I: pbuilder: network access will be disabled during build I: Current time: Thu Jun 20 10:44:15 +14 2024 I: pbuilder-time-stamp: 1718829855 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [augustus_3.5.0+dfsg-2.dsc] I: copying [./augustus_3.5.0+dfsg.orig.tar.xz] I: copying [./augustus_3.5.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Nov 21 13:29:04 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./augustus_3.5.0+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting augustus in augustus-3.5.0+dfsg dpkg-source: info: unpacking augustus_3.5.0+dfsg.orig.tar.xz dpkg-source: info: unpacking augustus_3.5.0+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying search_config_path dpkg-source: info: applying set_installdir dpkg-source: info: applying interpreter_paths.patch dpkg-source: info: applying switch_cgp_testing_off.patch dpkg-source: info: applying disable-compare.patch dpkg-source: info: applying s390x-disable-filterbam-tests.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29453/tmp/hooks/D01_modify_environment starting debug: Running on codethink13-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 20 10:44 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/29453/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/29453/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=29453 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WJYUBPNS/pbuilderrc_1Dk2 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WJYUBPNS/b2 --logfile b2/build.log --extrapackages usrmerge augustus_3.5.0+dfsg-2.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 19 06:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/29453/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. 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 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however: Package libboost-iostreams-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on liblpsolve55-dev; however: Package liblpsolve55-dev is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libncurses5-dev; however: Package libncurses5-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-serialization-dev; however: Package libboost-serialization-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libmysql++-dev; however: Package libmysql++-dev is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} chrpath{a} debhelper{a} default-libmysqlclient-dev{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libamd2{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization-dev{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libbtf1{a} libbz2-dev{a} libcamd2{a} libccolamd2{a} libcholmod3{a} libcolamd2{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libcxsparse3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libklu1{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldl2{a} liblpsolve55-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmariadb-dev{a} libmariadb-dev-compat{a} libmariadb3{a} libmetis5{a} libmongoose2{a} libmysql++-dev{a} libmysql++3v5{a} libncurses-dev{a} libncurses5-dev{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} librbio2{a} libreadline8{a} librtmp1{a} libruby{a} libruby3.1{a} libsasl2-2{a} libsasl2-modules-db{a} libsliplu1{a} libspqr2{a} libsqlite3-dev{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsuitesparse-dev{a} libsuitesparseconfig5{a} libtool{a} libuchardet0{a} libumfpack5{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} mariadb-common{a} media-types{a} mysql-common{a} openssl{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-net-telnet{a} ruby-rubygems{a} ruby-sdbm{a} ruby-webrick{a} ruby-xmlrpc{a} ruby3.1{a} rubygems-integration{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl fonts-lato libarchive-cpio-perl libgpm2 libgraphblas-dev libjs-jquery libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget zip 0 packages upgraded, 130 newly installed, 0 to remove and 0 not upgraded. Need to get 74.1 MB of archives. After unpacking 438 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 openssl arm64 3.0.8-1 [1373 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 ca-certificates all 20230311 [153 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 rubygems-integration all 1.18 [6704 B] Get: 25 http://deb.debian.org/debian bookworm/main arm64 rake all 13.0.6-3 [83.9 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 ruby-webrick all 1.8.1-1 [51.4 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libruby arm64 1:3.1 [4968 B] Get: 30 http://deb.debian.org/debian bookworm/main arm64 ruby-sdbm arm64 1.0.0-5+b1 [14.5 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libncurses6 arm64 6.4-4 [93.9 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libruby3.1 arm64 3.1.2-7 [5248 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 ruby3.1 arm64 3.1.2-7 [663 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 ruby-rubygems all 3.3.15-2 [293 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 ruby arm64 1:3.1 [5868 B] Get: 39 http://deb.debian.org/debian bookworm/main arm64 ruby-asciidoctor all 2.0.18-2 [211 