Diff of the two buildlogs: -- --- b1/build.log 2024-04-29 09:54:33.036550604 +0000 +++ b2/build.log 2024-04-29 09:56:06.148580129 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 28 21:51:09 -12 2024 -I: pbuilder-time-stamp: 1714384269 +I: Current time: Mon Jun 2 06:17:38 +14 2025 +I: pbuilder-time-stamp: 1748794658 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying fix_shebang.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/24406/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/90725/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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 1 16:17 /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/90725/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/90725/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='50364444e7244ca69e0950668a3d0454' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='24406' - PS1='# ' - PS2='> ' + INVOCATION_ID=aca331a37bdc406884fba03bd5cbc60f + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-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=90725 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.gxDbHY2f/pbuilderrc_jVKt --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gxDbHY2f/b1 --logfile b1/build.log lumpy-sv_0.3.1+dfsg-7.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.gxDbHY2f/pbuilderrc_LpTH --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.gxDbHY2f/b2 --logfile b2/build.log lumpy-sv_0.3.1+dfsg-7.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos2-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:13 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/24406/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 27 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/90725/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -91,7 +123,7 @@ Depends: debhelper-compat (= 13), dh-python, python3, libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, python3-pysam dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. -(Reading database ... 19885 files and directories currently installed.) +(Reading database ... 19709 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: @@ -152,55 +184,61 @@ Install the following packages: 3) dh-python [6.20240422 (testing)] 4) libbrotli1 [1.1.0-2+b3 (testing)] -5) libcurl3t64-gnutls [8.7.1-3 (testing)] -6) libcurl4-gnutls-dev [8.7.1-3 (testing)] -7) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] -8) libdeflate-dev [1.20-1 (testing)] -9) libdeflate0 [1.20-1 (testing)] -10) libexpat1 [2.6.2-1 (testing)] -11) libhts-dev [1.19+ds-1 (testing)] -12) libhts3 [1.19+ds-1 (testing)] -13) libhtscodecs2 [1.6.0-1+b1 (testing)] -14) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] -15) liblzma-dev [5.6.1+really5.4.5-1 (testing)] -16) libncurses6 [6.4+20240414-1 (testing)] -17) libnghttp2-14 [1.59.0-1 (testing)] -18) libpsl5t64 [0.21.2-1.1 (testing)] -19) libpython3-stdlib [3.11.8-1 (testing)] -20) libpython3.11-minimal [3.11.9-1 (testing)] -21) libpython3.11-stdlib [3.11.9-1 (testing)] -22) libreadline8t64 [8.2-4 (testing)] -23) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] -24) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] -25) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] -26) libssh2-1t64 [1.11.0-4.1+b2 (testing)] -27) libssl-dev [3.2.1-3 (testing)] -28) libssl3t64 [3.2.1-3 (testing)] -29) media-types [10.1.0 (testing)] -30) netbase [6.4 (testing)] -31) python3 [3.11.8-1 (testing)] -32) python3-distutils [3.12.3-1 (testing)] -33) python3-lib2to3 [3.12.3-1 (testing)] -34) python3-minimal [3.11.8-1 (testing)] -35) python3-pkg-resources [68.1.2-2 (testing)] -36) python3-pysam [0.22.0+ds-1+b1 (testing)] -37) python3-setuptools [68.1.2-2 (testing)] -38) python3.11 [3.11.9-1 (testing)] -39) python3.11-minimal [3.11.9-1 (testing)] -40) readline-common [8.2-4 (testing)] -41) samtools [1.19.2-1 (testing)] -42) tzdata [2024a-3 (testing)] +5) libcom-err2 [1.47.0-2.4 (testing)] +6) libcurl3t64-gnutls [8.7.1-3 (testing)] +7) libcurl4-gnutls-dev [8.7.1-3 (testing)] +8) libdb5.3t64 [5.3.28+dfsg2-7 (testing)] +9) libdeflate-dev [1.20-1 (testing)] +10) libdeflate0 [1.20-1 (testing)] +11) libexpat1 [2.6.2-1 (testing)] +12) libgssapi-krb5-2 [1.20.1-5+b1 (testing)] +13) libhts-dev [1.19+ds-1 (testing)] +14) libhts3 [1.19+ds-1 (testing)] +15) libhtscodecs2 [1.6.0-1+b1 (testing)] +16) libk5crypto3 [1.20.1-5+b1 (testing)] +17) libkeyutils1 [1.6.3-3 (testing)] +18) libkrb5-3 [1.20.1-5+b1 (testing)] +19) libkrb5support0 [1.20.1-5+b1 (testing)] +20) libldap-2.5-0 [2.5.13+dfsg-5+b3 (testing)] +21) liblzma-dev [5.6.1+really5.4.5-1 (testing)] +22) libncurses6 [6.4+20240414-1 (testing)] +23) libnghttp2-14 [1.59.0-1 (testing)] +24) libpsl5t64 [0.21.2-1.1 (testing)] +25) libpython3-stdlib [3.11.8-1 (testing)] +26) libpython3.11-minimal [3.11.9-1 (testing)] +27) libpython3.11-stdlib [3.11.9-1 (testing)] +28) libreadline8t64 [8.2-4 (testing)] +29) librtmp1 [2.4+20151223.gitfa8646d.1-2+b4 (testing)] +30) libsasl2-2 [2.1.28+dfsg1-4+b1 (testing)] +31) libsasl2-modules-db [2.1.28+dfsg1-4+b1 (testing)] +32) libssh2-1t64 [1.11.0-4.1+b2 (testing)] +33) libssl-dev [3.2.1-3 (testing)] +34) libssl3t64 [3.2.1-3 (testing)] +35) media-types [10.1.0 (testing)] +36) netbase [6.4 (testing)] +37) python3 [3.11.8-1 (testing)] +38) python3-distutils [3.12.3-1 (testing)] +39) python3-lib2to3 [3.12.3-1 (testing)] +40) python3-minimal [3.11.8-1 (testing)] +41) python3-pkg-resources [68.1.2-2 (testing)] +42) python3-pysam [0.22.0+ds-1+b1 (testing)] +43) python3-setuptools [68.1.2-2 (testing)] +44) python3.11 [3.11.9-1 (testing)] +45) python3.11-minimal [3.11.9-1 (testing)] +46) readline-common [8.2-4 (testing)] +47) samtools [1.19.2-1 (testing)] +48) tzdata [2024a-3 (testing)] The following NEW packages will be installed: - autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libbrotli1{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdb5.3t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} + autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdb5.3t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libgzstream-dev{a} libgzstream0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsqlite3-dev{a} libssh2-1t64{a} libssl-dev{a} libssl3t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages will be REMOVED: libdb5.3{a} libssl3{a} The following packages are RECOMMENDED but will NOT be installed: - ca-certificates curl libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget -0 packages upgraded, 78 newly installed, 2 to remove and 0 not upgraded. -Need to get 44.1 MB of archives. After unpacking 172 MB will be used. + ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget +0 packages upgraded, 84 newly installed, 2 to remove and 0 not upgraded. +Need to get 44.7 MB of archives. After unpacking 174 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libdb5.3t64 i386 5.3.28+dfsg2-7 [759 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libssl3t64 i386 3.2.1-3 [2234 kB] @@ -256,56 +294,61 @@ Get: 52 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg-3.1 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 libbamtools-dev i386 2.5.2+dfsg-5 [240 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b3 [314 kB] -Get: 55 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] -Get: 56 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] -Get: 57 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] -Get: 58 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] -Get: 59 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] -Get: 60 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] -Get: 61 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] -Get: 62 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.7.1-3 [467 kB] -Get: 63 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.7.1-3 [589 kB] -Get: 64 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] -Get: 65 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.20-1 [56.0 kB] -Get: 66 http://deb.debian.org/debian trixie/main i386 libfastahack0 i386 1.0.0+dfsg-11+b1 [28.7 kB] -Get: 67 http://deb.debian.org/debian trixie/main i386 libfastahack-dev i386 1.0.0+dfsg-11+b1 [30.3 kB] -Get: 68 http://deb.debian.org/debian trixie/main i386 libgzstream0 