https://launchpad.net/ubuntu/+source/augustus/3.5.0+dfsg-2/+build/24855919 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lgw01-084 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_222~591~ubuntu20.04.1 python3-lpbuildd_222~591~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 21 Nov 05:21:54 ntpdate[2319730]: adjust time server 10.211.37.1 offset -0.000743 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 --image-type chroot /home/buildd/filecache-default/c560a61c9a55d4d83030a3a869b3e28cada4bbf4 Creating target for build PACKAGEBUILD-24855919 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 Starting target for build PACKAGEBUILD-24855919 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 'deb http://ftpmaster.internal/ubuntu lunar main universe' 'deb http://ftpmaster.internal/ubuntu lunar-security main universe' 'deb http://ftpmaster.internal/ubuntu lunar-updates main universe' 'deb http://ftpmaster.internal/ubuntu lunar-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-24855919 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 Updating target for build PACKAGEBUILD-24855919 Get:1 http://ftpmaster.internal/ubuntu lunar InRelease [251 kB] Get:2 http://ftpmaster.internal/ubuntu lunar-security InRelease [74.9 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-updates InRelease [74.9 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed InRelease [102 kB] Get:5 http://ftpmaster.internal/ubuntu lunar/main riscv64 Packages [1299 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/universe riscv64 Packages [13.5 MB] Get:8 http://ftpmaster.internal/ubuntu lunar/universe Translation-en [5831 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 Packages [306 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main Translation-en [132 kB] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 Packages [1891 kB] Get:12 http://ftpmaster.internal/ubuntu lunar-proposed/universe Translation-en [830 kB] Fetched 24.8 MB in 45s (556 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.34 perl-modules-5.34 sgml-base Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libperl5.36 perl-modules-5.36 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-riscv64-linux-gnu cpp-12 debianutils fakeroot g++-12 gcc-12 gcc-12-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libapparmor1 libapt-pkg6.0 libasan8 libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libfakeroot libffi8 libgcc-12-dev libgcc-s1 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libjson-c5 libk5crypto3 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpng16-16 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsqlite3-0 libssl3 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libtasn1-6 libudev1 libunistring2 linux-libc-dev lto-disabled-list openssl perl perl-base pinentry-curses readline-common sgml-base systemd systemd-sysv tar tzdata usrmerge xz-utils zlib1g 92 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 80.6 MB of archives. After this operation, 45.7 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcrypt-dev riscv64 1:4.4.33-1 [235 kB] Get:2 http://ftpmaster.internal/ubuntu lunar/main riscv64 libc6-dev riscv64 2.36-0ubuntu4 [3146 kB] Get:3 http://ftpmaster.internal/ubuntu lunar/main riscv64 libc-dev-bin riscv64 2.36-0ubuntu4 [18.4 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcrypt1 riscv64 1:4.4.33-1 [93.4 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 linux-libc-dev riscv64 5.19.0-23.24 [1314 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcc1-0 riscv64 12.2.0-9ubuntu1 [42.9 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-12-base riscv64 12.2.0-9ubuntu1 [19.5 kB] Get:8 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcc-s1 riscv64 12.2.0-9ubuntu1 [43.9 kB] Get:9 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgomp1 riscv64 12.2.0-9ubuntu1 [111 kB] Get:10 http://ftpmaster.internal/ubuntu lunar/main riscv64 libatomic1 riscv64 12.2.0-9ubuntu1 [7854 B] Get:11 http://ftpmaster.internal/ubuntu lunar/main riscv64 libasan8 riscv64 12.2.0-9ubuntu1 [2333 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main riscv64 g++-12 riscv64 12.2.0-9ubuntu1 [9557 kB] Get:13 http://ftpmaster.internal/ubuntu lunar/main riscv64 libstdc++-12-dev riscv64 12.2.0-9ubuntu1 [4855 kB] Get:14 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgcc-12-dev riscv64 12.2.0-9ubuntu1 [2645 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main riscv64 gcc-12 riscv64 12.2.0-9ubuntu1 [16.3 MB] Get:16 http://ftpmaster.internal/ubuntu lunar/main riscv64 cpp-12 riscv64 12.2.0-9ubuntu1 [8286 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main riscv64 libstdc++6 riscv64 12.2.0-9ubuntu1 [673 kB] Get:18 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 zlib1g riscv64 1:1.2.13.dfsg-1ubuntu2 [53.9 kB] Get:19 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libctf0 riscv64 2.39-8ubuntu2 [87.0 kB] Get:20 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libctf-nobfd0 riscv64 2.39-8ubuntu2 [88.4 kB] Get:21 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libbinutils riscv64 2.39-8ubuntu2 [409 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 binutils-common riscv64 2.39-8ubuntu2 [216 kB] Get:23 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 binutils riscv64 2.39-8ubuntu2 [3022 B] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 binutils-riscv64-linux-gnu riscv64 2.39-8ubuntu2 [814 kB] Get:25 http://ftpmaster.internal/ubuntu lunar/main riscv64 libc6 riscv64 2.36-0ubuntu4 [2598 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main riscv64 base-files riscv64 12.3ubuntu1 [73.0 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 debianutils riscv64 5.7-0.4 [102 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main riscv64 bash riscv64 5.2-1ubuntu2 [671 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 grep riscv64 3.8-3 [154 kB] Get:30 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 perl-modules-5.36 all 5.36.0-4ubuntu2 [2984 kB] Get:31 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libperl5.36 riscv64 5.36.0-4ubuntu2 [4200 kB] Get:32 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 perl riscv64 5.36.0-4ubuntu2 [235 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 perl-base riscv64 5.36.0-4ubuntu2 [1649 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgdbm6 riscv64 1.23-3 [29.3 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgdbm-compat4 riscv64 1.23-3 [5910 B] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 tar riscv64 1.34+dfsg-1.1 [271 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libselinux1 riscv64 3.4-1build1 [71.3 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main riscv64 base-passwd riscv64 3.6.1 [49.4 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main riscv64 usrmerge all 29ubuntu2 [55.8 kB] Get:40 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 init-system-helpers all 1.65.2 [38.1 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/main riscv64 libc-bin riscv64 2.36-0ubuntu4 [556 kB] Get:42 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 liblz4-1 riscv64 1.9.4-1 [74.7 kB] Get:43 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 liblzma5 riscv64 5.2.7-0.1 [94.7 kB] Get:44 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libapparmor1 riscv64 3.0.7-1ubuntu3 [33.4 kB] Get:45 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libaudit-common all 1:3.0.7-1ubuntu2 [5018 B] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcap-ng0 riscv64 0.8.3-1build1 [13.5 kB] Get:47 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libaudit1 riscv64 1:3.0.7-1ubuntu2 [44.0 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libip4tc2 riscv64 1.8.7-1ubuntu7 [17.9 kB] Get:49 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpam0g riscv64 1.5.2-5ubuntu1 [56.1 kB] Get:50 