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 asciidoctor all 2.0.18-2 [86.6 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 mysql-common all 5.8+1.1.0 [6636 B] Get: 63 http://deb.debian.org/debian bookworm/main arm64 mariadb-common all 1:10.11.2-1 [22.4 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libmariadb3 arm64 1:10.11.2-1 [155 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libssl-dev arm64 3.0.8-1 [2296 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libmariadb-dev arm64 1:10.11.2-1 [248 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libmariadb-dev-compat arm64 1:10.11.2-1 [21.2 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 default-libmysqlclient-dev arm64 1.1.0 [3092 B] Get: 70 http://deb.debian.org/debian bookworm/main arm64 icu-devtools arm64 72.1-3 [192 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libsuitesparseconfig5 arm64 1:5.12.0+dfsg-2 [23.8 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libamd2 arm64 1:5.12.0+dfsg-2 [33.8 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-4 [134 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libbamtools-dev arm64 2.5.2+dfsg-4 [204 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libblas-dev arm64 3.11.0-2 [97.6 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74.0 arm64 1.74.0+ds1-20 [448 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libicu-dev arm64 72.1-3 [10.2 MB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74-dev arm64 1.74.0+ds1-20 [525 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libboost-iostreams1.74-dev arm64 1.74.0+ds1-20 [247 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libboost-iostreams-dev arm64 1.74.0.3 [4316 B] Get: 83 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74.0 arm64 1.74.0+ds1-20 [308 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74-dev arm64 1.74.0+ds1-20 [357 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization-dev arm64 1.74.0.3 [4560 B] Get: 86 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libbtf1 arm64 1:5.12.0+dfsg-2 [25.2 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 libbz2-dev arm64 1.0.8-5+b1 [31.5 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libcamd2 arm64 1:5.12.0+dfsg-2 [34.9 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 libccolamd2 arm64 1:5.12.0+dfsg-2 [37.6 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 libcolamd2 arm64 1:5.12.0+dfsg-2 [31.8 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libmetis5 arm64 5.1.0.dfsg-7 [154 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 libcholmod3 arm64 1:5.12.0+dfsg-2 [285 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-9 [357 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-9 [466 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libcxsparse3 arm64 1:5.12.0+dfsg-2 [73.4 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libgslcblas0 arm64 2.7.1+dfsg-3+b1 [82.3 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libgsl27 arm64 2.7.1+dfsg-3+b1 [824 kB] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libgsl-dev arm64 2.7.1+dfsg-3+b1 [1035 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 113 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libklu1 arm64 1:5.12.0+dfsg-2 [77.1 kB] Get: 116 http://deb.debian.org/debian bookworm/main arm64 liblapack-dev arm64 3.11.0-2 [3065 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libldl2 arm64 1:5.12.0+dfsg-2 [24.8 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libmongoose2 arm64 1:5.12.0+dfsg-2 [44.3 kB] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libumfpack5 arm64 1:5.12.0+dfsg-2 [201 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 librbio2 arm64 1:5.12.0+dfsg-2 [38.9 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libspqr2 arm64 1:5.12.0+dfsg-2 [75.1 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libsliplu1 arm64 1:5.12.0+dfsg-2 [46.6 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libsuitesparse-dev arm64 1:5.12.0+dfsg-2 [885 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 liblpsolve55-dev arm64 5.5.2.5-2 [364 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libmysql++3v5 arm64 3.2.5-2.1+b1 [150 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libmysql++-dev arm64 3.2.5-2.1+b1 [150 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libncurses-dev arm64 6.4-4 [336 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libncurses5-dev arm64 6.4-4 [932 B] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libsqlite3-dev arm64 3.40.1-2 [979 kB] Get: 130 http://deb.debian.org/debian bookworm/main arm64 samtools arm64 1.16.1-1 [580 kB] Fetched 74.1 MB in 2s (46.