg6.0 amd64 2.7.7 [945 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 tar amd64 1.34+dfsg-1.2ubuntu2 [293 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg amd64 1.22.1ubuntu5 [1387 kB] Get:76 http://ftpmaster.internal/ubuntu noble/main amd64 grep amd64 3.11-3 [161 kB] Get:77 http://ftpmaster.internal/ubuntu noble/main amd64 login amd64 1:4.13+dfsg1-3ubuntu1 [201 kB] Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-bin amd64 6.4+20231209-1 [187 kB] Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libperl5.36 amd64 5.36.0-10ubuntu1 [4782 kB] Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 perl amd64 5.36.0-10ubuntu1 [235 kB] Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 perl-base amd64 5.36.0-10ubuntu1 [1770 kB] Get:82 http://ftpmaster.internal/ubuntu noble/main amd64 perl-modules-5.36 all 5.36.0-10ubuntu1 [2984 kB] Get:83 http://ftpmaster.internal/ubuntu noble/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4 [736 kB] Get:84 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm6 amd64 1.23-5 [33.3 kB] Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libgdbm-compat4 amd64 1.23-5 [6498 B] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 util-linux amd64 2.39.2-6ubuntu1 [1120 kB] Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libdebconfclient0 amd64 0.271ubuntu1 [11.3 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 base-passwd amd64 3.6.3 [51.2 kB] Get:89 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 init-system-helpers all 1.66ubuntu1 [39.4 kB] Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.38-3ubuntu1 [680 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 ncurses-base all 6.4+20231209-1 [25.2 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 sysvinit-utils amd64 3.08-3ubuntu1 [33.7 kB] Get:93 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt amd64 2.7.7 [1376 kB] Get:94 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 apt-utils amd64 2.7.7 [216 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 ubuntu-keyring all 2023.11.28.1 [11.1 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libunistring5 amd64 1.1-2 [537 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libidn2-0 amd64 2.3.4-1build1 [64.3 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 libffi8 amd64 3.4.4-2 [24.4 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libp11-kit0 amd64 0.25.3-2ubuntu2 [298 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libgnutls30 amd64 3.8.1-4ubuntu6 [988 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules-bin amd64 1.5.2-9.1ubuntu1 [47.6 kB] Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-modules amd64 1.5.2-9.1ubuntu1 [284 kB] Get:103 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 init amd64 1.66ubuntu1 [6186 B] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libsmartcols1 amd64 2.39.2-6ubuntu1 [63.3 kB] Get:105 http://ftpmaster.internal/ubuntu noble/main amd64 uuid-runtime amd64 2.39.2-6ubuntu1 [32.9 kB] Get:106 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error-l10n all 1.47-3build1 [8024 B] Get:107 http://ftpmaster.internal/ubuntu noble/main amd64 libgpg-error0 amd64 1.47-3build1 [70.0 kB] Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libpam-runtime all 1.5.2-9.1ubuntu1 [41.5 kB] Get:109 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage-common all 3.5-1build1 [9982 B] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libsepol2 amd64 3.5-2 [300 kB] Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libsemanage2 amd64 3.5-1build1 [92.9 kB] Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libncursesw6 amd64 6.4+20231209-1 [147 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 libtinfo6 amd64 6.4+20231209-1 [107 kB] Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 passwd amd64 1:4.13+dfsg1-3ubuntu1 [844 kB] Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libproc2-0 amd64 2:4.0.4-2ubuntu1 [59.0 kB] Get:116 http://ftpmaster.internal/ubuntu noble/main amd64 mawk amd64 1.3.4.20231126-1 [126 kB] Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 procps amd64 2:4.0.4-2ubuntu1 [708 kB] Get:118 http://ftpmaster.internal/ubuntu noble/main amd64 krb5-locales all 1.20.1-5build1 [13.7 kB] Get:119 http://ftpmaster.internal/ubuntu noble/main amd64 readline-common all 8.2-3 [56.2 kB] Get:120 http://ftpmaster.internal/ubuntu noble/main amd64 libreadline8 amd64 8.2-3 [152 kB] Get:121 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-0 amd64 3.44.2-1 [685 kB] Get:122 http://ftpmaster.internal/ubuntu noble/main amd64 openssl amd64 3.0.10-1ubuntu3 [1188 kB] Get:123 http://ftpmaster.internal/ubuntu noble/main amd64 bash-completion all 1:2.11-8 [180 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 bsdextrautils amd64 2.39.2-6ubuntu1 [73.5 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 libpng16-16 amd64 1.6.40-2 [186 kB] Get:126 http://ftpmaster.internal/ubuntu noble/main amd64 xz-utils amd64 5.4.5-0.1 [268 kB] Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-2ubuntu1 [1122 B] Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-2ubuntu1 [5166 B] Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-2ubuntu1 [29.0 kB] Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 dpkg-dev all 1.22.1ubuntu5 [1147 kB] Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 libdpkg-perl all 1.22.1ubuntu5 [286 kB] Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 lto-disabled-list all 44 [12.4 kB] Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 libfakeroot amd64 1.32.2-1 [32.1 kB] Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 fakeroot amd64 1.32.2-1 [67.1 kB] Get:135 http://ftpmaster.internal/ubuntu noble/main amd64 optipng amd64 0.7.7-3 [83.3 kB] Get:136 http://ftpmaster.internal/ubuntu noble/main amd64 pinentry-curses amd64 1.2.1-3ubuntu1 [34.9 kB] Preconfiguring packages ... 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Setting up libtirpc-dev:amd64 (1.3.4+ds-1) ... Setting up gcc-13 (13.2.0-9ubuntu1) ... Setting up libdpkg-perl (1.22.1ubuntu5) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up gcc (4:13.2.0-2ubuntu1) ... Setting up dpkg-dev (1.22.1ubuntu5) ... Setting up libnsl-dev:amd64 (1.3.0-3) ... Setting up libc6-dev:amd64 (2.38-3ubuntu1) ... Setting up libstdc++-13-dev:amd64 (13.2.0-9ubuntu1) ... Setting up g++-13 (13.2.0-9ubuntu1) ... Setting up g++ (4:13.2.0-2ubuntu1) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for debianutils (5.14) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-27576140 amd64 noble-proposed -c chroot:build-PACKAGEBUILD-27576140 --arch=amd64 --dist=noble-proposed --nolog -A augustus_3.5.0+dfsg-4build1.dsc Initiating build PACKAGEBUILD-27576140 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lcy02-amd64-120.buildd +==============================================================================+ | augustus 3.5.0+dfsg-4build1 (amd64) Tue, 19 Dec 2023 15:09:10 +0000 | +==============================================================================+ Package: augustus Version: 3.5.0+dfsg-4build1 Source Version: 3.5.0+dfsg-4build1 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-27576140/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-Nen4mX/resolver-zwKmfX' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- augustus_3.5.0+dfsg-4build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/augustus-Nen4mX/augustus-3.5.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-Nen4mX' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath, 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 [474 B] Get:5 copy:/<>/apt_archive ./ Packages [559 B] Fetched 1990 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 libip4tc2 liblocale-gettext-perl libnss-nis libnss-nisplus libtext-charwidth-perl libtext-iconv-perl libtext-wrapi18n-perl libunistring2 psmisc uuid-runtime Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev chrpath debhelper debugedit default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd3 libarchive-zip-perl libbamtools-dev libbamtools2.5.2 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libbsd0 libbtf2 libbz2-dev libcamd3 libccolamd3 libcholmod5 libcolamd3 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse4 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu74 libklu2 liblapack-dev liblapack3 libldap2 libldl3 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmongoose3 libmysql++-dev libmysql++3v5 libmysqlclient-dev libmysqlclient21 libncurses-dev libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librbio4 librtmp1 libruby libruby3.1 libsasl2-2 libsasl2-modules-db libspex2 libspqr4 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig7 libtool libuchardet0 libumfpack6 libxml2 libyaml-0-2 libzstd-dev m4 man-db media-types mysql-common netbase po-debconf python3 python3-minimal python3.11 python3.11-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc liblapack-doc libboost1.83-doc libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph1.83-dev libboost-graph-parallel1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi1.83-dev libboost-mpi-python1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-python1.83-dev libboost-random1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.83-dev libcurl4-doc libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html icu-doc liblzma-doc libmysql++-doc ncurses-doc sqlite3-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support ri ruby-dev bundler cwltool Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libgraphblas-dev libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev chrpath debhelper debugedit default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd3 libarchive-zip-perl libbamtools-dev libbamtools2.5.2 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.83-dev libboost-iostreams1.83.0 libboost-regex1.83-dev libboost-regex1.83.0 libboost-serialization-dev libboost-serialization1.83-dev libboost-serialization1.83.0 libboost1.83-dev libbrotli1 libbsd0 libbtf2 libbz2-dev libcamd3 libccolamd3 libcholmod5 libcolamd3 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse4 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu74 libklu2 liblapack-dev liblapack3 libldap2 libldl3 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmongoose3 libmysql++-dev libmysql++3v5 libmysqlclient-dev libmysqlclient21 libncurses-dev libncurses6 libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librbio4 librtmp1 libruby libruby3.1 libsasl2-2 libsasl2-modules-db libspex2 libspqr4 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig7 libtool libuchardet0 libumfpack6 libxml2 libyaml-0-2 libzstd-dev m4 man-db media-types mysql-common netbase po-debconf python3 python3-minimal python3.11 python3.11-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration samtools sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 87.6 MB of archives. After this operation, 473 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [774 B] Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.11-minimal amd64 3.11.7-2 [840 kB] Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 libexpat1 amd64 2.5.0-2 [85.2 kB] Get:4 http://ftpmaster.internal/ubuntu noble/main amd64 python3.11-minimal amd64 3.11.7-2 [2219 kB] Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3-minimal amd64 3.11.4-5ubuntu1 [26.9 kB] Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 media-types all 10.1.0 [27.5 kB] Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 netbase all 6.4 [13.1 kB] Get:8 http://ftpmaster.internal/ubuntu noble/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1927 kB] Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 python3.11 amd64 3.11.7-2 [583 kB] Get:10 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libpython3-stdlib amd64 3.11.4-5ubuntu1 [9562 B] Get:11 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 python3 amd64 3.11.4-5ubuntu1 [22.9 kB] Get:12 http://ftpmaster.internal/ubuntu noble/main amd64 libbsd0 amd64 0.11.7-4 [41.4 kB] Get:13 http://ftpmaster.internal/ubuntu noble/main amd64 libelf1 amd64 0.190-1 [57.0 kB] Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libicu74 amd64 74.2-1ubuntu1 [10.9 MB] Get:15 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libxml2 amd64 2.9.14+dfsg-1.3build3 [762 kB] Get:16 http://ftpmaster.internal/ubuntu noble/main amd64 libyaml-0-2 amd64 0.2.5-1 [52.8 kB] Get:17 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic-mgc amd64 1:5.45-2 [307 kB] Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libmagic1 amd64 1:5.45-2 [86.1 kB] Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 file amd64 1:5.45-2 [21.9 kB] Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 gettext-base amd64 0.21-14 [38.3 kB] Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 libuchardet0 amd64 0.0.8-1 [75.3 kB] Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 groff-base amd64 1.23.0-3 [1023 kB] Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libedit2 amd64 3.1-20230828-1 [95.8 kB] Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses6 amd64 6.4+20231209-1 [111 kB] Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 libnghttp2-14 amd64 1.58.0-1 [73.2 kB] Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 libpipeline1 amd64 1.5.7-1 [23.3 kB] Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 libpsl5 amd64 0.21.2-1build1 [56.8 kB] Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 man-db amd64 2.12.0-1 [1229 kB] Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 rubygems-integration all 1.18 [5336 B] Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 rake all 13.0.6-3 [61.6 kB] Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-net-telnet all 0.2.0-1 [13.3 kB] Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-webrick all 1.8.1-1 [52.3 kB] Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 libruby amd64 1:3.1 [3938 B] Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-sdbm amd64 1.0.0-5build2 [16.4 kB] Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libruby3.1 amd64 3.1.2-7ubuntu3 [5169 kB] Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 ruby3.1 amd64 3.1.2-7ubuntu3 [48.9 kB] Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 ruby-rubygems all 3.4.20-1 [238 kB] Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 ruby amd64 1:3.1 [3470 B] Get:40 http://ftpmaster.internal/ubuntu noble/universe amd64 ruby-asciidoctor all 2.0.20-1 [174 kB] Get:41 http://ftpmaster.internal/ubuntu noble/universe amd64 asciidoctor all 2.0.20-1 [44.2 kB] Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 m4 amd64 1.4.19-4 [243 kB] Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 autoconf all 2.71-3 [339 kB] Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 autopoint all 0.21-14 [422 kB] Get:47 http://ftpmaster.internal/ubuntu noble/universe amd64 chrpath amd64 0.16-2 [13.2 kB] Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 libdebhelper-perl all 13.11.8ubuntu1 [85.9 kB] Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 libtool all 2.4.7-7 [166 kB] Get:50 http://ftpmaster.internal/ubuntu noble/main amd64 dh-autoreconf all 20 [16.1 kB] Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-override-perl all 0.10-1 [10.0 kB] Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB] Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 dh-strip-nondeterminism all 1.13.1-1 [5362 B] Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 libdw1 amd64 0.190-1 [260 kB] Get:56 http://ftpmaster.internal/ubuntu noble/main amd64 debugedit amd64 1:5.0-5 [46.1 kB] Get:57 http://ftpmaster.internal/ubuntu noble/main amd64 dwz amd64 0.15-1 [112 kB] Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 gettext amd64 0.21-14 [865 kB] Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 po-debconf all 1.0.21+nmu1 [233 kB] Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 debhelper all 13.11.8ubuntu1 [940 kB] Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 mysql-common all 5.8+1.1.0 [6626 B] Get:63 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmysqlclient21 amd64 8.0.35-1ubuntu2 [1283 kB] Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libssl-dev amd64 3.0.10-1ubuntu3 [2402 kB] Get:65 http://ftpmaster.internal/ubuntu noble/main amd64 libzstd-dev amd64 1.5.5+dfsg2-2 [364 kB] Get:66 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3ubuntu1 [896 kB] Get:67 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libmysqlclient-dev amd64 8.0.35-1ubuntu2 [1596 kB] Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 default-libmysqlclient-dev amd64 1.1.0 [3014 B] Get:69 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 icu-devtools amd64 74.2-1ubuntu1 [212 kB] Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libsuitesparseconfig7 amd64 1:7.3.1+dfsg-2 [11.7 kB] Get:71 http://ftpmaster.internal/ubuntu noble/universe amd64 libamd3 amd64 1:7.3.1+dfsg-2 [26.8 kB] Get:72 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-5 [137 kB] Get:73 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libbamtools-dev amd64 2.5.2+dfsg-5 [240 kB] Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.11.0-2build1 [237 kB] Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libblas-dev amd64 3.11.0-2build1 [170 kB] Get:76 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost1.83-dev amd64 1.83.0-1ubuntu3 [10.7 MB] Get:77 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-regex1.83.0 amd64 1.83.0-1ubuntu3 [339 kB] Get:78 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libicu-dev amd64 74.2-1ubuntu1 [11.9 MB] Get:79 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-regex1.83-dev amd64 1.83.0-1ubuntu3 [355 kB] Get:80 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-iostreams1.83.0 amd64 1.83.0-1ubuntu3 [259 kB] Get:81 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-iostreams1.83-dev amd64 1.83.0-1ubuntu3 [264 kB] Get:82 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-iostreams-dev amd64 1.83.0.1ubuntu2 [4046 B] Get:83 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-serialization1.83.0 amd64 1.83.0-1ubuntu3 [341 kB] Get:84 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 libboost-serialization1.83-dev amd64 1.83.0-1ubuntu3 [387 kB] Get:85 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 libboost-serialization-dev amd64 1.83.0.1ubuntu2 [4280 B] Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libbrotli1 amd64 1.1.0-2 [332 kB] Get:87 http://ftpmaster.internal/ubuntu noble/universe amd64 libbtf2 amd64 1:7.3.1+dfsg-2 [12.4 kB] Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libbz2-dev amd64 1.0.8-5build1 [32.5 kB] Get:89 http://ftpmaster.internal/ubuntu noble/universe amd64 libcamd3 amd64 1:7.3.1+dfsg-2 [23.4 kB] Get:90 http://ftpmaster.internal/ubuntu noble/universe amd64 libccolamd3 amd64 1:7.3.1+dfsg-2 [25.3 kB] Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libcolamd3 amd64 1:7.3.1+dfsg-2 [18.6 kB] Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 13.2.0-9ubuntu1 [891 kB] Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.11.0-2build1 [2623 kB] Get:94 http://ftpmaster.internal/ubuntu noble/universe amd64 libcholmod5 amd64 1:7.3.1+dfsg-2 [511 kB] Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4 [20.1 kB] Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4 [53.3 kB] Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libldap2 amd64 2.6.6+dfsg-1~exp1ubuntu1 [193 kB] Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libssh-4 amd64 0.10.5-3ubuntu1 [187 kB] Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libcurl3-gnutls amd64 8.4.0-2ubuntu1 [328 kB] Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libcurl4-gnutls-dev amd64 8.4.0-2ubuntu1 [436 kB] Get:102 http://ftpmaster.internal/ubuntu noble/universe amd64 libcxsparse4 amd64 1:7.3.1+dfsg-2 [74.5 kB] Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.18-1 [43.1 kB] Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate-dev amd64 1.18-1 [49.8 kB] Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 libgslcblas0 amd64 2.7.1+dfsg-6ubuntu1 [104 kB] Get:106 http://ftpmaster.internal/ubuntu noble/universe amd64 libgsl27 amd64 2.7.1+dfsg-6ubuntu1 [987 kB] Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 libgsl-dev amd64 2.7.1+dfsg-6ubuntu1 [1259 kB] Get:108 http://ftpmaster.internal/ubuntu noble/universe amd64 libhtscodecs2 amd64 1.6.0-1 [98.9 kB] Get:109 http://ftpmaster.internal/ubuntu noble/universe amd64 libhts3 amd64 1.18+ds-1 [428 kB] Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 liblzma-dev amd64 5.4.5-0.1 [178 kB] Get:111 http://ftpmaster.internal/ubuntu noble/universe amd64 libhts-dev amd64 1.18+ds-1 [5837 kB] Get:112 http://ftpmaster.internal/ubuntu noble/universe amd64 libklu2 amd64 1:7.3.1+dfsg-2 [78.6 kB] Get:113 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack-dev amd64 3.11.0-2build1 [5104 kB] Get:114 http://ftpmaster.internal/ubuntu noble/universe amd64 libldl3 amd64 1:7.3.1+dfsg-2 [12.1 kB] Get:115 http://ftpmaster.internal/ubuntu noble/universe amd64 libmongoose3 amd64 1:7.3.1+dfsg-2 [33.0 kB] Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 libumfpack6 amd64 1:7.3.1+dfsg-2 [272 kB] Get:117 http://ftpmaster.internal/ubuntu noble/universe amd64 librbio4 amd64 1:7.3.1+dfsg-2 [26.3 kB] Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 libspqr4 amd64 1:7.3.1+dfsg-2 [136 kB] Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 libspex2 amd64 1:7.3.1+dfsg-2 [34.7 kB] Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 libsuitesparse-dev amd64 1:7.3.1+dfsg-2 [1329 kB] Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 liblpsolve55-dev amd64 5.5.2.5-2build3 [463 kB] Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 libmysql++3v5 amd64 3.2.5-2.1 [104 kB] Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 libmysql++-dev amd64 3.2.5-2.1 [96.4 kB] Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 libncurses-dev amd64 6.4+20231209-1 [382 kB] Get:125 http://ftpmaster.internal/ubuntu noble/main amd64 libsqlite3-dev amd64 3.44.2-1 [902 kB] Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 samtools amd64 1.19-1 [592 kB] Preconfiguring packages ... Fetched 87.6 MB in 1s (88.6 MB/s) Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... 13841 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.7-2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.7-2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.7-2_amd64.deb ... Unpacking python3.11-minimal (3.11.7-2) ... Setting up libpython3.11-minimal:amd64 (3.11.7-2) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.7-2) ... Selecting previously unselected package python3-minimal. (Reading database ... 14155 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.4-5ubuntu1_amd64.deb ... Unpacking python3-minimal (3.11.4-5ubuntu1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../3-libpython3.11-stdlib_3.11.7-2_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.7-2) ... Selecting previously unselected package python3.11. Preparing to unpack .../4-python3.11_3.11.7-2_amd64.deb ... Unpacking python3.11 (3.11.7-2) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../5-libpython3-stdlib_3.11.4-5ubuntu1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.4-5ubuntu1) ... Setting up python3-minimal (3.11.4-5ubuntu1) ... Selecting previously unselected package python3. (Reading database ... 14589 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.4-5ubuntu1_amd64.deb ... Unpacking python3 (3.11.4-5ubuntu1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../001-libbsd0_0.11.7-4_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-4) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../002-libelf1_0.190-1_amd64.deb ... Unpacking libelf1:amd64 (0.190-1) ... Selecting previously unselected package libicu74:amd64. Preparing to unpack .../003-libicu74_74.2-1ubuntu1_amd64.deb ... Unpacking libicu74:amd64 (74.2-1ubuntu1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../004-libxml2_2.9.14+dfsg-1.3build3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3build3) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../005-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... 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Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4) ... Setting up libssh-4:amd64 (0.10.5-3ubuntu1) ... Setting up libgfortran5:amd64 (13.2.0-9ubuntu1) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:amd64 (5.4.5-0.1) ... Setting up libicu74:amd64 (74.2-1ubuntu1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3ubuntu1) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up libsuitesparseconfig7:amd64 (1:7.3.1+dfsg-2) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... Setting up libbsd0:amd64 (0.11.7-4) ... Setting up libdeflate-dev:amd64 (1.18-1) ... Setting up libelf1:amd64 (0.190-1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3build3) ... Setting up libldap2:amd64 (2.6.6+dfsg-1~exp1ubuntu1) ... Setting up chrpath (0.16-2) ... Setting up libblas-dev:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libmysqlclient-dev (8.0.35-1ubuntu2) ... Setting up libbz2-dev:amd64 (1.0.8-5build1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up default-libmysqlclient-dev:amd64 (1.1.0) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libdw1:amd64 (0.190-1) ... Setting up liblapack3:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libncurses-dev:amd64 (6.4+20231209-1) ... Setting up gettext (0.21-14) ... Setting up libgsl-dev (2.7.1+dfsg-6ubuntu1) ... Setting up libamd3:amd64 (1:7.3.1+dfsg-2) ... Setting up libtool (2.4.7-7) ... Setting up libcolamd3:amd64 (1:7.3.1+dfsg-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.7-2) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libboost-serialization1.83-dev:amd64 (1.83.0-1ubuntu3) ... Setting up libcurl3-gnutls:amd64 (8.4.0-2ubuntu1) ... Setting up libcurl4-gnutls-dev:amd64 (8.4.0-2ubuntu1) ... Setting up libcamd3:amd64 (1:7.3.1+dfsg-2) ... Setting up libmongoose3:amd64 (1:7.3.1+dfsg-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libmysql++-dev:amd64 (3.2.5-2.1) ... Setting up dh-autoreconf (20) ... Setting up librbio4:amd64 (1:7.3.1+dfsg-2) ... Setting up libbamtools-dev:amd64 (2.5.2+dfsg-5) ... Setting up liblapack-dev:amd64 (3.11.0-2build1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up icu-devtools (74.2-1ubuntu1) ... Setting up libboost-serialization-dev:amd64 (1.83.0.1ubuntu2) ... Setting up libccolamd3:amd64 (1:7.3.1+dfsg-2) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up debugedit (1:5.0-5) ... Setting up libicu-dev:amd64 (74.2-1ubuntu1) ... Setting up libpython3-stdlib:amd64 (3.11.4-5ubuntu1) ... Setting up python3.11 (3.11.7-2) ... Setting up libcholmod5:amd64 (1:7.3.1+dfsg-2) ... Setting up libhts3:amd64 (1.18+ds-1) ... Setting up libspex2:amd64 (1:7.3.1+dfsg-2) ... Setting up libspqr4:amd64 (1:7.3.1+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libhts-dev:amd64 (1.18+ds-1) ... Setting up python3 (3.11.4-5ubuntu1) ... Setting up man-db (2.12.0-1) ... 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 samtools (1.19-1) ... Setting up libklu2:amd64 (1:7.3.1+dfsg-2) ... Setting up libboost-regex1.83-dev:amd64 (1.83.0-1ubuntu3) ... Setting up libumfpack6:amd64 (1:7.3.1+dfsg-2) ... Setting up libsuitesparse-dev:amd64 (1:7.3.1+dfsg-2) ... Setting up libboost-iostreams1.83-dev:amd64 (1.83.0-1ubuntu3) ... Setting up debhelper (13.11.8ubuntu1) ... Setting up libboost-iostreams-dev:amd64 (1.83.0.1ubuntu2) ... Setting up liblpsolve55-dev (5.5.2.5-2build3) ... Setting up libruby:amd64 (1:3.1) ... Setting up ruby-rubygems (3.4.20-1) ... Setting up ruby (1:3.1) ... 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-sdbm:amd64 (1.0.0-5build2) ... Setting up libruby3.1:amd64 (3.1.2-7ubuntu3) ... Setting up ruby3.1 (3.1.2-7ubuntu3) ... Processing triggers for libc-bin (2.38-3ubuntu1) ... Processing triggers for systemd (255-1ubuntu1) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-169-generic #187-Ubuntu SMP Thu Nov 23 14:52:28 UTC 2023 amd64 (x86_64) Toolchain package versions: binutils_2.41.50.20231214-1ubuntu1 dpkg-dev_1.22.1ubuntu5 g++-13_13.2.0-9ubuntu1 gcc-13_13.2.0-9ubuntu1 libc6-dev_2.38-3ubuntu1 libstdc++-13-dev_13.2.0-9ubuntu1 libstdc++6_13.2.0-9ubuntu1 linux-libc-dev_6.6.0-14.14 Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1 apt_2.7.7 apt-utils_2.7.7 asciidoctor_2.0.20-1 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13ubuntu5 base-passwd_3.6.3 bash_5.2.21-2ubuntu1 bash-completion_1:2.11-8 binutils_2.41.50.20231214-1ubuntu1 binutils-common_2.41.50.20231214-1ubuntu1 binutils-x86-64-linux-gnu_2.41.50.20231214-1ubuntu1 bsdextrautils_2.39.2-6ubuntu1 bsdutils_1:2.39.2-6ubuntu1 build-essential_12.10ubuntu1 bzip2_1.0.8-5build1 ca-certificates_20230311ubuntu1 chrpath_0.16-2 coreutils_9.4-2ubuntu1 cpp_4:13.2.0-2ubuntu1 cpp-13_13.2.0-9ubuntu1 dash_0.5.12-6ubuntu1 debconf_1.5.82 debconf-i18n_1.5.82 debhelper_13.11.8ubuntu1 debianutils_5.14 debugedit_1:5.0-5 default-libmysqlclient-dev_1.1.0 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.1ubuntu5 dpkg-dev_1.22.1ubuntu5 dwz_0.15-1 e2fsprogs_1.47.0-2ubuntu1 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-2ubuntu1 g++-13_13.2.0-9ubuntu1 gcc_4:13.2.0-2ubuntu1 gcc-13_13.2.0-9ubuntu1 gcc-13-base_13.2.0-9ubuntu1 gettext_0.21-14 gettext-base_0.21-14 gpg_2.2.40-1.1ubuntu1 gpg-agent_2.2.40-1.1ubuntu1 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util-linux_2.39.2-6ubuntu1 uuid-runtime_2.39.2-6ubuntu1 xz-utils_5.4.5-0.1 zlib1g_1:1.3.dfsg-3ubuntu1 zlib1g-dev_1:1.3.dfsg-3ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: augustus Binary: augustus, augustus-data, augustus-doc Architecture: any all Version: 3.5.0+dfsg-4build1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://bioinf.uni-greifswald.de/augustus/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/augustus Vcs-Git: https://salsa.debian.org/med-team/augustus.