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libseccomp2 riscv64 2.5.4-1ubuntu2 [44.2 kB] Get:51 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libssl3 riscv64 3.0.5-2ubuntu2 [1437 kB] Get:52 http://ftpmaster.internal/ubuntu lunar/main riscv64 systemd-sysv riscv64 251.4-1ubuntu7 [11.2 kB] Get:53 http://ftpmaster.internal/ubuntu lunar/main riscv64 systemd riscv64 251.4-1ubuntu7 [2632 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsystemd-shared riscv64 251.4-1ubuntu7 [1505 kB] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libjson-c5 riscv64 0.16-2 [28.6 kB] Get:56 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcryptsetup12 riscv64 2:2.5.0-6ubuntu1 [190 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsystemd0 riscv64 251.4-1ubuntu7 [296 kB] Get:58 http://ftpmaster.internal/ubuntu lunar/main riscv64 libudev1 riscv64 251.4-1ubuntu7 [72.8 kB] Get:59 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libapt-pkg6.0 riscv64 2.5.4 [918 kB] Get:60 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libgpg-error0 riscv64 1.46-1 [62.1 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 gpgv riscv64 2.2.40-1ubuntu1 [202 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main riscv64 libunistring2 riscv64 1.0-2 [533 kB] Get:63 http://ftpmaster.internal/ubuntu lunar/main riscv64 libidn2-0 riscv64 2.3.3-1build1 [94.2 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libffi8 riscv64 3.4.4-1 [21.2 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main riscv64 libp11-kit0 riscv64 0.24.1-1ubuntu2 [197 kB] Get:66 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtasn1-6 riscv64 4.19.0-2 [38.6 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgnutls30 riscv64 3.7.7-2ubuntu2 [891 kB] Get:68 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 apt riscv64 2.5.4 [1338 kB] Get:69 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpam-modules-bin riscv64 1.5.2-5ubuntu1 [43.1 kB] Get:70 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpam-modules riscv64 1.5.2-5ubuntu1 [265 kB] Get:71 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 init riscv64 1.65.2 [4812 B] Get:72 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 sgml-base all 1.31 [11.4 kB] Get:73 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpam-runtime all 1.5.2-5ubuntu1 [40.0 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsemanage-common all 3.4-1build1 [9544 B] Get:75 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsemanage2 riscv64 3.4-1build1 [83.4 kB] Get:76 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libgssapi-krb5-2 riscv64 1.20.1-1 [125 kB] Get:77 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libkrb5-3 riscv64 1.20.1-1 [329 kB] Get:78 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libkrb5support0 riscv64 1.20.1-1 [30.0 kB] Get:79 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libk5crypto3 riscv64 1.20.1-1 [96.5 kB] Get:80 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 readline-common all 8.2-1.1 [55.1 kB] Get:81 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libreadline8 riscv64 8.2-1.1 [130 kB] Get:82 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsqlite3-0 riscv64 3.40.0-1 [583 kB] Get:83 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 openssl riscv64 3.0.5-2ubuntu2 [1140 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main riscv64 tzdata all 2022f-0ubuntu2 [400 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpng16-16 riscv64 1.6.38-2 [174 kB] Get:86 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 xz-utils riscv64 5.2.7-0.1 [138 kB] Get:87 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libfakeroot riscv64 1.30.1-1ubuntu1 [26.4 kB] Get:88 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 fakeroot riscv64 1.30.1-1ubuntu1 [67.9 kB] Get:89 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libassuan0 riscv64 2.5.5-5 [31.7 kB] Get:90 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 pinentry-curses riscv64 1.2.1-1ubuntu1 [36.0 kB] Get:91 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 gpg riscv64 2.2.40-1ubuntu1 [491 kB] Get:92 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 gpgconf riscv64 2.2.40-1ubuntu1 [119 kB] Get:93 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 gpg-agent riscv64 2.2.40-1ubuntu1 [239 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/main riscv64 lto-disabled-list all 36 [12.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 80.6 MB in 21s (3901 kB/s) (Reading database ... 13488 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.33-1_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.33-1) over (1:4.4.28-2) ... Preparing to unpack .../libc6-dev_2.36-0ubuntu4_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.36-0ubuntu4) over (2.36-0ubuntu2) ... Preparing to unpack .../libc-dev-bin_2.36-0ubuntu4_riscv64.deb ... Unpacking libc-dev-bin (2.36-0ubuntu4) over (2.36-0ubuntu2) ... Preparing to unpack .../libcrypt1_1%3a4.4.33-1_riscv64.deb ... Unpacking libcrypt1:riscv64 (1:4.4.33-1) over (1:4.4.28-2) ... Setting up libcrypt1:riscv64 (1:4.4.33-1) ... (Reading database ... 13489 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_5.19.0-23.24_riscv64.deb ... Unpacking linux-libc-dev:riscv64 (5.19.0-23.24) over (5.15.0-27.28) ... Preparing to unpack .../libcc1-0_12.2.0-9ubuntu1_riscv64.deb ... Unpacking libcc1-0:riscv64 (12.2.0-9ubuntu1) over (12.2.0-1ubuntu1) ... Preparing to unpack .../gcc-12-base_12.2.0-9ubuntu1_riscv64.deb ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24855919 riscv64 lunar-proposed -c chroot:build-PACKAGEBUILD-24855919 --arch=riscv64 --dist=lunar-proposed --nolog augustus_3.5.0+dfsg-2.dsc Initiating build PACKAGEBUILD-24855919 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lgw01-084.buildd +==============================================================================+ | augustus 3.5.0+dfsg-2 (riscv64) Mon, 21 Nov 2022 05:35:23 +0000 | +==============================================================================+ Package: augustus Version: 3.5.0+dfsg-2 Source Version: 3.5.0+dfsg-2 Distribution: lunar-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24855919/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-h07rSJ/resolver-lpCdXx' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- augustus_3.5.0+dfsg-2.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/augustus-h07rSJ/augustus-3.5.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-h07rSJ' 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 1s (3192 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: libperl5.34 perl-modules-5.34 sgml-base Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdextrautils chrpath debhelper debugedit default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libbamtools-dev libbamtools2.5.2 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization-dev libboost-serialization1.74-dev libboost-serialization1.74.0 libboost1.74-dev libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu71 libklu1 liblapack-dev liblapack3 libldap-2.5-0 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmd0 libmetis5 libmongoose2 libmpdec3 libmysql++-dev libmysql++3v5 libmysqlclient-dev libmysqlclient21 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librbio2 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsliplu1 libspqr2 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5 libxml2 libyaml-0-2 libzstd-dev m4 man-db media-types mysql-common po-debconf python3 python3-minimal python3.10 python3.10-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.0 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 libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcurl4-doc libgnutls28-dev libidn11-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 python3.10-venv python3.10-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 bsdextrautils chrpath