i386 1.5+git20171107.9a20658-2 [7384 B] -Get: 69 http://deb.debian.org/debian trixie/main i386 libgzstream-dev i386 1.5+git20171107.9a20658-2 [7576 B] -Get: 70 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] -Get: 71 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] -Get: 72 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.1+really5.4.5-1 [304 kB] -Get: 73 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] -Get: 74 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.4+20240414-1 [112 kB] -Get: 75 http://deb.debian.org/debian trixie/main i386 libsqlite3-dev i386 3.45.1-1 [1171 kB] -Get: 76 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.2.1-3 [2744 kB] -Get: 77 http://deb.debian.org/debian trixie/main i386 python3-pysam i386 0.22.0+ds-1+b1 [4120 kB] -Get: 78 http://deb.debian.org/debian trixie/main i386 samtools i386 1.19.2-1 [680 kB] -Fetched 44.1 MB in 1s (50.4 MB/s) +Get: 55 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.0-2.4 [20.6 kB] +Get: 56 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.20.1-5+b1 [35.9 kB] +Get: 57 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.20.1-5+b1 [83.2 kB] +Get: 58 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-3 [9432 B] +Get: 59 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.20.1-5+b1 [359 kB] +Get: 60 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.20.1-5+b1 [145 kB] +Get: 61 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-4+b1 [20.7 kB] +Get: 62 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-4+b1 [60.7 kB] +Get: 63 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5+b3 [196 kB] +Get: 64 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.59.0-1 [82.5 kB] +Get: 65 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1 [57.4 kB] +Get: 66 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b4 [62.0 kB] +Get: 67 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.0-4.1+b2 [225 kB] +Get: 68 http://deb.debian.org/debian trixie/main i386 libcurl3t64-gnutls i386 8.7.1-3 [467 kB] +Get: 69 http://deb.debian.org/debian trixie/main i386 libcurl4-gnutls-dev i386 8.7.1-3 [589 kB] +Get: 70 http://deb.debian.org/debian trixie/main i386 libdeflate0 i386 1.20-1 [46.9 kB] +Get: 71 http://deb.debian.org/debian trixie/main i386 libdeflate-dev i386 1.20-1 [56.0 kB] +Get: 72 http://deb.debian.org/debian trixie/main i386 libfastahack0 i386 1.0.0+dfsg-11+b1 [28.7 kB] +Get: 73 http://deb.debian.org/debian trixie/main i386 libfastahack-dev i386 1.0.0+dfsg-11+b1 [30.3 kB] +Get: 74 http://deb.debian.org/debian trixie/main i386 libgzstream0 i386 1.5+git20171107.9a20658-2 [7384 B] +Get: 75 http://deb.debian.org/debian trixie/main i386 libgzstream-dev i386 1.5+git20171107.9a20658-2 [7576 B] +Get: 76 http://deb.debian.org/debian trixie/main i386 libhtscodecs2 i386 1.6.0-1+b1 [68.5 kB] +Get: 77 http://deb.debian.org/debian trixie/main i386 libhts3 i386 1.19+ds-1 [490 kB] +Get: 78 http://deb.debian.org/debian trixie/main i386 liblzma-dev i386 5.6.1+really5.4.5-1 [304 kB] +Get: 79 http://deb.debian.org/debian trixie/main i386 libhts-dev i386 1.19+ds-1 [1660 kB] +Get: 80 http://deb.debian.org/debian trixie/main i386 libncurses6 i386 6.4+20240414-1 [112 kB] +Get: 81 http://deb.debian.org/debian trixie/main i386 libsqlite3-dev i386 3.45.1-1 [1171 kB] +Get: 82 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.2.1-3 [2744 kB] +Get: 83 http://deb.debian.org/debian trixie/main i386 python3-pysam i386 0.22.0+ds-1+b1 [4120 kB] +Get: 84 http://deb.debian.org/debian trixie/main i386 samtools i386 1.19.2-1 [680 kB] +Fetched 44.7 MB in 1s (87.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed dpkg: libdb5.3:i386: dependency problems, but removing anyway as you requested: libperl5.38:i386 depends on libdb5.3. libpam-modules:i386 depends on libdb5.3. -(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 ... 19885 files and directories currently installed.) +(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 ... 19709 files and directories currently installed.) Removing libdb5.3:i386 (5.3.28+dfsg2-4+b1) ... Selecting previously unselected package libdb5.3t64:i386. -(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 ... 