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools, chrpath Package-List: augustus deb science optional arch=any augustus-data deb science optional arch=all augustus-doc deb doc optional arch=all Checksums-Sha1: a926ee500e46fc39c81376be09bbcca055b8a8ad 151813456 augustus_3.5.0+dfsg.orig.tar.xz 6a8da6627837382c9cd2a353b0dca83e6e07552a 20332 augustus_3.5.0+dfsg-4build1.debian.tar.xz Checksums-Sha256: 30a2a5200e7201a28383bebb98350eab9e043e38d0f7b825a1c8a614a6e68dc8 151813456 augustus_3.5.0+dfsg.orig.tar.xz 5ca71587bcf5ac1a84d1038e18c9a115ca76c92237c482b21949f6553fb68e3d 20332 augustus_3.5.0+dfsg-4build1.debian.tar.xz Files: 11cc56baea3047c128e2da42f7cf9dd0 151813456 augustus_3.5.0+dfsg.orig.tar.xz ce7122b3d11ece2520c82f0084e174e7 20332 augustus_3.5.0+dfsg-4build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEVovyKmYzfL/Jprm3LIPbyOm9DjcFAmWBsBYACgkQLIPbyOm9 DjcDAA/9F51YRrUgYtM2RoGDlXSH46Q7Hf2sk4c4s/e76uNgssgOAJKVAfM/BNNu 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dpkg-source: info: unpacking augustus_3.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking augustus_3.5.0+dfsg-4build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying search_config_path dpkg-source: info: applying set_installdir dpkg-source: info: applying interpreter_paths.patch dpkg-source: info: applying switch_cgp_testing_off.patch dpkg-source: info: applying disable-compare.patch dpkg-source: info: applying s390x-disable-filterbam-tests.patch dpkg-source: info: applying cstdint.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-27576140 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-27576140 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-27576140 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 augustus dpkg-buildpackage: info: source version 3.5.0+dfsg-4build1 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 '/<>' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/<>/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/<>/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/<>/auxprogs/homGeneMapping' cd src; make clean make[3]: Entering directory '/<>/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o sqliteDB.o rm -f ../../../bin/homGeneMapping make[3]: Leaving directory '/<>/auxprogs/homGeneMapping/src' if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean homGeneMapping ; fi make[2]: Leaving directory '/<>/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/<>/auxprogs/joingenes' rm -f *.o joingenes ../../bin/joingenes make[2]: Leaving directory '/<>/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/<>/auxprogs/aln2wig' rm -f aln2wig aln2wig.o ../../bin/aln2wig make[2]: Leaving directory '/<>/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/<>/auxprogs/bam2wig' rm -f bam2wig.o bam2wig rm -f ../../bin/bam2wig if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean bam2wig ; fi make[2]: Leaving directory '/<>/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/<>/auxprogs/compileSpliceCands' rm -f compileSpliceCands *.o ../../bin/compileSpliceCands make[2]: Leaving directory '/<>/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/<>/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/<>/auxprogs/filterBam/src' rm -f *~ filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o rm -f filterBam rm -f ../../../bin/filterBam make[3]: Leaving directory '/<>/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/auxprogs/filterBam' /usr/bin/make -C auxprogs/utrrnaseq clean make[2]: Entering directory '/<>/auxprogs/utrrnaseq' rm -rf build/test *.gff rm -rf build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o build/Compute_UTRs.d build/Coord_Transform.d build/Genomic_Data.d build/Splice_Sites.d build/Supporting_Methods.d build/Test.d build/UTRs.d build/main.d build utrrnaseq make[2]: Leaving directory '/<>/auxprogs/utrrnaseq' rm -rf bin rm -f debian/*substvars rm -f debian/mansrc/*.1 find . -name "__pycache__" | xargs -r rm -r find src -name "*.o" | xargs -r rm find tests -name "*.sam.bam" | xargs -r rm find auxprogs -name "*.o" | xargs -r rm rm -rf tests/short/examples/results \ tests/short/auxprogs/bam2hints/tmp/ \ tests/short/auxprogs/bam2hints/result_files/ \ tests/short/auxprogs/filterbam/result_files/ rm -f auxprogs/utrrnaseq/Debug/utrrnaseq \ src/augustus \ src/cxxflags \ src/etraining \ src/fastBlockSearch \ src/getSeq \ src/load2db \ src/load2sqlitedb \ src/pp_simScore \ src/prepareAlign 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 '/<>' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/<>/auxprogs/aln2wig' cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-sign-compare -ansi -pedantic -O2 -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/augustus-3.5.0+dfsg-4build1 -c aln2wig.c cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wno-sign-compare -ansi -pedantic -O2 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o mkdir -p ../../bin cp -f aln2wig ../../bin make[2]: Leaving directory '/<>/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/<>/auxprogs/bam2hints' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O3 -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/augustus-3.5.0+dfsg-4build1 -I/usr/include/bamtools -c bam2hints.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O3 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -I/usr/include/bamtools -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp -f bam2hints ../../bin make[2]: Leaving directory '/<>/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/<>/auxprogs/bam2wig' cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O2 -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/augustus-3.5.0+dfsg-4build1 -I/usr/include/htslib -I/usr/local/include/htslib/ -c bam2wig.c cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O2 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o bam2wig bam2wig.o -lhts -lz -lpthread mkdir -p ../../bin cp -f bam2wig ../../bin/bam2wig make[2]: Leaving directory '/<>/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/<>/auxprogs/compileSpliceCands' cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -pedantic -ansi -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/augustus-3.5.0+dfsg-4build1 -c compileSpliceCands.c compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:216:9: warning: ‘__strncat_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^ compileSpliceCands.c:216:9: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function ‘parseLine’: compileSpliceCands.c:292:9: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 292 | strncpy(d->name,tokens[0],LINEBUFFER); | ^ compileSpliceCands.c: In function ‘parseList’: compileSpliceCands.c:333:69: warning: ‘left’ may be used uninitialized [-Wmaybe-uninitialized] 333 | isCandidate = ((right->averageCoverage>=left->averageCoverage*threshold) || | ~~~~^~~~~~~~~~~~~~~~~ compileSpliceCands.c:314:14: note: ‘left’ was declared here 314 | Data left; | ^~~~ compileSpliceCands.c: In function ‘main’: compileSpliceCands.c:563:17: warning: ‘chromosomeLength’ may be used uninitialized [-Wmaybe-uninitialized] 563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c:416:18: note: ‘chromosomeLength’ was declared here 416 | long int chromosomeLength; | ^~~~~~~~~~~~~~~~ cc -Wall -pedantic -ansi -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/augustus-3.5.0+dfsg-4build1 -Wdate-time -D_FORTIFY_SOURCE=3 -c -o list.o list.c cc -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -pedantic -ansi -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:216:9: warning: ‘__builtin___strncat_chk’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^ compileSpliceCands.c:216:9: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^ cp -f compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/<>/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/<>/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/<>/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -I./headers -I/usr/include/bamtools -c filterBam.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -I./headers -I/usr/include/bamtools -c functions/initOptions.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -I./headers -I/usr/include/bamtools -c functions/printElapsedTime.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -I./headers -I/usr/include/bamtools -c functions/MatePairs.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -I./headers -I/usr/include/bamtools -c functions/PairednessCoverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -I./headers -I/usr/include/bamtools -c BamToolsAccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/<>/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/<>/auxprogs/homGeneMapping/src' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -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/augustus-3.5.0+dfsg-4build1 -I../include -c gene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -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/augustus-3.5.0+dfsg-4build1 -I../include -c genome.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -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/augustus-3.5.0+dfsg-4build1 -I../include -c sqliteDB.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -lsqlite3 mkdir -p ../../../bin/ cp -f homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/<>/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/<>/auxprogs/joingenes' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -std=gnu++0x -O2 -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/augustus-3.5.0+dfsg-4build1 -c joingenes.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -std=gnu++0x -O2 -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/augustus-3.5.0+dfsg-4build1 -c jg_transcript.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -std=gnu++0x -O2 -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/augustus-3.5.0+dfsg-4build1 -c jg_ios.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -std=gnu++0x -O2 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o joingenes joingenes.o jg_transcript.o jg_ios.o mkdir -p ../../bin/ cp -f joingenes ../../bin/ make[2]: Leaving directory '/<>/auxprogs/joingenes' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>' mkdir -p bin mkdir -p bin cd src && make cd auxprogs && make make[3]: Entering directory '/<>/src' make[3]: Entering directory '/<>/auxprogs' cd aln2wig; make; make[4]: Entering directory '/<>/auxprogs/aln2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'aln2wig' is up to date. make[4]: Leaving directory '/<>/auxprogs/aln2wig' cd bam2hints; make; g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc make[4]: Entering directory '/<>/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/bam2hints' cd compileSpliceCands; make; make[4]: Entering directory '/<>/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/<>/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[5]: Entering directory '/<>/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/<>/auxprogs/filterBam/src' make[4]: Leaving directory '/<>/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/<>/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/<>/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/<>/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/<>/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/<>/auxprogs/joingenes' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/joingenes' cd utrrnaseq; make; make[4]: Entering directory '/<>/auxprogs/utrrnaseq' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p build Building file: src/Compute_UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/Compute_UTRs.d" -MT"build/Compute_UTRs.o" -o "build/Compute_UTRs.o" "src/Compute_UTRs.cpp" src/Compute_UTRs.cpp: In function ‘compute_UTRs(std::__cxx11::basic_string, std::allocator >)’: src/Compute_UTRs.cpp:142:18: warning: ‘chrom_pos’ may be used uninitialized [-Wmaybe-uninitialized] 142 | unsigned chrom_pos; //position for fixedStep only | ^~~~~~~~~ src/Compute_UTRs.cpp:251:69: warning: ‘step’ may be used uninitialized [-Wmaybe-uninitialized] 251 | for (int i = 0; i < (int)step; ++i) { | ^~~~~~~~~ src/Compute_UTRs.cpp:143:18: note: ‘step’ was declared here 143 | unsigned step; //Step for fixedStep only | ^~~~ src/Compute_UTRs.cpp:199:141: warning: ‘idx_former_scaff’ may be used uninitialized [-Wmaybe-uninitialized] 199 | const Genomic_Data::Scaff_plus_Gen_Data& curr_scaff = Genomic_Data::get_all_genes()[idx_former_scaff]; | ^ src/Compute_UTRs.cpp:150:18: note: ‘idx_former_scaff’ was declared here 150 | unsigned idx_former_scaff; | ^~~~~~~~~~~~~~~~ Finished building: src/Compute_UTRs.cpp Building file: src/Coord_Transform.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/Coord_Transform.d" -MT"build/Coord_Transform.o" -o "build/Coord_Transform.o" "src/Coord_Transform.