debhelper debugedit default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libbamtools-dev libbamtools2.5.2 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization-dev libboost-serialization1.74-dev libboost-serialization1.74.0 libboost1.74-dev libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu71 libklu1 liblapack-dev liblapack3 libldap-2.5-0 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmd0 libmetis5 libmongoose2 libmpdec3 libmysql++-dev libmysql++3v5 libmysqlclient-dev libmysqlclient21 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal libpython3.10-stdlib librbio2 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsliplu1 libspqr2 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5 libxml2 libyaml-0-2 libzstd-dev m4 man-db media-types mysql-common po-debconf python3 python3-minimal python3.10 python3.10-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-sdbm ruby-webrick ruby-xmlrpc ruby3.0 rubygems-integration samtools sbuild-build-depends-main-dummy zlib1g-dev 0 upgraded, 128 newly installed, 0 to remove and 0 not upgraded. Need to get 103 MB of archives. After this operation, 669 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [776 B] Get:2 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpython3.10-minimal riscv64 3.10.8-3 [788 kB] Get:3 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libexpat1 riscv64 2.5.0-1 [77.1 kB] Get:4 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 python3.10-minimal riscv64 3.10.8-3 [1787 kB] Get:5 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 python3-minimal riscv64 3.10.6-1ubuntu1 [24.1 kB] Get:6 http://ftpmaster.internal/ubuntu lunar/main riscv64 media-types all 8.0.0 [24.9 kB] Get:7 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmpdec3 riscv64 2.5.1-2build2 [85.3 kB] Get:8 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpython3.10-stdlib riscv64 3.10.8-3 [1695 kB] Get:9 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 python3.10 riscv64 3.10.8-3 [499 kB] Get:10 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpython3-stdlib riscv64 3.10.6-1ubuntu1 [6880 B] Get:11 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 python3 riscv64 3.10.6-1ubuntu1 [22.3 kB] Get:12 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmd0 riscv64 1.0.4-2 [29.4 kB] Get:13 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libbsd0 riscv64 0.11.7-1 [40.1 kB] Get:14 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libelf1 riscv64 0.188-1 [47.0 kB] Get:15 http://ftpmaster.internal/ubuntu lunar/main riscv64 libicu71 riscv64 71.1-3ubuntu1 [10.5 MB] Get:16 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libxml2 riscv64 2.9.14+dfsg-1.1 [598 kB] Get:17 http://ftpmaster.internal/ubuntu lunar/main riscv64 libyaml-0-2 riscv64 0.2.5-1 [50.4 kB] Get:18 http://ftpmaster.internal/ubuntu lunar/main riscv64 bsdextrautils riscv64 2.38-4ubuntu1 [81.5 kB] Get:19 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmagic-mgc riscv64 1:5.41-4 [257 kB] Get:20 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmagic1 riscv64 1:5.41-4 [88.7 kB] Get:21 http://ftpmaster.internal/ubuntu lunar/main riscv64 file riscv64 1:5.41-4 [20.6 kB] Get:22 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 gettext-base riscv64 0.21-10 [38.4 kB] Get:23 http://ftpmaster.internal/ubuntu lunar/main riscv64 libuchardet0 riscv64 0.0.7-1build2 [78.9 kB] Get:24 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 groff-base riscv64 1.22.4-9 [906 kB] Get:25 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libedit2 riscv64 3.1-20221030-1 [81.9 kB] Get:26 http://ftpmaster.internal/ubuntu lunar/main riscv64 libnghttp2-14 riscv64 1.50.0-1 [71.0 kB] Get:27 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libpipeline1 riscv64 1.5.7-1 [26.8 kB] Get:28 http://ftpmaster.internal/ubuntu lunar/main riscv64 libpsl5 riscv64 0.21.0-1.2build2 [57.3 kB] Get:29 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 man-db riscv64 2.11.1-1 [1178 kB] Get:30 http://ftpmaster.internal/ubuntu lunar/main riscv64 rubygems-integration all 1.18 [5336 B] Get:31 http://ftpmaster.internal/ubuntu lunar/main riscv64 rake all 13.0.6-3 [61.6 kB] Get:32 http://ftpmaster.internal/ubuntu lunar/main riscv64 ruby-net-telnet all 0.1.1-2.1 [13.1 kB] Get:33 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 ruby-webrick all 1.7.0-4 [51.9 kB] Get:34 http://ftpmaster.internal/ubuntu lunar/main riscv64 ruby-xmlrpc all 0.3.2-2 [24.8 kB] Get:35 http://ftpmaster.internal/ubuntu lunar/universe riscv64 ruby-sdbm riscv64 1.0.0-5 [14.0 kB] Get:36 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libruby3.0 riscv64 3.0.4-8 [4941 kB] Get:37 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 ruby3.0 riscv64 3.0.4-8 [49.8 kB] Get:38 http://ftpmaster.internal/ubuntu lunar/main riscv64 ruby-rubygems all 3.3.15-1 [231 kB] Get:39 http://ftpmaster.internal/ubuntu lunar/main riscv64 ruby riscv64 1:3.0~exp1 [5096 B] Get:40 http://ftpmaster.internal/ubuntu lunar/universe riscv64 ruby-asciidoctor all 2.0.17-1 [172 kB] Get:41 http://ftpmaster.internal/ubuntu lunar/universe riscv64 asciidoctor all 2.0.17-1 [44.0 kB] Get:42 http://ftpmaster.internal/ubuntu lunar/main riscv64 m4 riscv64 1.4.19-1 [243 kB] Get:43 http://ftpmaster.internal/ubuntu lunar/main riscv64 autoconf all 2.71-2 [338 kB] Get:44 http://ftpmaster.internal/ubuntu lunar/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:45 http://ftpmaster.internal/ubuntu lunar/main riscv64 automake all 1:1.16.5-1.3 [558 kB] Get:46 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 autopoint all 0.21-10 [421 kB] Get:47 http://ftpmaster.internal/ubuntu lunar/universe riscv64 chrpath riscv64 0.16-2 [12.9 kB] Get:48 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libdebhelper-perl all 13.10.1ubuntu1 [67.1 kB] Get:49 http://ftpmaster.internal/ubuntu lunar/main riscv64 libtool all 2.4.7-4 [166 kB] Get:50 http://ftpmaster.internal/ubuntu lunar/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:51 http://ftpmaster.internal/ubuntu lunar/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:52 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsub-override-perl all 0.09-4 [8706 B] Get:53 http://ftpmaster.internal/ubuntu lunar/main riscv64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:54 http://ftpmaster.internal/ubuntu lunar/main riscv64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:55 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libdw1 riscv64 0.188-1 [227 kB] Get:56 http://ftpmaster.internal/ubuntu lunar/main riscv64 debugedit riscv64 1:5.0-5 [48.8 kB] Get:57 http://ftpmaster.internal/ubuntu lunar/main riscv64 dwz riscv64 0.14+20220924-2 [115 kB] Get:58 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 gettext riscv64 0.21-10 [811 kB] Get:59 http://ftpmaster.internal/ubuntu lunar/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB] Get:60 http://ftpmaster.internal/ubuntu lunar/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:61 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 debhelper all 13.10.1ubuntu1 [924 kB] Get:62 http://ftpmaster.internal/ubuntu lunar/main riscv64 mysql-common all 5.8+1.0.8 [7212 B] Get:63 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmysqlclient21 riscv64 8.0.31-0ubuntu2 [1325 kB] Get:64 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libssl-dev riscv64 3.0.5-2ubuntu2 [4406 kB] Get:65 http://ftpmaster.internal/ubuntu lunar/main riscv64 libzstd-dev riscv64 1.5.2+dfsg-1 [1688 kB] Get:66 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 zlib1g-dev riscv64 1:1.2.13.dfsg-1ubuntu2 [957 kB] Get:67 http://ftpmaster.internal/ubuntu lunar/main riscv64 libmysqlclient-dev riscv64 8.0.31-0ubuntu2 [2569 kB] Get:68 http://ftpmaster.internal/ubuntu lunar/main riscv64 default-libmysqlclient-dev riscv64 1.0.8 [3588 B] Get:69 http://ftpmaster.internal/ubuntu lunar/main riscv64 icu-devtools