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20366 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.8-1_arm64.deb ... Unpacking openssl (3.0.8-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../005-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../013-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../014-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../015-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../016-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../017-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package libruby:arm64. Preparing to unpack .../018-libruby_1%3a3.1_arm64.deb ... Unpacking libruby:arm64 (1:3.1) ... Selecting previously unselected package ruby-sdbm:arm64. Preparing to unpack .../019-ruby-sdbm_1.0.0-5+b1_arm64.deb ... Unpacking ruby-sdbm:arm64 (1.0.0-5+b1) ... Selecting previously unselected package libbsd0:arm64. 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Preparing to unpack .../026-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../027-ruby_1%3a3.1_arm64.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../028-ruby-asciidoctor_2.0.18-2_all.deb ... Unpacking ruby-asciidoctor (2.0.18-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../029-asciidoctor_2.0.18-2_all.deb ... Unpacking asciidoctor (2.0.18-2) ... Selecting previously unselected package m4. Preparing to unpack .../030-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../031-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../032-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../033-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../034-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package chrpath. Preparing to unpack .../035-chrpath_0.16-2+b1_arm64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../036-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../037-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../038-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../039-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../040-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../041-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../042-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../043-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../044-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../045-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../046-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../047-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../048-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../049-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../050-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package mysql-common. Preparing to unpack .../051-mysql-common_5.8+1.1.0_all.deb ... Unpacking mysql-common (5.8+1.1.0) ... Selecting previously unselected package mariadb-common. Preparing to unpack .../052-mariadb-common_1%3a10.11.2-1_all.deb ... Unpacking mariadb-common (1:10.11.2-1) ... Selecting previously unselected package libmariadb3:arm64. Preparing to unpack .../053-libmariadb3_1%3a10.11.2-1_arm64.deb ... Unpacking libmariadb3:arm64 (1:10.11.2-1) ... Selecting previously unselected package libssl-dev:arm64. Preparing to unpack .../054-libssl-dev_3.0.8-1_arm64.deb ... Unpacking libssl-dev:arm64 (3.0.8-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../055-zlib1g-dev_1%3a1.2.13.dfsg-1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libmariadb-dev. Preparing to unpack .../056-libmariadb-dev_1%3a10.11.2-1_arm64.deb ... Unpacking libmariadb-dev (1:10.11.2-1) ... Selecting previously unselected package libmariadb-dev-compat:arm64. Preparing to unpack .../057-libmariadb-dev-compat_1%3a10.11.2-1_arm64.deb ... Unpacking libmariadb-dev-compat:arm64 (1:10.11.2-1) ... Selecting previously unselected package default-libmysqlclient-dev:arm64. Preparing to unpack .../058-default-libmysqlclient-dev_1.1.0_arm64.deb ... Unpacking default-libmysqlclient-dev:arm64 (1.1.0) ... Selecting previously unselected package icu-devtools. Preparing to unpack .../059-icu-devtools_72.1-3_arm64.deb ... Unpacking icu-devtools (72.1-3) ... Selecting previously unselected package libsuitesparseconfig5:arm64. Preparing to unpack .../060-libsuitesparseconfig5_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libsuitesparseconfig5:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libamd2:arm64. Preparing to unpack .../061-libamd2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libamd2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libbamtools2.5.2:arm64. Preparing to unpack .../062-libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb ... Unpacking libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... Selecting previously unselected package libbamtools-dev:arm64. Preparing to unpack .../063-libbamtools-dev_2.5.2+dfsg-4_arm64.deb ... Unpacking libbamtools-dev:arm64 (2.5.2+dfsg-4) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../064-libblas3_3.11.0-2_arm64.deb ... Unpacking libblas3:arm64 (3.11.0-2) ... Selecting previously unselected package libblas-dev:arm64. Preparing to unpack .../065-libblas-dev_3.11.0-2_arm64.deb ... Unpacking libblas-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libboost1.74-dev:arm64. Preparing to unpack .../066-libboost1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-regex1.74.0:arm64. Preparing to unpack .../067-libboost-regex1.74.0_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-regex1.74.0:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libicu-dev:arm64. Preparing