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc src/Coord_Transform.cpp:25:59: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 25 | template struct finding_intron_greater_s : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from src/flex_vec.hpp:8, from src/Coord_Transform.cpp:5: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp:33:58: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 33 | template struct finding_intron_lesser_s : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp:41:59: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | template struct finding_intron_greater_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp:49:58: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 49 | template struct finding_intron_lesser_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/Coord_Transform.cpp: In constructor ‘Coord_Transform::Coord_Transform(unsigned int, int, unsigned int, unsigned int, unsigned int, unsigned int, std::vector*)’: src/Coord_Transform.cpp:77:56: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 77 | bind2nd(finding_intron_greater_s(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp:81:56: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 81 | bind2nd(finding_intron_greater_e(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp:89:56: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 89 | bind2nd(finding_intron_lesser_e(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp:93:56: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 93 | bind2nd(finding_intron_lesser_s(), i)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/Coord_Transform.cpp: In member function ‘Coord_Transform::Coord_Transform(unsigned int, int, unsigned int, unsigned int, unsigned int, unsigned int, std::vector >*)’: src/Coord_Transform.cpp:148:70: warning: ‘skip_end’ may be used uninitialized [-Wmaybe-uninitialized] 148 | if (skip_start*dir > skip_end*dir) { | ~~~~~~~~^~~~ src/Coord_Transform.cpp:65:13: note: ‘skip_end’ was declared here 65 | int skip_end; //normally end position + W for this next intron | ^~~~~~~~ Finished building: src/Coord_Transform.cpp Building file: src/Genomic_Data.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/Genomic_Data.d" -MT"build/Genomic_Data.o" -o "build/Genomic_Data.o" "src/Genomic_Data.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc Finished building: src/Genomic_Data.cpp Building file: src/Splice_Sites.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/Splice_Sites.d" -MT"build/Splice_Sites.o" -o "build/Splice_Sites.o" "src/Splice_Sites.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc Finished building: src/Splice_Sites.cpp Building file: src/Supporting_Methods.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" Finished building: src/Supporting_Methods.cpp Building file: src/Test.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc Finished building: src/Test.cpp Building file: src/UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" src/UTRs.cpp:83:9: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 83 | binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from src/Genomic_Data.hpp:8, from src/UTRs.cpp:5: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:92:9: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 92 | binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:100:59: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 100 | template struct finding_intron_greater_s : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:108:58: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 108 | template struct finding_intron_lesser_s : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:116:59: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 116 | template struct finding_intron_greater_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:124:58: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 124 | template struct finding_intron_lesser_e : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp:133:49: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 133 | template struct finding_repeat : binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ src/UTRs.cpp: In static member function ‘static unsigned int UTRs::get_max_pos(unsigned int, int, unsigned int, unsigned int, std::vector*)’: src/UTRs.cpp:181:64: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_greater; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 181 | bind2nd(finding_coding_region_greater(), pos)) : | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:183:65: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_coding_region_lesser; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 183 | bind2nd(finding_coding_region_lesser(), pos)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp: In static member function ‘static bool UTRs::repeat_in_UTR(unsigned int, unsigned int, std::vector*)’: src/UTRs.cpp:196:63: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_repeat; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 196 | it = find_if(repeats->begin(), repeats->end(), bind2nd(finding_repeat(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp: In static member function ‘static std::vector UTRs::find_introns_in_range(unsigned int, unsigned int, int, std::vector*)’: src/UTRs.cpp:233:79: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_s; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 233 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_s(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:240:79: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_greater_e; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 240 | it = find_if(introns->begin(), introns->end(), bind2nd(finding_intron_greater_e(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:252:93: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_e; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 252 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_e(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ src/UTRs.cpp:259:93: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = finding_intron_lesser_s; _Tp = unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 259 | it = find_if(reverse_introns.begin(), reverse_introns.end(), bind2nd(finding_intron_lesser_s(), start)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc Finished building: src/UTRs.cpp Building file: src/main.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc Finished building: src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -O0 -pedantic -fmessage-length=0 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o utrrnaseq build/Compute_UTRs.o build/Coord_Transform.o build/Genomic_Data.o build/Splice_Sites.o build/Supporting_Methods.o build/Test.o build/UTRs.o build/main.o g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc Finished building target: utrrnaseq make[4]: Leaving directory '/<>/auxprogs/utrrnaseq' cd bam2wig; make; make[4]: Entering directory '/<>/auxprogs/bam2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/bam2wig' make[3]: Leaving directory '/<>/auxprogs' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp -f prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp -f load2sqlitedb ../bin/ echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 In member function ‘__ct ’, inlined from ‘addRow’ at pp_simscore.cc:71:18: pp_simscore.cc:33:30: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 33 | row = new Cell[length]; | ^ /usr/include/c++/13/new: In member function ‘addRow’: /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ cp -f load2db ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 extrinsicinfo.cc: In member function ‘__ct_base ’: extrinsicinfo.cc:1992:38: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1992 | sourceKey = new string[numSources]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ cp -f pp_simScore ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp -f getSeq ../bin/ ../include/vitmatrix.hh: In member function ‘assign’: ../include/vitmatrix.hh:696:43: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 696 | data = new ViterbiColumnType[count]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ motif.cc: In member function ‘setProperties.constprop’: motif.cc:460:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 460 | zus = new BaseCount[n]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ cp -f fastBlockSearch ../bin/ motif.cc: In member function ‘__ct_base ’: motif.cc:265:39: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 265 | windowProbs = new vector[n]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ motif.cc:266:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 266 | windowCounts = new vector[n]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc: In function ‘init’: utrmodel.cc:264:56: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 264 | GCttsMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:262:57: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 262 | GCtataMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:260:60: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 260 | GCtssMotifTATA = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:258:56: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 258 | GCtssMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:256:71: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 256 | GCtssup_emiprobs = new vector[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:254:66: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 254 | GCutr3_emiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:252:66: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 252 | GCutr5_emiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:250:70: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 250 | GCutr5init_emiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ motif.cc: In member function ‘read’: motif.cc:399:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 399 | windowProbs = new vector[n]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In member function ‘setProperties’, inlined from ‘__ct ’ at ../include/motif.hh:138:15, inlined from ‘computeStairs’ at motif.cc:544:24: motif.cc:460:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 460 | zus = new BaseCount[n]; | ^ /usr/include/c++/13/new: In member function ‘computeStairs’: /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc: In function ‘init’: exonmodel.cc:396:67: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 396 | GCemiprobs = new FramedPatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc:380:73: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 380 | GCtransInitBinProbs = new BinnedMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc:378:62: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 378 | GCtransInitMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc:376:69: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 376 | GCPls = new Matrix >[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ igenicmodel.cc: In function ‘init’: igenicmodel.cc:52:61: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 52 | GCemiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ igenicmodel.cc:54:69: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 54 | GCPls = new vector >[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ motif.cc: In member function ‘operator=.isra’: motif.cc:246:39: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 246 | windowProbs = new vector[n]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ motif.cc:247:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 247 | windowCounts = new vector[n]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc: In function ‘init’: exonmodel.cc:396:67: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 396 | GCemiprobs = new FramedPatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc:380:73: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 380 | GCtransInitBinProbs = new BinnedMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc:378:62: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 378 | GCtransInitMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ exonmodel.cc:376:69: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 376 | GCPls = new Matrix >[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc: In function ‘init’: utrmodel.cc:264:56: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 264 | GCttsMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:262:57: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 262 | GCtataMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:260:60: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 260 | GCtssMotifTATA = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:258:56: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 258 | GCtssMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:256:71: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 256 | GCtssup_emiprobs = new vector[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:254:66: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 254 | GCutr3_emiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:252:66: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 252 | GCutr5_emiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ utrmodel.cc:250:70: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 250 | GCutr5init_emiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ cp -f etraining ../bin/ igenicmodel.cc: In function ‘init’: igenicmodel.cc:52:61: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 52 | GCemiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ igenicmodel.cc:54:69: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 54 | GCPls = new vector >[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ ../include/vitmatrix.hh: In member function ‘assign’: ../include/vitmatrix.hh:696:43: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 696 | data = new ViterbiColumnType[count]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ intronmodel.cc: In function ‘init’: intronmodel.cc:166:61: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 166 | GCemiprobs = new PatMMGroup[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ intronmodel.cc:164:56: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 164 | GCassMotif = new Motif[Constant::decomp_num_steps]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ extrinsicinfo.cc: In member function ‘__ct_base ’: extrinsicinfo.cc:1992:38: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 1992 | sourceKey = new string[numSources]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ cp -f augustus ../bin/ make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc make[1]: Leaving directory '/<>' dh_auto_test make -j4 test make[1]: Entering directory '/<>' mkdir -p bin mkdir -p bin cd src && make cd auxprogs && make make[2]: Entering directory '/<>/auxprogs' cd aln2wig; make; make[2]: Entering directory '/<>/src' make[3]: Entering directory '/<>/auxprogs/aln2wig' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: 'aln2wig' is up to date. make[3]: Leaving directory '/<>/auxprogs/aln2wig' cd bam2hints; make; echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -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/augustus-3.5.0+dfsg-4build1 -Wdate-time -D_FORTIFY_SOURCE=3 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags make[3]: Entering directory '/<>/auxprogs/bam2hints' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[2]: Leaving directory '/<>/src' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/auxprogs/bam2hints' cd compileSpliceCands; make; make[3]: Entering directory '/<>/auxprogs/compileSpliceCands' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/auxprogs/compileSpliceCands' cd filterBam; make; make[3]: Entering directory '/<>/auxprogs/filterBam' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[4]: Entering directory '/<>/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=3 -Wall -Wextra -Wpedantic -std=c++11 -O3 -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/augustus-3.5.0+dfsg-4build1 -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[4]: Leaving directory '/<>/auxprogs/filterBam/src' make[3]: Leaving directory '/<>/auxprogs/filterBam' cd homGeneMapping; make; make[3]: Entering directory '/<>/auxprogs/homGeneMapping' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[4]: Entering directory '/<>/auxprogs/homGeneMapping/src' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/homGeneMapping/src' make[3]: Leaving directory '/<>/auxprogs/homGeneMapping' cd joingenes; make; make[3]: Entering directory '/<>/auxprogs/joingenes' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/auxprogs/joingenes' cd utrrnaseq; make; make[3]: Entering directory '/<>/auxprogs/utrrnaseq' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p build make[3]: Leaving directory '/<>/auxprogs/utrrnaseq' cd bam2wig; make; make[3]: Entering directory '/<>/auxprogs/bam2wig' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/auxprogs/bam2wig' make[2]: Leaving directory '/<>/auxprogs' cd tests/short && ./execute_test.py --html examples test_utr_on (examples.test_examples.TestExamples.test_utr_on) ... ok test_hints_MPE (examples.test_examples.TestExamples.test_hints_MPE) ... ok test_training_new_species (examples.test_examples.TestExamples.test_training_new_species) ... ok test_ab_initio_prediction (examples.test_examples.TestExamples.test_ab_initio_prediction) ... ok test_format_and_error_out (examples.test_examples.TestExamples.test_format_and_error_out) ... ok test_cgp (examples.test_examples.TestExamples.test_cgp) ... ok test_cgp_sqlite (examples.test_examples.TestExamples.test_cgp_sqlite) ... ok test_cgp_sqlite_hints (examples.test_examples.TestExamples.test_cgp_sqlite_hints) ... ok ---------------------------------------------------------------------- Ran 8 tests in 347.759s OK Removing generated test files... ---------------------------------------------------------------------- Executing small test suite ---------------------------------------------------------------------- Creating SQLite database for cgp test cases... cd tests/short && ./execute_test.py --html bam2hints test_bam2hints (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints) ... ok test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints_pipes) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.008s OK cd tests/short && ./execute_test.py --html bam2wig test_bam2wig (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig) ... ok test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig_region) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.021s OK cd tests/short && ./execute_test.py --html filterbam test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_options) ... ok test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId_no_minCover) ... ok test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId) ... ok test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minCover) ... ok test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_minCover99) ... ok test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniq) ... ok test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniqThresh) ... ok test_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_best) ... ok test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons) ... ok test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons_insertLimit) ... ok test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_not_paired) ... ok test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired) ... ok test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairwiseAlignments) ... ok test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_pairwiseAlignments_2) ... ok test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_maxIntronLen) ... ok test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairBedFile) ... ok test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_commonGeneFile) ... ok test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_no_options) ... ok test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_no_options) ... ok test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_uniq) ... ok test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_uniq) ... ok test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_best) ... ok test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_best) ... ok test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_paired_pairwiseAlignments) ... ok test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok ---------------------------------------------------------------------- Ran 25 tests in 0.526s OK make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' mkdir -p debian/augustus/usr/bin install bin/* debian/augustus/usr/bin install auxprogs/bam2wig/bam2wig \ debian/augustus/usr/bin install auxprogs/compileSpliceCands/compileSpliceCands \ debian/augustus/usr/bin install auxprogs/homGeneMapping/src/homGeneMapping \ debian/augustus/usr/bin install auxprogs/joingenes/joingenes \ debian/augustus/usr/bin mkdir -p debian/augustus/usr/share/augustus cp -r scripts debian/augustus/usr/share/augustus chmod -R -x debian/augustus/usr/share/augustus/scripts/* rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \ debian/augustus/usr/share/augustus/scripts/executeTestCGP.py \ debian/augustus/usr/share/augustus/scripts/*.txt chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \ debian/augustus/usr/share/augustus/scripts/*.pl* mkdir -p debian/augustus-doc/usr/share/doc/augustus cp README* debian/augustus-doc/usr/share/doc/augustus cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus cp docs/RUNNING* debian/augustus-doc/usr/share/doc/augustus cp docs/README* debian/augustus-doc/usr/share/doc/augustus cp docs/EXONCAND-MSAS-CGP.md \ debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial \ debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial-cgp \ debian/augustus-doc/usr/share/doc/augustus mkdir -p debian/augustus-data/usr/share/augustus cp -r config debian/augustus-data/usr/share/augustus find debian/augustus-data/usr/share/augustus \ -type f -exec chmod -x {} \; make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' chrpath -d debian/*/usr/bin/bam2hints chrpath -d debian/*/usr/bin/filterBam dh_install make[1]: Leaving directory '/<>' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs -k docs/HISTORY.TXT make[1]: Leaving directory '/<>' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -Xtutorial make[1]: Leaving directory '/<>' dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/augustus/usr/bin/getSeq: Unknown DWARF DW_FORM_0x1f21 fd6badc039dc3d30dbbbda0ed5b95317e27e71ed debugedit: debian/augustus/usr/bin/pp_simScore: Unknown DWARF DW_FORM_0x1f20 bf43a6ec8ac086caf7100134da9a4162422b2885 debugedit: debian/augustus/usr/bin/homGeneMapping: Unknown DWARF DW_FORM_0x1f21 b39e509cc08610275df4dcfaf9f91252b205ba09 debugedit: debian/augustus/usr/bin/fastBlockSearch: Unknown DWARF DW_FORM_0x1f20 33205556480056084157aeaea0e13550416aecb5 debugedit: debian/augustus/usr/bin/load2sqlitedb: Unknown DWARF DW_FORM_0x1f21 d93338c95eef0004dc5f176e5af6b9d979795c8d debugedit: debian/augustus/usr/bin/prepareAlign: Unknown DWARF DW_FORM_0x1f20 f19bcf9a323dec837943ba68e9ac66b73932930e debugedit: debian/augustus/usr/bin/compileSpliceCands: Unknown DWARF DW_FORM_0x1f21 ea35e82599d88bb5904ebaf9b95e3d9ca86ea80a debugedit: debian/augustus/usr/bin/joingenes: Unknown DWARF DW_FORM_0x1f20 0e5d613a72d2031e6955e770e4ae44fa4670d38d debugedit: debian/augustus/usr/bin/bam2hints: Unknown DWARF DW_FORM_0x1f20 ec271be451160f3a457812bce0511cd561a2bb84 debugedit: debian/augustus/usr/bin/augustus: Unknown DWARF DW_FORM_0x1f21 5198b5347784754d8128b87a0a2090906801ac43 debugedit: debian/augustus/usr/bin/etraining: Unknown DWARF DW_FORM_0x1f21 f3a5276ff8a570a9443c7a31ac1d5f44a19e3d79 debugedit: debian/augustus/usr/bin/bam2wig: Unknown DWARF DW_FORM_0x1f20 bf4247244dd9ba90b5a34e249434ce7bd02bf5fd debugedit: debian/augustus/usr/bin/aln2wig: Unknown DWARF DW_FORM_0x1f20 192ce367d02ec0efbd23e67cb87b13a7d72ab3b1 debugedit: debian/augustus/usr/bin/filterBam: Unknown DWARF DW_FORM_0x1f20 3b2bbc6215cce58b95ef783ccef3634610c75ea9 debugedit: debian/augustus/usr/bin/load2db: Unknown DWARF DW_FORM_0x1f21 ee027ceca26448d79cc66f570de8f6df1904b54a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing augustus (in debian/augustus); do_strip: , oemstrip: INFO: pkgstriptranslations version 154 INFO: pkgstriptranslations version 154 pkgstriptranslations: processing augustus-data (in debian/augustus-data); do_strip: , oemstrip: pkgstriptranslations: processing augustus-doc (in debian/augustus-doc); do_strip: , oemstrip: pkgstriptranslations: processing augustus-dbgsym (in debian/.debhelper/augustus/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/augustus/DEBIAN/control, package augustus, directory debian/augustus .. removing usr/share/doc/augustus/changelog.gz Skipping arch: any to arch: all dependency to augustus-data pkgstripfiles: processing control file: debian/.debhelper/augustus/dbgsym-root/DEBIAN/control, package augustus-dbgsym, directory debian/.debhelper/augustus/dbgsym-root pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus ... dpkg-deb: building package 'augustus-dbgsym' in 'debian/.debhelper/scratch-space/build-augustus/augustus-dbgsym_3.5.0+dfsg-4build1_amd64.deb'. pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-4build1_amd64.deb'. pkgstripfiles: processing control file: debian/augustus-data/DEBIAN/control, package augustus-data, directory debian/augustus-data .. removing usr/share/doc/augustus-data/changelog.gz pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus-data ... pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-4build1_all.deb'. pkgstripfiles: processing control file: debian/augustus-doc/DEBIAN/control, package augustus-doc, directory debian/augustus-doc .. removing usr/share/doc/augustus-doc/changelog.gz pkgstripfiles: Disabled PNG optimization for -doc package augustus-doc (to save build time) dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.5.0+dfsg-4build1_all.deb'. Renaming augustus-dbgsym_3.5.0+dfsg-4build1_amd64.deb to augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb dpkg-genbuildinfo --build=binary -O../augustus_3.5.0+dfsg-4build1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../augustus_3.5.0+dfsg-4build1_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 2023-12-19T15:19:42Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ augustus_3.5.0+dfsg-4build1_amd64.changes: ------------------------------------------ Format: 1.8 Date: Tue, 19 Dec 2023 15:46:05 +0100 Source: augustus Binary: augustus augustus-data augustus-doc Built-For-Profiles: noudeb Architecture: all amd64 Version: 3.5.0+dfsg-4build1 Distribution: noble-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: augustus - gene prediction in eukaryotic genomes augustus-data - data files for AUGUSTUS augustus-doc - documentation files for AUGUSTUS Changes: augustus (3.5.0+dfsg-4build1) noble; urgency=medium . * No-change rebuild for boost defaults change. Checksums-Sha1: 4708301d56ca6df4da2935dcd4256d5851a971ba 22773158 augustus-data_3.5.0+dfsg-4build1_all.deb f3079e55bc0783016ff1109f8d6430333b10cb1f 28636900 augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb 6c1b118d5fbdec66208f89d33feae65f42b76016 23506680 augustus-doc_3.5.0+dfsg-4build1_all.deb 4c556841bcf37a7a6ace985bdb5ce63a697250f1 9941 augustus_3.5.0+dfsg-4build1_amd64.buildinfo 8f2db3f0f1d349a57c16bed7460da6dbd56c9908 1743834 augustus_3.5.0+dfsg-4build1_amd64.deb Checksums-Sha256: 7d05cdf259f2be278a99cf588b8a380cb7d75e1c6bea98f928752bb496403482 22773158 augustus-data_3.5.0+dfsg-4build1_all.deb ecc49ea65283e41cf7fc09153b185fb17f69eaff537555093cc1e7e60ddf40c6 28636900 augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb fc107313d1f60dd1d35335f09a7760f49e46e911ef37c8cdf16ddd50f79698e9 23506680 augustus-doc_3.5.0+dfsg-4build1_all.deb 178a3d81da216bacf5453e42a9ac88866c451dfd7f9d766596d5fc25bb7309a5 9941 augustus_3.5.0+dfsg-4build1_amd64.buildinfo 5b182e7ff1e42f32935c1693b88439e1c1ebf1c677473dd1e35d398fb1e76dbd 1743834 augustus_3.5.0+dfsg-4build1_amd64.deb Files: 6984517816864c5cae6b0b87b5996445 22773158 science optional augustus-data_3.5.0+dfsg-4build1_all.deb 931efb20669c7aca5eefb6c939a034c8 28636900 debug optional augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb 3397cbbbd254ab707e9e3d19372bac90 23506680 doc optional augustus-doc_3.5.0+dfsg-4build1_all.deb 8bd4c8b577a436648c15e7c31cb34c9e 9941 science optional augustus_3.5.0+dfsg-4build1_amd64.buildinfo 97e095f2815664255d01d12470e84271 1743834 science optional augustus_3.5.0+dfsg-4build1_amd64.deb /<>/augustus_3.5.0+dfsg-4build1_amd64.changes.new could not be renamed to /<>/augustus_3.5.0+dfsg-4build1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: augustus Binary: augustus augustus-data augustus-dbgsym augustus-doc Architecture: all amd64 Version: 3.5.0+dfsg-4build1 Checksums-Md5: 