riscv64 71.1-3ubuntu1 [201 kB] Get:70 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsuitesparseconfig5 riscv64 1:5.12.0+dfsg-2 [9226 B] Get:71 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libamd2 riscv64 1:5.12.0+dfsg-2 [18.8 kB] Get:72 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libbamtools2.5.2 riscv64 2.5.2+dfsg-2 [156 kB] Get:73 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libbamtools-dev riscv64 2.5.2+dfsg-2 [971 kB] Get:74 http://ftpmaster.internal/ubuntu lunar/main riscv64 libblas3 riscv64 3.10.1-2 [119 kB] Get:75 http://ftpmaster.internal/ubuntu lunar/main riscv64 libblas-dev riscv64 3.10.1-2 [277 kB] Get:76 http://ftpmaster.internal/ubuntu lunar/main riscv64 libboost1.74-dev riscv64 1.74.0-17ubuntu2 [9589 kB] Get:77 http://ftpmaster.internal/ubuntu lunar/main riscv64 libboost-regex1.74.0 riscv64 1.74.0-17ubuntu2 [489 kB] Get:78 http://ftpmaster.internal/ubuntu lunar/main riscv64 libicu-dev riscv64 71.1-3ubuntu1 [16.1 MB] Get:79 http://ftpmaster.internal/ubuntu lunar/main riscv64 libboost-regex1.74-dev riscv64 1.74.0-17ubuntu2 [2092 kB] Get:80 http://ftpmaster.internal/ubuntu lunar/main riscv64 libboost-iostreams1.74.0 riscv64 1.74.0-17ubuntu2 [243 kB] Get:81 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libboost-iostreams1.74-dev riscv64 1.74.0-17ubuntu2 [334 kB] Get:82 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libboost-iostreams-dev riscv64 1.74.0.3ubuntu7 [3242 B] Get:83 http://ftpmaster.internal/ubuntu lunar/main riscv64 libboost-serialization1.74.0 riscv64 1.74.0-17ubuntu2 [329 kB] Get:84 http://ftpmaster.internal/ubuntu lunar/main riscv64 libboost-serialization1.74-dev riscv64 1.74.0-17ubuntu2 [848 kB] Get:85 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libboost-serialization-dev riscv64 1.74.0.3ubuntu7 [3464 B] Get:86 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libbrotli1 riscv64 1.0.9-2build7 [324 kB] Get:87 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libbtf1 riscv64 1:5.12.0+dfsg-2 [10.9 kB] Get:88 http://ftpmaster.internal/ubuntu lunar/main riscv64 libbz2-dev riscv64 1.0.8-5build1 [88.9 kB] Get:89 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libcamd2 riscv64 1:5.12.0+dfsg-2 [20.4 kB] Get:90 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libccolamd2 riscv64 1:5.12.0+dfsg-2 [22.4 kB] Get:91 http://ftpmaster.internal/ubuntu lunar/main riscv64 libcolamd2 riscv64 1:5.12.0+dfsg-2 [15.8 kB] Get:92 http://ftpmaster.internal/ubuntu lunar/main riscv64 libgfortran5 riscv64 12.2.0-9ubuntu1 [386 kB] Get:93 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblapack3 riscv64 3.10.1-2 [1869 kB] Get:94 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libmetis5 riscv64 5.1.0.dfsg-7build2 [153 kB] Get:95 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libcholmod3 riscv64 1:5.12.0+dfsg-2 [313 kB] Get:96 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsasl2-modules-db riscv64 2.1.28+dfsg-6ubuntu2 [19.0 kB] Get:97 http://ftpmaster.internal/ubuntu lunar/main riscv64 libsasl2-2 riscv64 2.1.28+dfsg-6ubuntu2 [55.1 kB] Get:98 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libldap-2.5-0 riscv64 2.5.13+dfsg-1ubuntu2 [162 kB] Get:99 http://ftpmaster.internal/ubuntu lunar/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build4 [54.6 kB] Get:100 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libssh-4 riscv64 0.10.4-2 [162 kB] Get:101 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcurl3-gnutls riscv64 7.86.0-2 [251 kB] Get:102 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libcurl4-gnutls-dev riscv64 7.86.0-2 [836 kB] Get:103 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libcxsparse3 riscv64 1:5.12.0+dfsg-2 [63.3 kB] Get:104 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libdeflate0 riscv64 1.14-1 [52.8 kB] Get:105 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libdeflate-dev riscv64 1.14-1 [110 kB] Get:106 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libgslcblas0 riscv64 2.7.1+dfsg-3 [80.0 kB] Get:107 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libgsl27 riscv64 2.7.1+dfsg-3 [996 kB] Get:108 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libgsl-dev riscv64 2.7.1+dfsg-3 [3473 kB] Get:109 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 libhtscodecs2 riscv64 1.3.0-4 [77.6 kB] Get:110 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 libhts3 riscv64 1.16+ds-3 [382 kB] Get:111 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 liblzma-dev riscv64 5.2.7-0.1 [271 kB] Get:112 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 libhts-dev riscv64 1.16+ds-3 [3180 kB] Get:113 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libklu1 riscv64 1:5.12.0+dfsg-2 [69.4 kB] Get:114 http://ftpmaster.internal/ubuntu lunar/main riscv64 liblapack-dev riscv64 3.10.1-2 [10.1 MB] Get:115 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libldl2 riscv64 1:5.12.0+dfsg-2 [10.8 kB] Get:116 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libmongoose2 riscv64 1:5.12.0+dfsg-2 [32.9 kB] Get:117 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libumfpack5 riscv64 1:5.12.0+dfsg-2 [228 kB] Get:118 http://ftpmaster.internal/ubuntu lunar/universe riscv64 librbio2 riscv64 1:5.12.0+dfsg-2 [24.3 kB] Get:119 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libspqr2 riscv64 1:5.12.0+dfsg-2 [63.8 kB] Get:120 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libsliplu1 riscv64 1:5.12.0+dfsg-2 [33.0 kB] Get:121 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libsuitesparse-dev riscv64 1:5.12.0+dfsg-2 [2483 kB] Get:122 http://ftpmaster.internal/ubuntu lunar/universe riscv64 liblpsolve55-dev riscv64 5.5.2.5-2build2 [688 kB] Get:123 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libmysql++3v5 riscv64 3.2.5-2.1 [114 kB] Get:124 http://ftpmaster.internal/ubuntu lunar/universe riscv64 libmysql++-dev riscv64 3.2.5-2.1 [96.4 kB] Get:125 http://ftpmaster.internal/ubuntu lunar/main riscv64 libncurses-dev riscv64 6.3+20220423-2 [867 kB] Get:126 http://ftpmaster.internal/ubuntu lunar/main riscv64 libncurses5-dev riscv64 6.3+20220423-2 [796 B] Get:127 http://ftpmaster.internal/ubuntu lunar-proposed/main riscv64 libsqlite3-dev riscv64 3.40.0-1 [1917 kB] Get:128 http://ftpmaster.internal/ubuntu lunar-proposed/universe riscv64 samtools riscv64 1.16.1-1 [574 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 103 MB in 22s (4679 kB/s) Selecting previously unselected package libpython3.10-minimal:riscv64. (Reading database ... 15456 files and directories currently installed.) Preparing to unpack .../libpython3.10-minimal_3.10.8-3_riscv64.deb ... Unpacking libpython3.10-minimal:riscv64 (3.10.8-3) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.5.0-1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.5.0-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.8-3_riscv64.deb ... Unpacking python3.10-minimal (3.10.8-3) ... Setting up libpython3.10-minimal:riscv64 (3.10.8-3) ... Setting up libexpat1:riscv64 (2.5.0-1) ... Setting up python3.10-minimal (3.10.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 15759 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.10.6-1ubuntu1_riscv64.deb ... Unpacking python3-minimal (3.10.6-1ubuntu1) ... Selecting previously unselected package media-types. 