to unpack .../068-libicu-dev_72.1-3_arm64.deb ... Unpacking libicu-dev:arm64 (72.1-3) ... Selecting previously unselected package libboost-regex1.74-dev:arm64. Preparing to unpack .../069-libboost-regex1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-regex1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-iostreams1.74-dev:arm64. Preparing to unpack .../070-libboost-iostreams1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-iostreams1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-iostreams-dev:arm64. Preparing to unpack .../071-libboost-iostreams-dev_1.74.0.3_arm64.deb ... Unpacking libboost-iostreams-dev:arm64 (1.74.0.3) ... Selecting previously unselected package libboost-serialization1.74.0:arm64. Preparing to unpack .../072-libboost-serialization1.74.0_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-serialization1.74.0:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-serialization1.74-dev:arm64. Preparing to unpack .../073-libboost-serialization1.74-dev_1.74.0+ds1-20_arm64.deb ... Unpacking libboost-serialization1.74-dev:arm64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-serialization-dev:arm64. Preparing to unpack .../074-libboost-serialization-dev_1.74.0.3_arm64.deb ... Unpacking libboost-serialization-dev:arm64 (1.74.0.3) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../075-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libbtf1:arm64. Preparing to unpack .../076-libbtf1_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libbtf1:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libbz2-dev:arm64. Preparing to unpack .../077-libbz2-dev_1.0.8-5+b1_arm64.deb ... Unpacking libbz2-dev:arm64 (1.0.8-5+b1) ... Selecting previously unselected package libcamd2:arm64. Preparing to unpack .../078-libcamd2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libcamd2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libccolamd2:arm64. Preparing to unpack .../079-libccolamd2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libccolamd2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libcolamd2:arm64. Preparing to unpack .../080-libcolamd2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libcolamd2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libgfortran5:arm64. Preparing to unpack .../081-libgfortran5_12.2.0-14_arm64.deb ... Unpacking libgfortran5:arm64 (12.2.0-14) ... Selecting previously unselected package liblapack3:arm64. Preparing to unpack .../082-liblapack3_3.11.0-2_arm64.deb ... Unpacking liblapack3:arm64 (3.11.0-2) ... 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Selecting previously unselected package libcxsparse3:arm64. Preparing to unpack .../094-libcxsparse3_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libcxsparse3:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libdeflate0:arm64. Preparing to unpack .../095-libdeflate0_1.14-1_arm64.deb ... Unpacking libdeflate0:arm64 (1.14-1) ... Selecting previously unselected package libdeflate-dev:arm64. Preparing to unpack .../096-libdeflate-dev_1.14-1_arm64.deb ... Unpacking libdeflate-dev:arm64 (1.14-1) ... Selecting previously unselected package libgslcblas0:arm64. Preparing to unpack .../097-libgslcblas0_2.7.1+dfsg-3+b1_arm64.deb ... Unpacking libgslcblas0:arm64 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libgsl27:arm64. Preparing to unpack .../098-libgsl27_2.7.1+dfsg-3+b1_arm64.deb ... Unpacking libgsl27:arm64 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../099-libgsl-dev_2.7.1+dfsg-3+b1_arm64.deb ... Unpacking libgsl-dev (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libhtscodecs2:arm64. Preparing to unpack .../100-libhtscodecs2_1.3.0-4_arm64.deb ... Unpacking libhtscodecs2:arm64 (1.3.0-4) ... Selecting previously unselected package libhts3:arm64. Preparing to unpack .../101-libhts3_1.16+ds-3_arm64.deb ... Unpacking libhts3:arm64 (1.16+ds-3) ... Selecting previously unselected package liblzma-dev:arm64. Preparing to unpack .../102-liblzma-dev_5.4.1-0.2_arm64.deb ... Unpacking liblzma-dev:arm64 (5.4.1-0.2) ... Selecting previously unselected package libhts-dev:arm64. Preparing to unpack .../103-libhts-dev_1.16+ds-3_arm64.deb ... Unpacking libhts-dev:arm64 (1.16+ds-3) ... Selecting previously unselected package libklu1:arm64. Preparing to unpack .../104-libklu1_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libklu1:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package liblapack-dev:arm64. Preparing to unpack .../105-liblapack-dev_3.11.0-2_arm64.deb ... Unpacking liblapack-dev:arm64 (3.11.0-2) ... Selecting previously unselected package libldl2:arm64. Preparing to unpack .../106-libldl2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libldl2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libmongoose2:arm64. Preparing to unpack .../107-libmongoose2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libmongoose2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libumfpack5:arm64. Preparing to unpack .../108-libumfpack5_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libumfpack5:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package