6984517816864c5cae6b0b87b5996445 22773158 augustus-data_3.5.0+dfsg-4build1_all.deb 931efb20669c7aca5eefb6c939a034c8 28636900 augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb 3397cbbbd254ab707e9e3d19372bac90 23506680 augustus-doc_3.5.0+dfsg-4build1_all.deb 97e095f2815664255d01d12470e84271 1743834 augustus_3.5.0+dfsg-4build1_amd64.deb Checksums-Sha1: 4708301d56ca6df4da2935dcd4256d5851a971ba 22773158 augustus-data_3.5.0+dfsg-4build1_all.deb f3079e55bc0783016ff1109f8d6430333b10cb1f 28636900 augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb 6c1b118d5fbdec66208f89d33feae65f42b76016 23506680 augustus-doc_3.5.0+dfsg-4build1_all.deb 8f2db3f0f1d349a57c16bed7460da6dbd56c9908 1743834 augustus_3.5.0+dfsg-4build1_amd64.deb Checksums-Sha256: 7d05cdf259f2be278a99cf588b8a380cb7d75e1c6bea98f928752bb496403482 22773158 augustus-data_3.5.0+dfsg-4build1_all.deb ecc49ea65283e41cf7fc09153b185fb17f69eaff537555093cc1e7e60ddf40c6 28636900 augustus-dbgsym_3.5.0+dfsg-4build1_amd64.ddeb fc107313d1f60dd1d35335f09a7760f49e46e911ef37c8cdf16ddd50f79698e9 23506680 augustus-doc_3.5.0+dfsg-4build1_all.deb 5b182e7ff1e42f32935c1693b88439e1c1ebf1c677473dd1e35d398fb1e76dbd 1743834 augustus_3.5.0+dfsg-4build1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Tue, 19 Dec 2023 15:19:41 +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 (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13ubuntu5), base-passwd (= 3.6.3), bash (= 5.2.21-2ubuntu1), binutils (= 2.41.50.20231214-1ubuntu1), binutils-common (= 2.41.50.20231214-1ubuntu1), binutils-x86-64-linux-gnu (= 2.41.50.20231214-1ubuntu1), bsdextrautils (= 2.39.2-6ubuntu1), bsdutils (= 1:2.39.2-6ubuntu1), build-essential (= 12.10ubuntu1), bzip2 (= 1.0.8-5build1), ca-certificates (= 20230311ubuntu1), chrpath (= 0.16-2), coreutils (= 9.4-2ubuntu1), cpp (= 4:13.2.0-2ubuntu1), cpp-13 (= 13.2.0-9ubuntu1), dash (= 0.5.12-6ubuntu1), debconf (= 1.5.82), debhelper (= 13.11.8ubuntu1), debianutils (= 5.14), debugedit (= 1:5.0-5), default-libmysqlclient-dev (= 1.1.0), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.1ubuntu5), dpkg-dev (= 1.22.1ubuntu5), dwz (= 0.15-1), file (= 1:5.45-2), findutils (= 4.9.0-5), g++ (= 4:13.2.0-2ubuntu1), g++-13 (= 13.2.0-9ubuntu1), gcc (= 4:13.2.0-2ubuntu1), gcc-13 (= 13.2.0-9ubuntu1), gcc-13-base (= 13.2.0-9ubuntu1), gettext (= 0.21-14), gettext-base (= 0.21-14), grep (= 3.11-3), groff-base (= 1.23.0-3), gzip (= 1.12-1ubuntu1), hostname (= 3.23+nmu1ubuntu1), icu-devtools (= 74.2-1ubuntu1), init-system-helpers (= 1.66ubuntu1), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-3), libamd3 (= 1:7.3.1+dfsg-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 13.2.0-9ubuntu1), libatomic1 (= 13.2.0-9ubuntu1), libattr1 (= 1:2.5.1-4), libaudit-common (= 1:3.1.2-1), libaudit1 (= 1:3.1.2-1), libbamtools-dev (= 2.5.2+dfsg-5), libbamtools2.5.2 (= 2.5.2+dfsg-5), libbinutils (= 2.41.50.20231214-1ubuntu1), libblas-dev (= 3.11.0-2build1), libblas3 (= 3.11.0-2build1), libblkid1 (= 2.39.2-6ubuntu1), libboost-iostreams-dev (= 1.83.0.1ubuntu2), libboost-iostreams1.83-dev (= 1.83.0-1ubuntu3), libboost-iostreams1.83.0 (= 1.83.0-1ubuntu3), libboost-regex1.83-dev (= 1.83.0-1ubuntu3), libboost-regex1.83.0 (= 1.83.0-1ubuntu3), libboost-serialization-dev (= 1.83.0.1ubuntu2), libboost-serialization1.83-dev (= 1.83.0-1ubuntu3), libboost-serialization1.83.0 (= 1.83.0-1ubuntu3), libboost1.83-dev (= 1.83.0-1ubuntu3), libbrotli1 (= 1.1.0-2), libbsd0 (= 0.11.7-4), libbtf2 (= 1:7.3.1+dfsg-2), libbz2-1.0 (= 1.0.8-5build1), libbz2-dev (= 1.0.8-5build1), libc-bin (= 2.38-3ubuntu1), libc-dev-bin (= 2.38-3ubuntu1), libc6 (= 2.38-3ubuntu1), libc6-dev (= 2.38-3ubuntu1), libcamd3 (= 1:7.3.1+dfsg-2), libcap-ng0 (= 0.8.3-3), libcap2 (= 1:2.66-4ubuntu1), libcc1-0 (= 13.2.0-9ubuntu1), libccolamd3 (= 1:7.3.1+dfsg-2), libcholmod5 (= 1:7.3.1+dfsg-2), libcolamd3 (= 1:7.3.1+dfsg-2), libcom-err2 (= 1.47.0-2ubuntu1), libcrypt-dev (= 1:4.4.36-2), libcrypt1 (= 1:4.4.36-2), libctf-nobfd0 (= 2.41.50.20231214-1ubuntu1), libctf0 (= 2.41.50.20231214-1ubuntu1), libcurl3-gnutls (= 8.4.0-2ubuntu1), libcurl4-gnutls-dev (= 8.4.0-2ubuntu1), libcxsparse4 (= 1:7.3.1+dfsg-2), libdb5.3 (= 5.3.28+dfsg2-4), libdebconfclient0 (= 0.271ubuntu1), libdebhelper-perl (= 13.11.8ubuntu1), libdeflate-dev (= 1.18-1), libdeflate0 (= 1.18-1), libdpkg-perl (= 1.22.1ubuntu5), libdw1 (= 0.190-1), libedit2 (= 3.1-20230828-1), libelf1 (= 0.190-1), libexpat1 (= 2.5.0-2), libffi8 (= 3.4.4-2), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-9ubuntu1), libgcc-s1 (= 13.2.0-9ubuntu1), libgcrypt20 (= 1.10.2-3ubuntu1), libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgfortran5 (= 13.2.0-9ubuntu1), libgmp10 (= 2:6.3.0+dfsg-2ubuntu4), libgnutls30 (= 3.8.1-4ubuntu6), libgomp1 (= 13.2.0-9ubuntu1), libgpg-error0 (= 1.47-3build1), libgprofng0 (= 2.41.50.20231214-1ubuntu1), libgsl-dev (= 2.7.1+dfsg-6ubuntu1), libgsl27 (= 2.7.1+dfsg-6ubuntu1), libgslcblas0 (= 2.7.1+dfsg-6ubuntu1), libgssapi-krb5-2 (= 1.20.1-5build1), libhogweed6 (= 3.9.1-2), libhts-dev (= 1.18+ds-1), libhts3 (= 1.18+ds-1), libhtscodecs2 (= 1.6.0-1), libhwasan0 (= 13.2.0-9ubuntu1), libicu-dev (= 74.2-1ubuntu1), libicu74 (= 74.2-1ubuntu1), libidn2-0 (= 2.3.4-1build1), libisl23 (= 0.26-3), libitm1 (= 13.2.0-9ubuntu1), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-5build1), libkeyutils1 (= 1.6.3-2), libklu2 (= 1:7.3.1+dfsg-2), libkrb5-3 (= 1.20.1-5build1), libkrb5support0 (= 1.20.1-5build1), liblapack-dev (= 3.11.0-2build1), liblapack3 (= 3.11.0-2build1), libldap2 (= 2.6.6+dfsg-1~exp1ubuntu1), libldl3 (= 1:7.3.1+dfsg-2), liblpsolve55-dev (= 5.5.2.5-2build3), liblsan0 (= 13.2.0-9ubuntu1), liblz4-1 (= 1.9.4-1), liblzma-dev (= 5.4.5-0.1), liblzma5 (= 5.4.5-0.1), libmagic-mgc (= 1:5.45-2), libmagic1 (= 1:5.45-2), libmd0 (= 1.1.0-1), libmongoose3 (= 1:7.3.1+dfsg-2), libmount1 (= 2.39.2-6ubuntu1), libmpc3 (= 1.3.1-1), libmpfr6 (= 4.2.1-1), libmysql++-dev (= 3.2.5-2.1), libmysql++3v5 (= 3.2.5-2.1), libmysqlclient-dev (= 8.0.35-1ubuntu2), libmysqlclient21 (= 8.0.35-1ubuntu2), libncurses-dev (= 6.4+20231209-1), libncurses6 (= 6.4+20231209-1), libncursesw6 (= 6.4+20231209-1), libnettle8 (= 3.9.1-2), libnghttp2-14 (= 1.58.0-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libp11-kit0 (= 0.25.3-2ubuntu2), libpam-modules (= 1.5.2-9.1ubuntu1), libpam-modules-bin (= 1.5.2-9.1ubuntu1), libpam-runtime (= 1.5.2-9.1ubuntu1), libpam0g (= 1.5.2-9.1ubuntu1), libpcre2-8-0 (= 10.42-4ubuntu1), libperl5.36 (= 5.36.0-10ubuntu1), libpipeline1 (= 1.5.7-1), libpsl5 (= 0.21.2-1build1), libpython3-stdlib (= 3.11.4-5ubuntu1), libpython3.11-minimal (= 3.11.7-2), libpython3.11-stdlib (= 3.11.7-2), libquadmath0 (= 13.2.0-9ubuntu1), librbio4 (= 1:7.3.1+dfsg-2), libreadline8 (= 8.2-3), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libruby (= 1:3.1), libruby3.1 (= 3.1.2-7ubuntu3), libsasl2-2 (= 2.1.28+dfsg1-4), libsasl2-modules-db (= 2.1.28+dfsg1-4), libseccomp2 (= 2.5.4-2ubuntu1), libselinux1 (= 3.5-1build2), libsframe1 (= 2.41.50.20231214-1ubuntu1), libsmartcols1 (= 2.39.2-6ubuntu1), libspex2 (= 1:7.3.1+dfsg-2), libspqr4 (= 1:7.3.1+dfsg-2), libsqlite3-0 (= 3.44.2-1), libsqlite3-dev (= 3.44.2-1), libssh-4 (= 0.10.5-3ubuntu1), libssl-dev (= 3.0.10-1ubuntu3), libssl3 (= 3.0.10-1ubuntu3), libstdc++-13-dev (= 13.2.0-9ubuntu1), libstdc++6 (= 13.2.0-9ubuntu1), libsub-override-perl (= 0.10-1), libsuitesparse-dev (= 1:7.3.1+dfsg-2), libsuitesparseconfig7 (= 1:7.3.1+dfsg-2), libsystemd0 (= 255-1ubuntu1), libtasn1-6 (= 4.19.0-3), libtinfo6 (= 6.4+20231209-1), libtirpc-common (= 1.3.4+ds-1), libtirpc-dev (= 1.3.4+ds-1), libtirpc3 (= 1.3.4+ds-1), libtool (= 2.4.7-7), libtsan2 (= 13.2.0-9ubuntu1), libubsan1 (= 13.2.0-9ubuntu1), libuchardet0 (= 0.0.8-1), libudev1 (= 255-1ubuntu1), libumfpack6 (= 1:7.3.1+dfsg-2), libunistring5 (= 1.1-2), libuuid1 (= 2.39.2-6ubuntu1), libxml2 (= 2.9.14+dfsg-1.3build3), libyaml-0-2 (= 0.2.5-1), libzstd-dev (= 1.5.5+dfsg2-2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.0-14.14), login (= 1:4.13+dfsg1-3ubuntu1), lto-disabled-list (= 44), m4 (= 1.4.19-4), make (= 4.3-4.1build1), man-db (= 2.12.0-1), mawk (= 1.3.4.20231126-1), media-types (= 10.1.0), mysql-common (= 5.8+1.1.0), ncurses-base (= 6.4+20231209-1), ncurses-bin (= 6.4+20231209-1), netbase (= 6.4), openssl (= 3.0.10-1ubuntu3), patch (= 2.7.6-7build2), perl (= 5.36.0-10ubuntu1), perl-base (= 5.36.0-10ubuntu1), perl-modules-5.36 (= 5.36.0-10ubuntu1), po-debconf (= 1.0.21+nmu1), python3 (= 3.11.4-5ubuntu1), python3-minimal (= 3.11.4-5ubuntu1), python3.11 (= 3.11.7-2), python3.11-minimal (= 3.11.7-2), rake (= 13.0.6-3), readline-common (= 8.2-3), rpcsvc-proto (= 1.4.2-0ubuntu6), ruby (= 1:3.1), ruby-asciidoctor (= 2.0.20-1), ruby-net-telnet (= 0.2.0-1), ruby-rubygems (= 3.4.20-1), ruby-sdbm (= 1.0.0-5build2), ruby-webrick (= 1.8.1-1), ruby-xmlrpc (= 0.3.2-2), ruby3.1 (= 3.1.2-7ubuntu3), rubygems-integration (= 1.18), samtools (= 1.19-1), sed (= 4.9-1), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-3ubuntu1), tar (= 1.34+dfsg-1.2ubuntu2), tzdata (= 2023c-9ubuntu1), util-linux (= 2.39.2-6ubuntu1), xz-utils (= 5.4.5-0.1), zlib1g (= 1:1.3.dfsg-3ubuntu1), zlib1g-dev (= 1:1.3.dfsg-3ubuntu1) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1702997165" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ augustus-data_3.5.0+dfsg-4build1_all.deb ---------------------------------------- new Debian package, version 2.0. size 22773158 bytes: control archive=24651 bytes. 632 bytes, 15 lines control 163064 bytes, 1391 lines md5sums Package: augustus-data Source: augustus Version: 3.5.0+dfsg-4build1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 140336 Section: science Priority: optional Multi-Arch: foreign Homepage: https://bioinf.uni-greifswald.de/augustus/ Description: data files for AUGUSTUS This package contains pre-trained species models and other required architecture-independent data files for the AUGUSTUS gene finder. These are needed to identify gene structures in these or related organisms. drwxr-xr-x root/root 0 2023-12-19 14:46 ./ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/cgp/ -rw-r--r-- root/root 1672 2023-12-19 14:46 ./usr/share/augustus/config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg -rw-r--r-- root/root 1173 2023-12-19 14:46 ./usr/share/augustus/config/cgp/log_reg_parameters_arabidopsis.cfg -rw-r--r-- root/root 1546 2023-12-19 14:46 ./usr/share/augustus/config/cgp/log_reg_parameters_default.cfg -rw-r--r-- root/root 2628 2023-12-19 14:46 ./usr/share/augustus/config/cgp/log_reg_parameters_fly.cfg -rw-r--r-- root/root 1161 2023-12-19 14:46 ./usr/share/augustus/config/cgp/log_reg_parameters_human.cfg -rw-r--r-- root/root 861 2023-12-19 14:46 ./usr/share/augustus/config/cgp/log_reg_parameters_primates.cfg -rw-r--r-- root/root 937 2023-12-19 14:46 ./usr/share/augustus/config/cgp/log_reg_parameters_s_aureus.cfg drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/ -rw-r--r-- root/root 6731 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic-cgp.cfg -rw-r--r-- root/root 2349 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.E.XNT.cfg -rw-r--r-- root/root 2033 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.E.cfg -rw-r--r-- root/root 2723 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.P.cfg -rw-r--r-- root/root 2552 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.M.RM.E.W.cfg -rw-r--r-- root/root 2441 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.M.RM.PB.cfg -rw-r--r-- root/root 2003 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.ME.cfg -rw-r--r-- root/root 2574 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.MEMS.cfg -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.MP.cfg -rw-r--r-- root/root 2809 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.MPE.cfg -rw-r--r-- root/root 2350 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.MT.cfg -rw-r--r-- root/root 9979 2023-12-19 14:46 ./usr/share/augustus/config/extrinsic/extrinsic.cfg drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/model/ -rw-r--r-- root/root 3384 2023-12-19 14:46 ./usr/share/augustus/config/model/constraints_shadow_partial.txt -rw-r--r-- root/root 4113 2023-12-19 14:46 ./usr/share/augustus/config/model/constraints_shadow_partial_utr.txt -rw-r--r-- root/root 2400 2023-12-19 14:46 ./usr/share/augustus/config/model/ovlp_len.pbl -rw-r--r-- root/root 2374 2023-12-19 14:46 ./usr/share/augustus/config/model/ovlp_len_archaea.pbl -rw-r--r-- root/root 5594 2023-12-19 14:46 ./usr/share/augustus/config/model/states_shadow.cfg -rw-r--r-- root/root 5672 2023-12-19 14:46 ./usr/share/augustus/config/model/states_shadow_2igenic.cfg -rw-r--r-- root/root 866 2023-12-19 14:46 ./usr/share/augustus/config/model/states_shadow_bacterium.cfg -rw-r--r-- root/root 856 2023-12-19 14:46 ./usr/share/augustus/config/model/states_shadow_intronless.cfg -rw-r--r-- root/root 8509 2023-12-19 14:46 ./usr/share/augustus/config/model/states_shadow_utr.cfg -rw-r--r-- root/root 10075 2023-12-19 14:46 ./usr/share/augustus/config/model/states_shadow_utr_nc.cfg -rw-r--r-- root/root 3019 2023-12-19 14:46 ./usr/share/augustus/config/model/states_singlestrand.cfg -rw-r--r-- root/root 3086 2023-12-19 14:46 ./usr/share/augustus/config/model/states_singlestrand_2igenic.cfg -rw-r--r-- root/root 6884 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_atleastone.pbl -rw-r--r-- root/root 1353 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_bacterium.pbl -rw-r--r-- root/root 6435 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_complete.pbl -rw-r--r-- root/root 9818 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_complete_utr.pbl -rw-r--r-- root/root 6518 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_exactlyone.pbl -rw-r--r-- root/root 1197 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_intronless.pbl -rw-r--r-- root/root 9052 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_partial.pbl -rw-r--r-- root/root 14414 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_partial_utr.pbl -rw-r--r-- root/root 17332 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_shadow_partial_utr_nc.pbl -rw-r--r-- root/root 3690 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_singlestrand_atleastone.pbl -rw-r--r-- root/root 3416 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_singlestrand_complete.pbl -rw-r--r-- root/root 3487 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_singlestrand_exactlyone.pbl -rw-r--r-- root/root 4536 2023-12-19 14:46 ./usr/share/augustus/config/model/trans_singlestrand_partial.pbl drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/parameters/ -rw-r--r-- root/root 1231 2023-12-19 14:46 ./usr/share/augustus/config/parameters/AUG_CMDLN_PARAMETERS.md -rw-r--r-- root/root 49849 2023-12-19 14:46 ./usr/share/augustus/config/parameters/aug_cmdln_parameters.json drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/profile/ -rw-r--r-- root/root 1752 2023-12-19 14:46 ./usr/share/augustus/config/profile/blosum55.qij -rw-r--r-- root/root 1752 2023-12-19 14:46 ./usr/share/augustus/config/profile/blosum62.qij lrwxrwxrwx root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/profile/default.qij -> blosum62.qij drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/ drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/ -rw-r--r-- root/root 265142 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl -rw-r--r-- root/root 32524 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl -rw-r--r-- root/root 316261 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg -rw-r--r-- root/root 7319 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt -rw-r--r-- root/root 1734 2023-12-19 14:46 ./usr/share/augustus/config/species/Anopheles_gambiae/README.