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Setting up libboost1.74-dev:riscv64 (1.74.0-17ubuntu2) ... Setting up libzstd-dev:riscv64 (1.5.2+dfsg-1) ... Setting up bsdextrautils (2.38-4ubuntu1) ... Setting up libgslcblas0:riscv64 (2.7.1+dfsg-3) ... Setting up libmagic-mgc (1:5.41-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:riscv64 (0.2.5-1) ... Setting up libboost-iostreams1.74.0:riscv64 (1.74.0-17ubuntu2) ... Setting up libdebhelper-perl (13.10.1ubuntu1) ... Setting up libbrotli1:riscv64 (1.0.9-2build7) ... Setting up libldl2:riscv64 (1:5.12.0+dfsg-2) ... Setting up libnghttp2-14:riscv64 (1.50.0-1) ... Setting up libmagic1:riscv64 (1:5.41-4) ... Setting up libdeflate0:riscv64 (1.14-1) ... Setting up gettext-base (0.21-10) ... Setting up libgsl27:riscv64 (2.7.1+dfsg-3) ... Setting up m4 (1.4.19-1) ... Setting up rubygems-integration (1.18) ... Setting up libmetis5:riscv64 (5.1.0.dfsg-7build2) ... Setting up file (1:5.41-4) ... Setting up libbtf1:riscv64 (1:5.12.0+dfsg-2) ... Setting up libsasl2-modules-db:riscv64 (2.1.28+dfsg-6ubuntu2) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:riscv64 (3.10.1-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode Setting up libsqlite3-dev:riscv64 (3.40.0-1) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build4) ... Setting up ruby-net-telnet (0.1.1-2.1) ... Setting up libboost-regex1.74.0:riscv64 (1.74.0-17ubuntu2) ... Setting up libssl-dev:riscv64 (3.0.5-2ubuntu2) ... Setting up autopoint (0.21-10) ... Setting up icu-devtools (71.1-3ubuntu1) ... Setting up libmysql++3v5:riscv64 (3.2.5-2.1) ... Setting up libbamtools2.5.2:riscv64 (2.5.2+dfsg-2) ... Setting up libsasl2-2:riscv64 (2.1.28+dfsg-6ubuntu2) ... Setting up libssh-4:riscv64 (0.10.4-2) ... Setting up libgfortran5:riscv64 (12.2.0-9ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up ruby-webrick (1.7.0-4) ... Setting up liblzma-dev:riscv64 (5.2.7-0.1) ... Setting up libboost-serialization1.74.0:riscv64 (1.74.0-17ubuntu2) ... Setting up zlib1g-dev:riscv64 (1:1.2.13.dfsg-1ubuntu2) ... Setting up libmd0:riscv64 (1.0.4-2) ... Setting up libuchardet0:riscv64 (0.0.7-1build2) ... Setting up libncurses5-dev:riscv64 (6.3+20220423-2) ... Setting up libmpdec3:riscv64 (2.5.1-2build2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libcxsparse3:riscv64 (1:5.12.0+dfsg-2) ... Setting up libbsd0:riscv64 (0.11.7-1) ... Setting up libdeflate-dev:riscv64 (1.14-1) ... Setting up libelf1:riscv64 (0.188-1) ... Setting up libicu-dev:riscv64 (71.1-3ubuntu1) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:riscv64 (2.9.14+dfsg-1.1) ... Setting up libsuitesparseconfig5:riscv64 (1:5.12.0+dfsg-2) ... Setting up chrpath (0.16-2) ... Setting up libblas-dev:riscv64 (3.10.1-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so to provide /usr/lib/riscv64-linux-gnu/libblas.so (libblas.so-riscv64-linux-gnu) in auto mode Setting up libmysqlclient-dev (8.0.31-0ubuntu2) ... Setting up librbio2:riscv64 (1:5.12.0+dfsg-2) ... Setting up libbz2-dev:riscv64 (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:riscv64 (1.0.8) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libamd2:riscv64 (1:5.12.0+dfsg-2) ... Setting up libdw1:riscv64 (0.188-1) ... Setting up liblapack3:riscv64 (3.10.1-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode Setting up gettext (0.21-10) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up libcolamd2:riscv64 (1:5.12.0+dfsg-2) ... Setting up libtool (2.4.7-4) ... Setting up libedit2:riscv64 (3.1-20221030-1) ... Setting up libldap-2.5-0:riscv64 (2.5.13+dfsg-1ubuntu2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libmysql++-dev:riscv64 (3.2.5-2.1) ... Setting up libsliplu1:riscv64 (1:5.12.0+dfsg-2) ... Setting up libpython3.10-stdlib:riscv64 (3.10.8-3) ... Setting up dh-autoreconf (20) ... Setting up libcamd2:riscv64 (1:5.12.0+dfsg-2) ... Setting up libmongoose2:riscv64 (1:5.12.0+dfsg-2) ... Setting up libbamtools-dev:riscv64 (2.5.2+dfsg-2) ... Setting up liblapack-dev:riscv64 (3.10.1-2) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so to provide /usr/lib/riscv64-linux-gnu/liblapack.so (liblapack.so-riscv64-linux-gnu) in auto mode Setting up libboost-serialization1.74-dev:riscv64 (1.74.0-17ubuntu2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14+20220924-2) ... Setting up libboost-regex1.74-dev:riscv64 (1.74.0-17ubuntu2) ... Setting up groff-base (1.22.4-9) ... Setting up libklu1:riscv64 (1:5.12.0+dfsg-2) ... Setting up libccolamd2:riscv64 (1:5.12.0+dfsg-2) ... Setting up debugedit (1:5.0-5) ... Setting up libcholmod3:riscv64 (1:5.12.0+dfsg-2) ... Setting up libpython3-stdlib:riscv64 (3.10.6-1ubuntu1) ... Setting up libspqr2:riscv64 (1:5.12.0+dfsg-2) ... Setting up python3.10 (3.10.8-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:riscv64 (7.86.0-2) ... Setting up python3 (3.10.6-1ubuntu1) ... Setting up libcurl4-gnutls-dev (7.86.0-2) ... Setting up man-db (2.11.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libboost-iostreams1.74-dev:riscv64 (1.74.0-17ubuntu2) ... Setting up libumfpack5:riscv64 (1:5.12.0+dfsg-2) ... Setting up libboost-serialization-dev:riscv64 (1.74.0.3ubuntu7) ... Setting up libhts3:riscv64 (1.16+ds-3) ... Setting up libsuitesparse-dev:riscv64 (1:5.12.0+dfsg-2) ... Setting up libhts-dev:riscv64 (1.16+ds-3) ... Setting up debhelper (13.10.1ubuntu1) ... Setting up libboost-iostreams-dev:riscv64 (1.74.0.3ubuntu7) ... Setting up samtools (1.16.1-1) ... Setting up liblpsolve55-dev (5.5.2.5-2build2) ... Setting up ruby-rubygems (3.3.15-1) ... Setting up ruby3.0 (3.0.4-8) ... Setting up ruby (1:3.0~exp1) ... Setting up ruby-asciidoctor (2.0.17-1) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.17-1) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libruby3.0:riscv64 (3.0.4-8) ... Setting up ruby-sdbm:riscv64 (1.0.0-5) ... Processing triggers for libc-bin (2.36-0ubuntu4) ... Processing triggers for systemd (251.4-1ubuntu7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.13.0-1019-generic #21~20.04.1-Ubuntu SMP Thu Mar 24 22:36:01 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.39-8ubuntu2 dpkg-dev_1.21.9ubuntu1 g++-12_12.2.0-9ubuntu1 gcc-12_12.2.0-9ubuntu1 libc6-dev_2.36-0ubuntu4 libstdc++-12-dev_12.2.0-9ubuntu1 libstdc++6_12.2.0-9ubuntu1 linux-libc-dev_5.19.0-23.24 Package versions: adduser_3.121ubuntu1 advancecomp_2.3-1 apt_2.5.4 asciidoctor_2.0.17-1 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3ubuntu1 base-passwd_3.6.1 bash_5.2-1ubuntu2 binutils_2.39-8ubuntu2 binutils-common_2.39-8ubuntu2 binutils-riscv64-linux-gnu_2.39-8ubuntu2 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 chrpath_0.16-2 coreutils_8.32-4.1ubuntu1 cpp_4:12.2.0-1ubuntu1 cpp-12_12.2.0-9ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-8ubuntu1 debconf_1.5.79ubuntu1 debhelper_13.10.1ubuntu1 debianutils_5.7-0.4 debugedit_1:5.0-5 default-libmysqlclient-dev_1.0.8 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dpkg_1.21.9ubuntu1 dpkg-dev_1.21.9ubuntu1 dwz_0.14+20220924-2 e2fsprogs_1.46.5-2ubuntu2 fakeroot_1.30.1-1ubuntu1 file_1:5.41-4 findutils_4.9.0-3ubuntu1 g++_4:12.2.0-1ubuntu1 g++-12_12.2.0-9ubuntu1 gcc_4:12.2.0-1ubuntu1 gcc-12_12.2.0-9ubuntu1 gcc-12-base_12.2.0-9ubuntu1 gettext_0.21-10 gettext-base_0.21-10 gpg_2.2.40-1ubuntu1 gpg-agent_2.2.40-1ubuntu1 gpgconf_2.2.40-1ubuntu1 gpgv_2.2.40-1ubuntu1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1ubuntu1 hostname_3.23ubuntu2 icu-devtools_71.1-3ubuntu1 init_1.65.2 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-1 libamd2_1:5.12.0+dfsg-2 libapparmor1_3.0.7-1ubuntu3 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan8_12.2.0-9ubuntu1 libassuan0_2.5.5-5 libatomic1_12.2.0-9ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1ubuntu2 libaudit1_1:3.0.7-1ubuntu2 libbamtools-dev_2.5.2+dfsg-2 libbamtools2.5.2_2.5.2+dfsg-2 libbinutils_2.39-8ubuntu2 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38-4ubuntu1 libboost-iostreams-dev_1.74.0.3ubuntu7 libboost-iostreams1.74-dev_1.74.0-17ubuntu2 libboost-iostreams1.74.0_1.74.0-17ubuntu2 libboost-regex1.74-dev_1.74.0-17ubuntu2 libboost-regex1.74.0_1.74.0-17ubuntu2 libboost-serialization-dev_1.74.0.3ubuntu7 libboost-serialization1.74-dev_1.74.0-17ubuntu2 libboost-serialization1.74.0_1.74.0-17ubuntu2 libboost1.74-dev_1.74.0-17ubuntu2 libbrotli1_1.0.9-2build7 libbsd0_0.11.7-1 libbtf1_1:5.12.0+dfsg-2 libbz2-1.0_1.0.8-5build1 libbz2-dev_1.0.8-5build1 libc-bin_2.36-0ubuntu4 libc-dev-bin_2.36-0ubuntu4 libc6_2.36-0ubuntu4 