librbio2:arm64. Preparing to unpack .../109-librbio2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking librbio2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libspqr2:arm64. Preparing to unpack .../110-libspqr2_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libspqr2:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libsliplu1:arm64. Preparing to unpack .../111-libsliplu1_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libsliplu1:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package libsuitesparse-dev:arm64. Preparing to unpack .../112-libsuitesparse-dev_1%3a5.12.0+dfsg-2_arm64.deb ... Unpacking libsuitesparse-dev:arm64 (1:5.12.0+dfsg-2) ... Selecting previously unselected package liblpsolve55-dev. Preparing to unpack .../113-liblpsolve55-dev_5.5.2.5-2_arm64.deb ... Unpacking liblpsolve55-dev (5.5.2.5-2) ... Selecting previously unselected package libmysql++3v5:arm64. Preparing to unpack .../114-libmysql++3v5_3.2.5-2.1+b1_arm64.deb ... Unpacking libmysql++3v5:arm64 (3.2.5-2.1+b1) ... Selecting previously unselected package libmysql++-dev:arm64. Preparing to unpack .../115-libmysql++-dev_3.2.5-2.1+b1_arm64.deb ... Unpacking libmysql++-dev:arm64 (3.2.5-2.1+b1) ... Selecting previously unselected package libncurses-dev:arm64. Preparing to unpack .../116-libncurses-dev_6.4-4_arm64.deb ... Unpacking libncurses-dev:arm64 (6.4-4) ... Selecting previously unselected package libncurses5-dev:arm64. Preparing to unpack .../117-libncurses5-dev_6.4-4_arm64.deb ... Unpacking libncurses5-dev:arm64 (6.4-4) ... Selecting previously unselected package libsqlite3-dev:arm64. Preparing to unpack .../118-libsqlite3-dev_3.40.1-2_arm64.deb ... Unpacking libsqlite3-dev:arm64 (3.40.1-2) ... Selecting previously unselected package samtools. Preparing to unpack .../119-samtools_1.16.1-1_arm64.deb ... Unpacking samtools (1.16.1-1) ... Setting up libhtscodecs2:arm64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up mysql-common (5.8+1.1.0) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libgslcblas0:arm64 (2.7.1+dfsg-3+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libldl2:arm64 (1:5.12.0+dfsg-2) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up libgsl27:arm64 (2.7.1+dfsg-3+b1) ... Setting up m4 (1.4.19-3) ... Setting up libmetis5:arm64 (5.1.0.dfsg-7) ... Setting up file (1:5.44-3) ... Setting up libbtf1:arm64 (1:5.12.0+dfsg-2) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up mariadb-common (1:10.11.2-1) ... update-alternatives: using /etc/mysql/mariadb.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up autotools-dev (20220109.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libsqlite3-dev:arm64 (3.40.1-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.4-4) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libboost-regex1.74.0:arm64 (1.74.0+ds1-20) ... Setting up libssl-dev:arm64 (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up icu-devtools (72.1-3) ... Setting up libmariadb3:arm64 (1:10.11.2-1) ... Setting up libmysql++3v5:arm64 (3.2.5-2.1+b1) ... Setting up libbamtools2.5.2:arm64 (2.5.2+dfsg-4) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up ruby-webrick (1.8.1-1) ... Setting up liblzma-dev:arm64 (5.4.1-0.2) ... Setting up libboost-serialization1.74.0:arm64 (1.74.0+ds1-20) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libcxsparse3:arm64 (1:5.12.0+dfsg-2) ... Setting up openssl (3.0.8-1) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libdeflate-dev:arm64 (1.14-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libicu-dev:arm64 (72.1-3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up libsuitesparseconfig5:arm64 (1:5.12.0+dfsg-2) ... Setting up chrpath (0.16-2+b1) ... Setting up libblas-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up librbio2:arm64 (1:5.12.0+dfsg-2) ... Setting up libbz2-dev:arm64 (1.0.8-5+b1) ... 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 libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses-dev:arm64 (6.4-4) ... Setting up gettext (0.21-12) ... Setting up libgsl-dev (2.7.1+dfsg-3+b1) ... Setting up libcolamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libsliplu1:arm64 (1:5.12.0+dfsg-2) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libcamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up libmongoose2:arm64 (1:5.12.0+dfsg-2) ... Setting up libbamtools-dev:arm64 (2.5.2+dfsg-4) ... Setting up liblapack-dev:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libboost-serialization1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libmariadb-dev (1:10.11.2-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up groff-base (1.22.4-10) ... Setting up libklu1:arm64 (1:5.12.0+dfsg-2) ... Setting up libccolamd2:arm64 (1:5.12.0+dfsg-2) ... Setting up libncurses5-dev:arm64 (6.4-4) ... Setting up libcholmod3:arm64 (1:5.12.0+dfsg-2) ... Setting up libmariadb-dev-compat:arm64 (1:10.11.2-1) ... Setting up libspqr2:arm64 (1:5.12.0+dfsg-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libcurl3-gnutls:arm64 (7.88.1-9) ... Setting up rubygems-integration (1.18) ... Setting up libcurl4-gnutls-dev:arm64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libboost-iostreams1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libumfpack5:arm64 (1:5.12.0+dfsg-2) ... Setting up libboost-serialization-dev:arm64 (1.74.0.3) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up default-libmysqlclient-dev:arm64 (1.1.0) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:arm64 (1.16+ds-3) ... Setting up libsuitesparse-dev:arm64 (1:5.12.0+dfsg-2) ... Setting up libhts-dev:arm64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libboost-iostreams-dev:arm64 (1.74.0.3) ... Setting up samtools (1.16.1-1) ... Setting up libmysql++-dev:arm64 (3.2.5-2.1+b1) ... Setting up liblpsolve55-dev (5.5.2.5-2) ... Setting up libruby:arm64 (1:3.1) ... Setting up ruby-rubygems (3.3.15-2) ... Setting up ruby (1:3.1) ... Setting up ruby-asciidoctor (2.0.18-2) ... Setting up rake (13.0.6-3) ... Setting up asciidoctor (2.0.18-2) ... Setting up ruby-sdbm:arm64 (1.0.0-5+b1) ... Setting up libruby3.1:arm64 (3.1.2-7) ... Setting up ruby3.1 (3.1.2-7) ... Processing triggers for libc-bin (2.36-9) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/29453/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... I: user script /srv/workspace/pbuilder/29453/tmp/hooks/A99_set_merged_usr finished hostname: Temporary failure in name resolution I: Running cd /build/augustus-3.5.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../augustus_3.5.0+dfsg-2_source.changes dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.5.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/augustus-3.5.0+dfsg' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' cd src; make clean make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o sqliteDB.o rm -f ../../../bin/homGeneMapping make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' if [ -n /usr/bin/python3 ] ; then cd ../../tests/short && ./execute_test.py --clean homGeneMapping ; fi make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' rm -f *.o joingenes ../../bin/joingenes make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' rm -f aln2wig aln2wig.o ../../bin/aln2wig make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/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 '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' rm -f compileSpliceCands *.o ../../bin/compileSpliceCands make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/build/augustus-3.5.0+dfsg/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 '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/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 '/build/augustus-3.5.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/augustus-3.5.0+dfsg' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o mkdir -p ../../bin cp -f aln2wig ../../bin make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -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/aarch64-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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o cp -f compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/build/augustus-3.5.0+dfsg/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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -std=gnu++0x -O2 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/augustus-3.5.0+dfsg' mkdir -p bin mkdir -p bin cd src && make cd auxprogs && make make[3]: Entering directory '/build/augustus-3.5.0+dfsg/src' make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' 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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genbank.o genbank.cc make[4]: 'aln2wig' is up to date. make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' cd bam2hints; 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=/build/augustus-3.5.0+dfsg=. -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]: Entering directory '/build/augustus-3.5.0+dfsg/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=/build/augustus-3.5.0+dfsg=. -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 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=/build/augustus-3.5.0+dfsg=. -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 make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' 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=/build/augustus-3.5.0+dfsg=. -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 '/build/augustus-3.5.0+dfsg/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 '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o statemodel.o statemodel.