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/ -rw-r--r-- root/root 405541 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_exon_probs.pbl -rw-r--r-- root/root 65224 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl -rw-r--r-- root/root 226608 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg -rw-r--r-- root/root 7356 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/Argopecten_irradians_weightmatrix.txt -rw-r--r-- root/root 1898 2023-12-19 14:46 ./usr/share/augustus/config/species/Argopecten_irradians/README.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/ -rw-r--r-- root/root 238812 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_exon_probs.pbl -rw-r--r-- root/root 32585 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl -rw-r--r-- root/root 306671 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg -rw-r--r-- root/root 7293 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/Aurelia_aurita_weightmatrix.txt -rw-r--r-- root/root 1609 2023-12-19 14:46 ./usr/share/augustus/config/species/Aurelia_aurita/README.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Bathycoccus_prasinos/ -rw-r--r-- root/root 265665 2023-12-19 14:46 ./usr/share/augustus/config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_exon_probs.pbl -rw-r--r-- root/root 32623 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14:46 ./usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg -rw-r--r-- root/root 7321 2023-12-19 14:46 ./usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt -rw-r--r-- root/root 1492 2023-12-19 14:46 ./usr/share/augustus/config/species/Naegleria_gruberi/README.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Nemopilema_nomurai/ -rw-r--r-- root/root 252774 2023-12-19 14:46 ./usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_exon_probs.pbl -rw-r--r-- root/root 32548 2023-12-19 14:46 ./usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_igenic_probs.pbl -rw-r--r-- root/root 147283 2023-12-19 14:46 ./usr/share/augustus/config/species/Nemopilema_nomurai/Nemopilema_nomurai_intron_probs.pbl -rw-r--r-- root/root 2057 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drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/ -rw-r--r-- root/root 234471 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl -rw-r--r-- root/root 32716 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl -rw-r--r-- root/root 37558 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg -rw-r--r-- root/root 7377 2023-12-19 14:46 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./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl -rw-r--r-- root/root 32539 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl -rw-r--r-- root/root 345143 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg -rw-r--r-- root/root 7389 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt -rw-r--r-- root/root 1626 2023-12-19 14:46 ./usr/share/augustus/config/species/Pycnopodia_helianthoides/README.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/ -rw-r--r-- root/root 1562 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/README.txt -rw-r--r-- root/root 233908 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_exon_probs.pbl -rw-r--r-- root/root 32715 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_igenic_probs.pbl -rw-r--r-- root/root 143386 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg -rw-r--r-- root/root 7395 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/ -rw-r--r-- root/root 1656 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/README.txt -rw-r--r-- root/root 231075 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_exon_probs.pbl -rw-r--r-- root/root 32612 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_igenic_probs.pbl -rw-r--r-- root/root 373024 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg -rw-r--r-- root/root 7353 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Rhopilema_esculentum/Rhopilema_esculentum_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/ -rw-r--r-- root/root 1730 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/README.txt -rw-r--r-- root/root 453639 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl -rw-r--r-- root/root 65337 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl -rw-r--r-- root/root 215736 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg -rw-r--r-- root/root 7310 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/ -rw-r--r-- root/root 1606 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/README.txt -rw-r--r-- root/root 256985 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl -rw-r--r-- root/root 32510 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl -rw-r--r-- root/root 88077 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg -rw-r--r-- root/root 7396 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/ -rw-r--r-- root/root 1676 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/README.txt -rw-r--r-- root/root 242394 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl -rw-r--r-- root/root 32530 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl -rw-r--r-- root/root 100312 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg -rw-r--r-- root/root 7353 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/ -rw-r--r-- root/root 1455 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/README.txt -rw-r--r-- root/root 249461 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_exon_probs.pbl -rw-r--r-- root/root 32485 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_igenic_probs.pbl -rw-r--r-- root/root 330638 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg -rw-r--r-- root/root 7337 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Sordaria_macrospora/Sordaria_macrospora_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/ -rw-r--r-- root/root 1487 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/README.txt -rw-r--r-- root/root 259057 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_exon_probs.pbl -rw-r--r-- root/root 32409 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_igenic_probs.pbl -rw-r--r-- root/root 320022 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg -rw-r--r-- root/root 7340 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/ -rw-r--r-- root/root 1821 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/README.txt -rw-r--r-- root/root 635833 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl -rw-r--r-- root/root 97608 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl -rw-r--r-- root/root 284956 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg -rw-r--r-- root/root 7343 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/ -rw-r--r-- root/root 1654 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/README.txt -rw-r--r-- root/root 257107 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_exon_probs.pbl -rw-r--r-- root/root 32504 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_igenic_probs.pbl -rw-r--r-- root/root 380615 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.utr.cfg -rw-r--r-- root/root 7493 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/ -rw-r--r-- root/root 1519 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/README.txt -rw-r--r-- root/root 229484 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_exon_probs.pbl -rw-r--r-- root/root 32565 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_igenic_probs.pbl -rw-r--r-- root/root 97582 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg -rw-r--r-- root/root 7351 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/ -rw-r--r-- root/root 1546 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/README.txt -rw-r--r-- root/root 762759 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl -rw-r--r-- root/root 130684 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl -rw-r--r-- root/root 198017 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg -rw-r--r-- root/root 7316 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/ -rw-r--r-- root/root 1568 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/README.txt -rw-r--r-- root/root 399405 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl -rw-r--r-- root/root 65292 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl -rw-r--r-- root/root 207609 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg -rw-r--r-- root/root 7288 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/ -rw-r--r-- root/root 1613 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/README.txt -rw-r--r-- root/root 260235 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_exon_probs.pbl -rw-r--r-- root/root 32484 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_igenic_probs.pbl -rw-r--r-- root/root 343629 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg -rw-r--r-- root/root 7387 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/Xenopus_tropicalis/ -rw-r--r-- root/root 243087 2023-12-19 14:46 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drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/ -rw-r--r-- root/root 336182 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_exon_probs.pbl -rw-r--r-- root/root 46627 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_igenic_probs.pbl -rw-r--r-- root/root 137431 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_metapars.cfg -rw-r--r-- root/root 6818 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/aspergillus_terreus/aspergillus_terreus_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/b_pseudomallei/ 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./usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_parameters.cfg.orig2 -rw-r--r-- root/root 1403 2023-12-19 14:46 ./usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_trans_shadow_bacterium.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/b_pseudomallei/b_pseudomallei_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/ -rw-r--r-- root/root 738558 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl -rw-r--r-- root/root 260808 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF -rw-r--r-- root/root 130533 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl -rw-r--r-- root/root 32599 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF -rw-r--r-- root/root 139244 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl -rw-r--r-- root/root 148305 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_metapars.utr.cfg -rw-r--r-- root/root 7310 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg -rw-r--r-- root/root 7310 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1 -rw-r--r-- root/root 7308 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2 -rw-r--r-- root/root 7314 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3 -rw-r--r-- root/root 7311 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4 -rw-r--r-- root/root 7313 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5 -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_impatiens1/bombus_impatiens1_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/ -rw-r--r-- root/root 1204455 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl -rw-r--r-- root/root 222280 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF -rw-r--r-- root/root 228232 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl -rw-r--r-- root/root 32679 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF -rw-r--r-- root/root 333779 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl -rw-r--r-- root/root 105391 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF -rw-r--r-- root/root 2058 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_metapars.utr.cfg -rw-r--r-- root/root 7336 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg -rw-r--r-- root/root 7221 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1 -rw-r--r-- root/root 7337 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2 -rw-r--r-- root/root 7336 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3 -rw-r--r-- root/root 7336 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4 -rw-r--r-- root/root 352514 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_utr_probs.