libc6-dev_2.36-0ubuntu4 libcamd2_1:5.12.0+dfsg-2 libcap-ng0_0.8.3-1build1 libcap2_1:2.44-1build3 libcc1-0_12.2.0-9ubuntu1 libccolamd2_1:5.12.0+dfsg-2 libcholmod3_1:5.12.0+dfsg-2 libcolamd2_1:5.12.0+dfsg-2 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libcryptsetup12_2:2.5.0-6ubuntu1 libctf-nobfd0_2.39-8ubuntu2 libctf0_2.39-8ubuntu2 libcurl3-gnutls_7.86.0-2 libcurl4-gnutls-dev_7.86.0-2 libcxsparse3_1:5.12.0+dfsg-2 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264ubuntu1 libdebhelper-perl_13.10.1ubuntu1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdevmapper1.02.1_2:1.02.185-1ubuntu1 libdpkg-perl_1.21.9ubuntu1 libdw1_0.188-1 libedit2_3.1-20221030-1 libelf1_0.188-1 libexpat1_2.5.0-1 libext2fs2_1.46.5-2ubuntu2 libfakeroot_1.30.1-1ubuntu1 libfdisk1_2.38-4ubuntu1 libffi8_3.4.4-1 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-9ubuntu1 libgcc-s1_12.2.0-9ubuntu1 libgcrypt20_1.10.1-2ubuntu1 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgfortran5_12.2.0-9ubuntu1 libgmp10_2:6.2.1+dfsg1-1ubuntu2 libgnutls30_3.7.7-2ubuntu2 libgomp1_12.2.0-9ubuntu1 libgpg-error0_1.46-1 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20.1-1 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-3 libhts3_1.16+ds-3 libhtscodecs2_1.3.0-4 libicu-dev_71.1-3ubuntu1 libicu71_71.1-3ubuntu1 libidn2-0_2.3.3-1build1 libip4tc2_1.8.7-1ubuntu7 libisl23_0.25-1 libjson-c5_0.16-2 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libklu1_1:5.12.0+dfsg-2 libkmod2_30+20220630-3ubuntu1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 liblapack-dev_3.10.1-2 liblapack3_3.10.1-2 libldap-2.5-0_2.5.13+dfsg-1ubuntu2 libldl2_1:5.12.0+dfsg-2 liblockfile-bin_1.17-1build2 liblockfile1_1.17-1build2 liblpsolve55-dev_5.5.2.5-2build2 liblz4-1_1.9.4-1 liblzma-dev_5.2.7-0.1 liblzma5_5.2.7-0.1 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ruby-net-telnet_0.1.1-2.1 ruby-rubygems_3.3.15-1 ruby-sdbm_1.0.0-5 ruby-webrick_1.7.0-4 ruby-xmlrpc_0.3.2-2 ruby3.0_3.0.4-8 rubygems-integration_1.18 samtools_1.16.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 sgml-base_1.31 systemd_251.4-1ubuntu7 systemd-sysv_251.4-1ubuntu7 sysvinit-utils_3.04-1ubuntu1 tar_1.34+dfsg-1.1 tzdata_2022f-0ubuntu2 ubuntu-keyring_2021.03.26 usrmerge_29ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.7-0.1 zlib1g_1:1.2.13.dfsg-1ubuntu2 zlib1g-dev_1:1.2.13.dfsg-1ubuntu2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: augustus Binary: augustus, augustus-data, augustus-doc Architecture: any all Version: 3.5.0+dfsg-2 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 94f8380e1b95690ab6321e1579d90e7f7cbcd44c 19920 augustus_3.5.0+dfsg-2.debian.tar.xz Checksums-Sha256: 30a2a5200e7201a28383bebb98350eab9e043e38d0f7b825a1c8a614a6e68dc8 151813456 augustus_3.5.0+dfsg.orig.tar.xz 2249cb77873071a191813ca9d4e828877aba1ae59ece01f237f0d942edd99ccb 19920 augustus_3.5.0+dfsg-2.debian.tar.xz Files: 11cc56baea3047c128e2da42f7cf9dd0 151813456 augustus_3.5.0+dfsg.orig.tar.xz ace135cf933aba3ec77fa12654ee84d2 19920 augustus_3.5.0+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAmN6uEAACgkQ6NN64vCf SHLk0A//be6j5pH7II0jOzpgXlnFh5NDUaTPYiWIWWp8x8gkEM9kgEJCAl8+psvN xnnsFlDFvmHML1iDbyIv/MQFsHXxb8yNyQKVlVqQ6pbDl9NcsA9vQoxin5YCPw9W gCDkDfjY1W+DuwfYJMjf2/IlMY+KV/U+qfiE9aE4cxDSFMDGRc16cCJf3BetFIAM A7vhQ4ioVDJZ0JAir0ZlwncyJPO1XMK+uUJ2ux2VotvfSmnrxJ94hNcICZq2+3aL Zi9k8uf9S/PbODLDJ6YNpXksyP6VoE8K/tYisqmu0IEvVOySyR3xB7Fwjo3aUorm yocmKGtV6HJGTKinocpK1d5U00YKBE1yN+CnNQwtKMxeKNjb3+Gghc2BHiURdlLZ 03R9IMUBjsYts5SeR/rJtxU8DaOXXFL4fseYi6lMb2f2cbINyMZn7rNFNNxTiviv FZn4Mjnt0PygXxhpZKrntc8O4eo8dbB7K8xa36HbnUHJSAih5uK95n1jvt9vmIQk IAm5PiQmV5ciQQjBnQeZvpYbmh/yuE9DZ5Y9qZPrFT5FU4DkZ+w179NHCpzaFmcl 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Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-24855919 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24855919 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24855919 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-2 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 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' 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 auxprogs -name "*.o" | xargs -r rm rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a 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=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/bamtools -c bam2hints.cc In file included from /usr/include/c++/12/list:63, from bam2hints.cc:9: In member function ‘std::_List_iterator< >::_Self std::_List_iterator< >::operator++(int) [with _Tp = hint_t]’, inlined from ‘void printHints(FILE*, const char*)’ at bam2hints.cc:326:121: /usr/include/c++/12/bits/stl_list.h:297:28: warning: pointer used after ‘void operator delete(void*, std::size_t)’ [-Wuse-after-free] 297 | _M_node = _M_node->_M_next; | ~~~~~~~~~^~~~~~~ In file included from /usr/include/riscv64-linux-gnu/c++/12/bits/c++allocator.h:33, from /usr/include/c++/12/bits/allocator.h:46, from /usr/include/c++/12/list:61: In member function ‘void std::__new_allocator<_Tp>::deallocate(_Tp*, size_type) [with _Tp = std::_List_node]’, inlined from ‘static void std::allocator_traits >::deallocate(allocator_type&, pointer, size_type) [with _Tp = std::_List_node]’ at /usr/include/c++/12/bits/alloc_traits.h:496:23, inlined from ‘void std::__cxx11::_List_base<_Tp, _Alloc>::_M_put_node(typename _Node_alloc_traits::pointer) [with _Tp = hint_t; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_list.h:522:39, inlined from ‘void std::__cxx11::list<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = hint_t; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/stl_list.h:2024:13, inlined from ‘std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::erase(const_iterator) [with _Tp = hint_t; _Alloc = std::allocator]’ at /usr/include/c++/12/bits/list.tcc:158:15, inlined from ‘void printHints(FILE*, const char*)’ at bam2hints.cc:334:26: /usr/include/c++/12/bits/new_allocator.h:158:33: note: call to ‘void operator delete(void*, std::size_t)’ here 158 | _GLIBCXX_OPERATOR_DELETE(_GLIBCXX_SIZED_DEALLOC(__p, __n)); | ^ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -Wall -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I/usr/include/htslib -I/usr/local/include/htslib/ -c bam2wig.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c compileSpliceCands.c compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:216:9: warning: ‘__builtin_strncat’ 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: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 292 | strncpy(d->name,tokens[0],LINEBUFFER); | ^ compileSpliceCands.c: In function ‘parseList’: compileSpliceCands.c:337:36: warning: ‘left’ may be used uninitialized [-Wmaybe-uninitialized] 337 | if(isCompatibleStrand(left->strand,right->strand)) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o 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=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c filterBam.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/initOptions.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/printElapsedTime.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/MatePairs.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c functions/PairednessCoverage.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I./headers -I/usr/include/bamtools -c BamToolsAccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c gene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c genome.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -c sqliteDB.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c joingenes.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jg_transcript.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c jg_ios.