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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o namgene.o namgene.cc make[5]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/build/augustus-3.5.0+dfsg/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 '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' cd utrrnaseq; make; make[4]: Entering directory '/build/augustus-3.5.0+dfsg/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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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 | ^~~~~~~~~ In file included from /usr/include/c++/12/vector:64, from src/Genomic_Data.hpp:9, from src/Compute_UTRs.cpp:5: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = Genomic_Data::Scaff_plus_Gen_Data; _Alloc = std::allocator]', inlined from 'void compute_UTRs(std::string)' at src/Compute_UTRs.cpp:199:106: /usr/include/c++/12/bits/stl_vector.h:1124:41: warning: 'idx_former_scaff' may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ src/Compute_UTRs.cpp: In function 'void compute_UTRs(std::string)': 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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc src/Genomic_Data.cpp: In function 'std::vector > lower_case_runs(std::string)': src/Genomic_Data.cpp:62:33: warning: 'start' may be used uninitialized [-Wmaybe-uninitialized] 62 | ret += make_pair(start, end); | ~~~~~~~~~^~~~~~~~~~~~ src/Genomic_Data.cpp:42:18: note: 'start' was declared here 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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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/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=/build/augustus-3.5.0+dfsg=. -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" 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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.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=/build/augustus-3.5.0+dfsg=. -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/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=/build/augustus-3.5.0+dfsg=. -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" 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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 Finished building target: utrrnaseq make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' cd bam2wig; make; make[4]: Entering directory '/build/augustus-3.5.0+dfsg/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 '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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 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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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=/build/augustus-3.5.0+dfsg=. -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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 getSeq ../bin/ cp -f pp_simScore ../bin/ cp -f fastBlockSearch ../bin/ cp -f etraining ../bin/ cp -f augustus ../bin/ make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/src' make[2]: Leaving directory '/build/augustus-3.5.0+dfsg' asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' dh_auto_test make -j8 test make[1]: Entering directory '/build/augustus-3.5.0+dfsg' mkdir -p bin cd src && make mkdir -p bin make[2]: Entering directory '/build/augustus-3.5.0+dfsg/src' cd auxprogs && make make[2]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs' cd aln2wig; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: 'aln2wig' is up to date. make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/aln2wig' cd bam2hints; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2hints' echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags cd compileSpliceCands; make; make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/src' make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/compileSpliceCands' cd filterBam; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wpedantic -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/augustus-3.5.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-rpath,/usr/lib -o filterBam filterBam.o initOptions.o printElapsedTime.o MatePairs.o PairednessCoverage.o BamToolsAccess.o -lbamtools -lz mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam/src' make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/filterBam' cd homGeneMapping; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[4]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping/src' make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/homGeneMapping' cd joingenes; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/joingenes' cd utrrnaseq; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. mkdir -p build make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/utrrnaseq' cd bam2wig; make; make[3]: Entering directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs/bam2wig' make[2]: Leaving directory '/build/augustus-3.5.0+dfsg/auxprogs' If you run make test on a non-AMD64 architecture or a non-Linux system (like macOS), most tests will run without the --compare option! cd tests/short && ./execute_test.py examples test_utr_on (examples.test_examples.TestExamples.test_utr_on) ... ok test_hints_MPE (examples.test_examples.TestExamples.test_hints_MPE) ... ok test_training_new_species (examples.test_examples.TestExamples.test_training_new_species) ... ok test_ab_initio_prediction (examples.test_examples.TestExamples.test_ab_initio_prediction) ... ok test_format_and_error_out (examples.test_examples.TestExamples.test_format_and_error_out) ... ok test_cgp (examples.test_examples.TestExamples.test_cgp) ... ok test_cgp_sqlite (examples.test_examples.TestExamples.test_cgp_sqlite) ... ok test_cgp_sqlite_hints (examples.test_examples.TestExamples.test_cgp_sqlite_hints) ... ok ---------------------------------------------------------------------- Ran 8 tests in 1170.526s OK Removing generated test files... ---------------------------------------------------------------------- Executing small test suite ---------------------------------------------------------------------- Creating SQLite database for cgp test cases... cd tests/short && ./execute_test.py --html bam2hints test_bam2hints (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints) ... ok test_bam2hints_pipes (auxprogs.bam2hints.test_bam2hints.TestBam2Hints.test_bam2hints_pipes) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.029s OK cd tests/short && ./execute_test.py --html bam2wig test_bam2wig (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig) ... ok test_bam2wig_region (auxprogs.bam2wig.test_bam2wig.TestBam2Wig.test_bam2wig_region) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.039s OK cd tests/short && ./execute_test.py --html filterbam test_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_options) ... ok test_no_minId_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId_no_minCover) ... ok test_no_minId (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minId) ... ok test_no_minCover (auxprogs.filterbam.test_filterbam.TestFilterBam.test_no_minCover) ... ok test_minCover99 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_minCover99) ... ok test_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniq) ... ok test_uniqThresh (auxprogs.filterbam.test_filterbam.TestFilterBam.test_uniqThresh) ... ok test_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_best) ... ok test_noIntrons (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons) ... ok test_noIntrons_insertLimit (auxprogs.filterbam.test_filterbam.TestFilterBam.test_noIntrons_insertLimit) ... ok test_not_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_not_paired) ... ok test_paired (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired) ... ok test_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairwiseAlignments) ... ok test_pairwiseAlignments_2 (auxprogs.filterbam.test_filterbam.TestFilterBam.test_pairwiseAlignments_2) ... ok test_paired_maxIntronLen (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_maxIntronLen) ... ok test_paired_pairBedFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_paired_pairBedFile) ... ok test_commonGeneFile (auxprogs.filterbam.test_filterbam.TestFilterBam.test_commonGeneFile) ... ok test_calmd_seq_with_equalsigns_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_no_options) ... ok test_calmd_no_options (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_no_options) ... ok test_calmd_seq_with_equalsigns_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_uniq) ... ok test_calmd_uniq (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_uniq) ... ok test_calmd_seq_with_equalsigns_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_best) ... ok test_calmd_best (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_best) ... ok test_calmd_seq_with_equalsigns_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_seq_with_equalsigns_paired_pairwiseAlignments) ... ok test_calmd_paired_pairwiseAlignments (auxprogs.filterbam.test_filterbam.TestFilterBam.test_calmd_paired_pairwiseAlignments) ... ok ---------------------------------------------------------------------- Ran 25 tests in 1.086s OK make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/augustus-3.5.0+dfsg' 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 '/build/augustus-3.5.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/augustus-3.5.0+dfsg' chrpath -d debian/*/usr/bin/bam2hints chrpath -d debian/*/usr/bin/filterBam dh_install make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/augustus-3.5.0+dfsg' dh_installchangelogs -k docs/HISTORY.TXT make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' dh_installman dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/augustus-3.5.0+dfsg' dh_compress -Xtutorial make[1]: Leaving directory '/build/augustus-3.5.0+dfsg' dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'augustus-data' in '../augustus-data_3.5.0+dfsg-2_all.deb'. dpkg-deb: building package 'augustus-doc' in '../augustus-doc_3.5.0+dfsg-2_all.deb'. dpkg-deb: building package 'augustus' in '../augustus_3.5.0+dfsg-2_arm64.deb'. dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.5.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../augustus_3.5.0+dfsg-2_arm64.buildinfo dpkg-genchanges --build=binary -O../augustus_3.5.0+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/29453/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29453/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29453 and its subdirectories I: Current time: Thu Jun 20 11:22:58 +14 2024 I: pbuilder-time-stamp: 1718832178