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/bombus_terrestris2/bombus_terrestris2_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/ -rw-r--r-- root/root 330915 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_exon_probs.pbl -rw-r--r-- root/root 46253 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_igenic_probs.pbl -rw-r--r-- root/root 147068 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_metapars.cfg -rw-r--r-- root/root 6779 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/botrytis_cinerea/botrytis_cinerea_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/ -rw-r--r-- root/root 2637768 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/brugia_exon_probs.pbl -rw-r--r-- root/root 367516 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/brugia_igenic_probs.pbl -rw-r--r-- root/root 288045 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/brugia_intron_probs.pbl -rw-r--r-- root/root 4029 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/brugia_parameters.cfg -rw-r--r-- root/root 404589 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/brugia_splicefile -rw-r--r-- root/root 805 2023-12-19 14:46 ./usr/share/augustus/config/species/brugia/brugia_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/ -rw-r--r-- root/root 227124 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl -rw-r--r-- root/root 227124 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF -rw-r--r-- root/root 32573 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl -rw-r--r-- root/root 32573 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF -rw-r--r-- root/root 151262 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl -rw-r--r-- root/root 151262 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_metapars.utr.cfg -rw-r--r-- root/root 7288 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_parameters.cfg -rw-r--r-- root/root 82480 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_utr_probs.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/c_elegans_trsk/c_elegans_trsk_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/ -rw-r--r-- root/root 227729 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_exon_probs.pbl -rw-r--r-- root/root 32621 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_igenic_probs.pbl -rw-r--r-- root/root 105835 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_metapars.utr.cfg -rw-r--r-- root/root 7311 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_parameters.cfg -rw-r--r-- root/root 84221 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_utr_probs.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/cacao/cacao_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/ -rw-r--r-- root/root 327878 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_exon_probs.pbl -rw-r--r-- root/root 45273 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_igenic_probs.pbl -rw-r--r-- root/root 50818 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_intron_probs.pbl -rw-r--r-- root/root 2523 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_metapars.cfg -rw-r--r-- root/root 6744 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_parameters.cfg -rw-r--r-- root/root 14444 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_trans_shadow_partial_utr.pbl -rw-r--r-- root/root 117067 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_utr_probs.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/caenorhabditis/caenorhabditis_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/ -rw-r--r-- root/root 2258 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/README.TXT -rw-r--r-- root/root 227917 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_exon_probs.pbl -rw-r--r-- root/root 32637 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_igenic_probs.pbl -rw-r--r-- root/root 110070 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_metapars.utr.cfg -rw-r--r-- root/root 7392 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/camponotus_floridanus/camponotus_floridanus_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/ -rw-r--r-- root/root 359498 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/candida_albicans_exon_probs.pbl -rw-r--r-- root/root 45152 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/candida_albicans_igenic_probs.pbl -rw-r--r-- root/root 86067 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/candida_albicans_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/candida_albicans_metapars.cfg -rw-r--r-- root/root 6781 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/candida_albicans_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_albicans/candida_albicans_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/ -rw-r--r-- root/root 343565 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_exon_probs.pbl -rw-r--r-- root/root 45629 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_igenic_probs.pbl -rw-r--r-- root/root 36792 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_metapars.cfg -rw-r--r-- root/root 6845 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_guilliermondii/candida_guilliermondii_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/ -rw-r--r-- root/root 338195 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_exon_probs.pbl -rw-r--r-- root/root 45158 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_igenic_probs.pbl -rw-r--r-- root/root 138501 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_metapars.cfg -rw-r--r-- root/root 6801 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/candida_tropicalis/candida_tropicalis_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/ -rw-r--r-- root/root 349242 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_exon_probs.pbl -rw-r--r-- root/root 46682 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_igenic_probs.pbl -rw-r--r-- root/root 375594 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_metapars.cfg -rw-r--r-- root/root 6812 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/chaetomium_globosum/chaetomium_globosum_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/ -rw-r--r-- root/root 999 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/README.TXT -rw-r--r-- root/root 2132567 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_exon_probs.pbl -rw-r--r-- root/root 325304 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_igenic_probs.pbl -rw-r--r-- root/root 1075557 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_metapars.utr.cfg -rw-r--r-- root/root 7198 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/chicken/chicken_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/ -rw-r--r-- root/root 236940 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_exon_probs.pbl -rw-r--r-- root/root 32468 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_igenic_probs.pbl -rw-r--r-- root/root 115762 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_metapars.utr.cfg -rw-r--r-- root/root 7346 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg -rw-r--r-- root/root 7270 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_parameters.cfg.orig1 -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/chiloscyllium/chiloscyllium_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/ -rw-r--r-- root/root 224245 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_exon_probs.pbl -rw-r--r-- root/root 32527 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_igenic_probs.pbl -rw-r--r-- root/root 336945 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_metapars.utr.cfg -rw-r--r-- root/root 7154 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_parameters.cfg -rw-r--r-- root/root 9052 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial.pbl -rw-r--r-- root/root 14434 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_trans_shadow_partial_utr.pbl -rw-r--r-- root/root 47666 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_utr_probs.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamy2011/chlamy2011_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamydomonas/ -rw-r--r-- root/root 318496 2023-12-19 14:46 ./usr/share/augustus/config/species/chlamydomonas/chlamydomonas_exon_probs.pbl -rw-r--r-- root/root 46118 2023-12-19 14:46 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14:46 ./usr/share/augustus/config/species/chlorella/ -rw-r--r-- root/root 340683 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_exon_probs.pbl -rw-r--r-- root/root 44208 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_igenic_probs.pbl -rw-r--r-- root/root 139655 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_metapars.cfg -rw-r--r-- root/root 1355 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_metapars.utr.cfg -rw-r--r-- root/root 6837 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_parameters.cfg -rw-r--r-- root/root 116709 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_utr_probs.pbl -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/chlorella/chlorella_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ -rw-r--r-- root/root 665 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/README.TXT -rw-r--r-- root/root 232373 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_exon_probs.pbl -rw-r--r-- root/root 32601 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_igenic_probs.pbl -rw-r--r-- root/root 61182 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_intron_probs.pbl -rw-r--r-- root/root 2057 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_metapars.cfg -rw-r--r-- root/root 1125 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_metapars.cgp.cfg -rw-r--r-- root/root 1356 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_metapars.utr.cfg -rw-r--r-- root/root 7212 2023-12-19 14:46 ./usr/share/augustus/config/species/ciona/ciona_parameters.cfg -rw-r--r-- root/root 7182 2023-12-19 14:46 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./usr/share/augustus/config/species/lodderomyces_elongisporus/ -rw-r--r-- root/root 1134920 2023-12-19 14:46 ./usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_exon_probs.pbl -rw-r--r-- root/root 182219 2023-12-19 14:46 ./usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_igenic_probs.pbl -rw-r--r-- root/root 239119 2023-12-19 14:46 ./usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_metapars.cfg -rw-r--r-- root/root 6876 2023-12-19 14:46 ./usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/lodderomyces_elongisporus/lodderomyces_elongisporus_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/ -rw-r--r-- root/root 330470 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_exon_probs.pbl -rw-r--r-- root/root 46909 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_igenic_probs.pbl -rw-r--r-- root/root 145474 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_metapars.cfg -rw-r--r-- root/root 6805 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/magnaporthe_grisea/magnaporthe_grisea_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/maize/ -rw-r--r-- root/root 2566678 2023-12-19 14:46 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./usr/share/augustus/config/species/nematostella_vectensis/nematostella_vectensis_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora/ -rw-r--r-- root/root 998409 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora/neurospora_exon_probs.pbl -rw-r--r-- root/root 140376 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora/neurospora_igenic_probs.pbl -rw-r--r-- root/root 175535 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora/neurospora_intron_probs.pbl -rw-r--r-- root/root 4133 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora/neurospora_parameters.cfg -rw-r--r-- root/root 800 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora/neurospora_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 ./usr/share/augustus/config/species/neurospora_crassa/ -rw-r--r-- root/root 1498946 2023-12-19 14:46 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./usr/share/augustus/config/species/schizosaccharomyces_pombe/ -rw-r--r-- root/root 318656 2023-12-19 14:46 ./usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_exon_probs.pbl -rw-r--r-- root/root 45204 2023-12-19 14:46 ./usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_igenic_probs.pbl -rw-r--r-- root/root 135537 2023-12-19 14:46 ./usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_intron_probs.pbl -rw-r--r-- root/root 1860 2023-12-19 14:46 ./usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_metapars.cfg -rw-r--r-- root/root 6877 2023-12-19 14:46 ./usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_parameters.cfg -rw-r--r-- root/root 810 2023-12-19 14:46 ./usr/share/augustus/config/species/schizosaccharomyces_pombe/schizosaccharomyces_pombe_weightmatrix.txt drwxr-xr-x root/root 0 2023-12-19 14:46 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./usr/share/doc/augustus-data/ lrwxrwxrwx root/root 0 2023-12-19 14:46 ./usr/share/doc/augustus-data/HISTORY.TXT.gz -> changelog.gz -rw-r--r-- root/root 1481 2023-12-19 14:46 ./usr/share/doc/augustus-data/changelog.Debian.gz -rw-r--r-- root/root 2741 2022-11-06 01:02 ./usr/share/doc/augustus-data/copyright augustus-doc_3.5.0+dfsg-4build1_all.deb --------------------------------------- new Debian package, version 2.0. size 23506680 bytes: control archive=9791 bytes. 628 bytes, 15 lines control 41794 bytes, 402 lines md5sums Package: augustus-doc Source: augustus Version: 3.5.0+dfsg-4build1 Architecture: all Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 145637 Section: doc Priority: optional Multi-Arch: foreign Homepage: https://bioinf.uni-greifswald.de/augustus/ Description: documentation files for AUGUSTUS This package contains documentation for AUGUSTUS: a comprehensive manual-style README both for AUGUSTUS in general as well as for its 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bytes, 24 lines control 10479 bytes, 140 lines md5sums Package: augustus Version: 3.5.0+dfsg-4build1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 6239 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-iostreams1.83.0 (>= 1.83.0), libc6 (>= 2.38), libcolamd3 (>= 1:7.0.1), libgcc-s1 (>= 3.3.1), libgsl27 (>= 2.7.1), libhts3 (>= 1.17), libmysql++3v5 (>= 3.2.5-1~), libmysqlclient21 (>= 8.0.11), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 13.1), augustus-data Recommends: samtools Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython Section: science Priority: optional Homepage: https://bioinf.uni-greifswald.de/augustus/ Description: gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 1635952 Build-Time: 609 Distribution: noble-proposed Host Architecture: amd64 Install-Time: 13 Job: augustus_3.5.0+dfsg-4build1.dsc Machine Architecture: amd64 Package: augustus Package-Time: 632 Source-Version: 3.5.0+dfsg-4build1 Space: 1635952 Status: successful Version: 3.5.0+dfsg-4build1 -------------------------------------------------------------------------------- Finished at 2023-12-19T15:19:42Z Build needed 00:10:32, 1635952k disk space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=amd64 PACKAGEBUILD-27576140 Scanning for processes to kill in build PACKAGEBUILD-27576140