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 -j8 "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 '/<>/auxprogs' cd aln2wig; make; make[3]: Entering directory '/<>/src' 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; make[4]: Entering directory '/<>/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o properties.o properties.cc make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/auxprogs/bam2hints' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_profile.o pp_profile.cc cd compileSpliceCands; make; g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_hitseq.o pp_hitseq.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_scoring.o pp_scoring.cc 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' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.cc cd filterBam; make; g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc 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=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Compute_UTRs.d" -MT"build/Compute_UTRs.o" -o "build/Compute_UTRs.o" "src/Compute_UTRs.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o types.o types.cc src/Compute_UTRs.cpp: In function ‘void compute_UTRs(std::string)’: src/Compute_UTRs.cpp:254:58: warning: ‘step’ may be used uninitialized [-Wmaybe-uninitialized] 254 | chrom_pos+=step; | ~~~~~~~~~^~~~~~ src/Compute_UTRs.cpp:143:18: note: ‘step’ was declared here 143 | unsigned step; //Step for fixedStep only | ^~~~ src/Compute_UTRs.cpp:254:58: warning: ‘chrom_pos’ may be used uninitialized [-Wmaybe-uninitialized] 254 | chrom_pos+=step; | ~~~~~~~~~^~~~~~ src/Compute_UTRs.cpp:142:18: note: ‘chrom_pos’ was declared here 142 | unsigned chrom_pos; //position 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=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Coord_Transform.d" -MT"build/Coord_Transform.o" -o "build/Coord_Transform.o" "src/Coord_Transform.cpp" 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++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from src/flex_vec.hpp:8, from src/Coord_Transform.cpp:5: /usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ 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:131:54: warning: ‘skip_end’ may be used uninitialized [-Wmaybe-uninitialized] 131 | i = 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=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o gene.o gene.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc src/Genomic_Data.cpp: In function ‘std::vector > lower_case_runs(std::string)’: src/Genomic_Data.cpp:42:18: warning: ‘start’ may be used uninitialized [-Wmaybe-uninitialized] 42 | unsigned start; | ^~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc Finished building: src/Genomic_Data.cpp Building file: src/Splice_Sites.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc Finished building: src/Splice_Sites.cpp Building file: src/Supporting_Methods.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Supporting_Methods.d" -MT"build/Supporting_Methods.o" -o "build/Supporting_Methods.o" "src/Supporting_Methods.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc Finished building: src/Supporting_Methods.cpp Building file: src/Test.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/Test.d" -MT"build/Test.o" -o "build/Test.o" "src/Test.cpp" Finished building: src/Test.cpp Building file: src/UTRs.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/UTRs.d" -MT"build/UTRs.o" -o "build/UTRs.o" "src/UTRs.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc 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++/12/string:48, from src/Genomic_Data.hpp:8, from src/UTRs.cpp:5: /usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/bits/stl_function.h:1438: /usr/include/c++/12/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++/12/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++/12/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++/12/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++/12/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++/12/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++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc Finished building: src/UTRs.cpp Building file: src/main.cpp Invoking: GCC C++ Compiler: g++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -MMD -MP -MF"build/main.d" -MT"build/main.o" -o "build/main.o" "src/main.cpp" g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc Finished building: src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O0 -pedantic -fmessage-length=0 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.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=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -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=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 cp -f prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 load2sqlitedb ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 cp -f load2db ../bin/ cp -f fastBlockSearch ../bin/ cp -f pp_simScore ../bin/ cp -f getSeq ../bin/ cp -f etraining ../bin/ 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: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a 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 -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>' dh_installchangelogs -k docs/HISTORY.TXT make[1]: Leaving directory '/<>' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>' dh_compress -Xtutorial make[1]: Leaving directory '/<>' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/augustus/usr/bin/etraining: Unknown DWARF DW_FORM_0x1f20 711ffb6c15ea27db5e96fc10adcd411ec0184925 debugedit: debian/augustus/usr/bin/augustus: Unknown DWARF DW_FORM_0x1f20 dd225ba01980f072d07e304da2af8f51ffdf3e0c debugedit: debian/augustus/usr/bin/homGeneMapping: Unknown DWARF DW_FORM_0x1f20 1bcd5400a4ed0034aa46129a322b97837e131e30 debugedit: debian/augustus/usr/bin/load2db: Unknown DWARF DW_FORM_0x1f21 49c39057dd534147872edeefc9f10486e9e3eec2 debugedit: debian/augustus/usr/bin/fastBlockSearch: Unknown DWARF DW_FORM_0x1f21 34feb799f2bc5fe21a0f2a5c276015ea9d293711 debugedit: debian/augustus/usr/bin/prepareAlign: Unknown DWARF DW_FORM_0x1f21 f0ac2f80b097251dbabb5f9686175222420ab2af debugedit: debian/augustus/usr/bin/compileSpliceCands: Unknown DWARF DW_FORM_0x1f20 a6e184bd9eea4ac90b0fe5f4b0b93c476b3fd190 debugedit: debian/augustus/usr/bin/load2sqlitedb: Unknown DWARF DW_FORM_0x1f21 ada250cf38c84cc82c75d8bce3fb92f8b0128d3c debugedit: debian/augustus/usr/bin/bam2wig: Unknown DWARF DW_FORM_0x1f20 21bc97e6465c122a851873ff68e08a65ad1ec300 debugedit: debian/augustus/usr/bin/filterBam: Unknown DWARF DW_FORM_0x1f21 fff7fd04b32147adb83375853bbe2b821553d1e6 debugedit: debian/augustus/usr/bin/joingenes: Unknown DWARF DW_FORM_0x1f20 fea46f1f725ff2eb4cfd3400958d7bd3266616fb debugedit: debian/augustus/usr/bin/aln2wig: Unknown DWARF DW_FORM_0x1f21 6e1cc108cf4ef4998f97b0585553be36548aed74 debugedit: debian/augustus/usr/bin/getSeq: Unknown DWARF DW_FORM_0x1f21 4e2dfbf5ca6106e6fe490cca6f3d6235223e7fac debugedit: debian/augustus/usr/bin/bam2hints: Unknown DWARF DW_FORM_0x1f21 5f72ebc3538ca5b0c13fc40f36ed4368539446ca debugedit: debian/augustus/usr/bin/pp_simScore: Unknown DWARF DW_FORM_0x1f21 6329742deb8d70e51f435ce3059d3b76a170ef69 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a 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 -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing augustus (in debian/augustus); 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 " pkgstripfiles: processing control file: debian/augustus/DEBIAN/control, package augustus, directory debian/augustus .. removing usr/share/doc/augustus/changelog.gz pkgstripfiles: processing control file: debian/.debhelper/augustus/dbgsym-root/DEBIAN/control, package augustus-dbgsym, directory debian/.debhelper/augustus/dbgsym-root dpkg-deb: building package 'augustus-dbgsym' in 'debian/.debhelper/scratch-space/build-augustus/augustus-dbgsym_3.5.0+dfsg-2_riscv64.deb'. pkgstripfiles: Running PNG optimization (using 8 cpus) for package augustus ... pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-2_riscv64.deb'. Renaming augustus-dbgsym_3.5.0+dfsg-2_riscv64.deb to augustus-dbgsym_3.5.0+dfsg-2_riscv64.ddeb dpkg-genbuildinfo --build=any -O../augustus_3.5.0+dfsg-2_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../augustus_3.5.0+dfsg-2_riscv64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-11-21T06:22:47Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ augustus_3.5.0+dfsg-2_riscv64.changes: -------------------------------------- Format: 1.8 Date: Mon, 21 Nov 2022 00:11:53 +0100 Source: augustus Binary: augustus Built-For-Profiles: noudeb Architecture: riscv64 Version: 3.5.0+dfsg-2 Distribution: lunar-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Sascha Steinbiss Description: augustus - gene prediction in eukaryotic genomes Changes: augustus (3.5.0+dfsg-2) unstable; urgency=medium . * Skip filterBam auxprogs test on s390x. 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/<>/augustus_3.5.0+dfsg-2_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: augustus Binary: augustus augustus-dbgsym Architecture: riscv64 Version: 3.5.0+dfsg-2 Checksums-Md5: 3c9502fb0c4f6ffb211d1f8ffd311f9d 37648818 augustus-dbgsym_3.5.0+dfsg-2_riscv64.ddeb 1432d4a1a3579ca75a8a16d6fc22bc04 2179476 augustus_3.5.0+dfsg-2_riscv64.deb Checksums-Sha1: 75b4efd091005d6b5c2081d3540ccf92a22bec98 37648818 augustus-dbgsym_3.5.0+dfsg-2_riscv64.ddeb c380765d3e6e5e351d1bc41cd10bc9ae5c927de0 2179476 augustus_3.5.0+dfsg-2_riscv64.deb Checksums-Sha256: ae0d7f0337bad32d05e46913bc71a1fda1b990b2d399e5f959603134948c4510 37648818 augustus-dbgsym_3.5.0+dfsg-2_riscv64.ddeb 3b3068f535f5d4a9578a5ad051b4e8ae0010b2045673361e4a15930fcf467945 2179476 augustus_3.5.0+dfsg-2_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Mon, 21 Nov 2022 06:22:39 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.17-1), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3ubuntu1), base-passwd (= 3.6.1), bash (= 5.2-1ubuntu2), binutils (= 2.39-8ubuntu2), binutils-common (= 2.39-8ubuntu2), binutils-riscv64-linux-gnu (= 2.39-8ubuntu2), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), ca-certificates (= 20211016), chrpath (= 0.16-2), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:12.2.0-1ubuntu1), cpp-12 (= 12.2.0-9ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-8ubuntu1), debconf (= 1.5.79ubuntu1), debhelper (= 13.10.1ubuntu1), debianutils (= 5.7-0.4), debugedit (= 1:5.0-5), default-libmysqlclient-dev (= 1.0.8), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-1), dpkg (= 1.21.9ubuntu1), dpkg-dev (= 1.21.9ubuntu1), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3ubuntu1), g++ (= 4:12.2.0-1ubuntu1), g++-12 (= 12.2.0-9ubuntu1), gcc (= 4:12.2.0-1ubuntu1), gcc-12 (= 12.2.0-9ubuntu1), gcc-12-base (= 12.2.0-9ubuntu1), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1ubuntu1), hostname (= 3.23ubuntu2), icu-devtools (= 71.1-3ubuntu1), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-1), libamd2 (= 1:5.12.0+dfsg-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 12.2.0-9ubuntu1), libatomic1 (= 12.2.0-9ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1ubuntu2), libaudit1 (= 1:3.0.7-1ubuntu2), libbamtools-dev (= 2.5.2+dfsg-2), libbamtools2.5.2 (= 2.5.2+dfsg-2), libbinutils (= 2.39-8ubuntu2), libblas-dev (= 3.10.1-2), libblas3 (= 3.10.1-2), libblkid1 (= 2.38-4ubuntu1), libboost-iostreams-dev (= 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libstdc++-12-dev (= 12.2.0-9ubuntu1), libstdc++6 (= 12.2.0-9ubuntu1), libsub-override-perl (= 0.09-4), libsuitesparse-dev (= 1:5.12.0+dfsg-2), libsuitesparseconfig5 (= 1:5.12.0+dfsg-2), libsystemd0 (= 251.4-1ubuntu7), libtasn1-6 (= 4.19.0-2), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-4), libuchardet0 (= 0.0.7-1build2), libudev1 (= 251.4-1ubuntu7), libumfpack5 (= 1:5.12.0+dfsg-2), libunistring2 (= 1.0-2), libuuid1 (= 2.38-4ubuntu1), libxml2 (= 2.9.14+dfsg-1.1), libyaml-0-2 (= 0.2.5-1), libzstd-dev (= 1.5.2+dfsg-1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.19.0-23.24), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.2ubuntu1), lto-disabled-list (= 36), m4 (= 1.4.19-1), make (= 4.3-4.1build1), man-db (= 2.11.1-1), mawk (= 1.3.4.20200120-3.1), media-types (= 8.0.0), mysql-common (= 5.8+1.0.8), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), openssl (= 3.0.5-2ubuntu2), patch (= 2.7.6-7build2), perl (= 5.36.0-4ubuntu2), perl-base (= 5.36.0-4ubuntu2), perl-modules-5.36 (= 5.36.0-4ubuntu2), po-debconf (= 1.0.21+nmu1), python3 (= 3.10.6-1ubuntu1), python3-minimal (= 3.10.6-1ubuntu1), python3.10 (= 3.10.8-3), python3.10-minimal (= 3.10.8-3), rake (= 13.0.6-3), readline-common (= 8.2-1.1), rpcsvc-proto (= 1.4.2-0ubuntu6), ruby (= 1:3.0~exp1), ruby-asciidoctor (= 2.0.17-1), ruby-net-telnet (= 0.1.1-2.1), ruby-rubygems (= 3.3.15-1), ruby-sdbm (= 1.0.0-5), ruby-webrick (= 1.7.0-4), ruby-xmlrpc (= 0.3.2-2), ruby3.0 (= 3.0.4-8), rubygems-integration (= 1.18), samtools (= 1.16.1-1), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.04-1ubuntu1), tar (= 1.34+dfsg-1.1), usrmerge (= 29ubuntu2), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.7-0.1), zlib1g (= 1:1.2.13.dfsg-1ubuntu2), zlib1g-dev (= 1:1.2.13.dfsg-1ubuntu2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1668985913" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ augustus_3.5.0+dfsg-2_riscv64.deb --------------------------------- new Debian package, version 2.0. size 2179476 bytes: control archive=5088 bytes. 1611 bytes, 24 lines control 10479 bytes, 140 lines md5sums Package: augustus Version: 3.5.0+dfsg-2 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 8809 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.34), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 4.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.10), libmysql++3v5 (>= 3.2.5-1~), libmysqlclient21 (>= 8.0.11), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 11), 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. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. drwxr-xr-x root/root 0 2022-11-20 23:11 ./ drwxr-xr-x root/root 0 2022-11-20 23:11 ./usr/ drwxr-xr-x root/root 0 2022-11-20 23:11 ./usr/bin/ -rwxr-xr-x root/root 14800 2022-11-20 23:11 ./usr/bin/aln2wig -rwxr-xr-x root/root 2075464 2022-11-20 23:11 ./usr/bin/augustus -rwxr-xr-x root/root 36448 2022-11-20 23:11 ./usr/bin/bam2hints -rwxr-xr-x root/root 10720 2022-11-20 23:11 ./usr/bin/bam2wig -rwxr-xr-x root/root 14824 2022-11-20 23:11 ./usr/bin/compileSpliceCands -rwxr-xr-x root/root 2244944 2022-11-20 23:11 ./usr/bin/etraining -rwxr-xr-x root/root 313264 2022-11-20 23:11 ./usr/bin/fastBlockSearch -rwxr-xr-x root/root 154992 2022-11-20 23:11 ./usr/bin/filterBam -rwxr-xr-x root/root 2055232 2022-11-20 23:11 ./usr/bin/getSeq -rwxr-xr-x root/root 118704 2022-11-20 23:11 ./usr/bin/homGeneMapping -rwxr-xr-x root/root 121984 2022-11-20 23:11 ./usr/bin/joingenes 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+------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 1667976 Build-Time: 2105 Distribution: lunar-proposed Host Architecture: riscv64 Install-Time: 571 Job: augustus_3.5.0+dfsg-2.dsc Machine Architecture: riscv64 Package: augustus Package-Time: 2844 Source-Version: 3.5.0+dfsg-2 Space: 1667976 Status: successful Version: 3.5.0+dfsg-2 -------------------------------------------------------------------------------- Finished at 2022-11-21T06:22:47Z Build needed 00:47:24, 1667976k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 Scanning for processes to kill in build PACKAGEBUILD-24855919 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 Stopping target for build PACKAGEBUILD-24855919 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=lunar --arch=riscv64 PACKAGEBUILD-24855919 Removing build PACKAGEBUILD-24855919