19878 files and directories currently installed.) +(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 ... 19702 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_i386.deb ... Unpacking libdb5.3t64:i386 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:i386 (5.3.28+dfsg2-7) ... dpkg: libssl3:i386: dependency problems, but removing anyway as you requested: - libkrb5-3:i386 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). -(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 ... 19884 files and directories currently installed.) +(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 ... 19708 files and directories currently installed.) Removing libssl3:i386 (3.1.5-1) ... Selecting previously unselected package libssl3t64:i386. -(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 ... 19871 files and directories currently installed.) +(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 ... 19695 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.1-3_i386.deb ... Unpacking libssl3t64:i386 (3.2.1-3) ... Setting up libssl3t64:i386 (3.2.1-3) ... Selecting previously unselected package libpython3.11-minimal:i386. -(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 ... 19886 files and directories currently installed.) +(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 ... 19710 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.9-1) ... Selecting previously unselected package libexpat1:i386. @@ -318,7 +361,7 @@ Setting up libexpat1:i386 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... 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 ... 20202 files and directories currently installed.) +(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 ... 20026 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_i386.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. @@ -351,7 +394,7 @@ Unpacking libpython3-stdlib:i386 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... 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 ... 21194 files and directories currently installed.) +(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 ... 21018 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_i386.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package sensible-utils. @@ -471,81 +514,100 @@ Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../39-libbrotli1_1.1.0-2+b3_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b3) ... +Selecting previously unselected package libcom-err2:i386. +Preparing to unpack .../40-libcom-err2_1.47.0-2.4_i386.deb ... +Unpacking libcom-err2:i386 (1.47.0-2.4) ... +Selecting previously unselected package libkrb5support0:i386. +Preparing to unpack .../41-libkrb5support0_1.20.1-5+b1_i386.deb ... +Unpacking libkrb5support0:i386 (1.20.1-5+b1) ... +Selecting previously unselected package libk5crypto3:i386. +Preparing to unpack .../42-libk5crypto3_1.20.1-5+b1_i386.deb ... +Unpacking libk5crypto3:i386 (1.20.1-5+b1) ... +Selecting previously unselected package libkeyutils1:i386. +Preparing to unpack .../43-libkeyutils1_1.6.3-3_i386.deb ... +Unpacking libkeyutils1:i386 (1.6.3-3) ... +Selecting previously unselected package libkrb5-3:i386. +Preparing to unpack .../44-libkrb5-3_1.20.1-5+b1_i386.deb ... +Unpacking libkrb5-3:i386 (1.20.1-5+b1) ... +Selecting previously unselected package libgssapi-krb5-2:i386. +Preparing to unpack .../45-libgssapi-krb5-2_1.20.1-5+b1_i386.deb ... +Unpacking libgssapi-krb5-2:i386 (1.20.1-5+b1) ... Selecting previously unselected package libsasl2-modules-db:i386. -Preparing to unpack .../40-libsasl2-modules-db_2.1.28+dfsg1-4+b1_i386.deb ... +Preparing to unpack .../46-libsasl2-modules-db_2.1.28+dfsg1-4+b1_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libsasl2-2:i386. -Preparing to unpack .../41-libsasl2-2_2.1.28+dfsg1-4+b1_i386.deb ... +Preparing to unpack .../47-libsasl2-2_2.1.28+dfsg1-4+b1_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Selecting previously unselected package libldap-2.5-0:i386. -Preparing to unpack .../42-libldap-2.5-0_2.5.13+dfsg-5+b3_i386.deb ... +Preparing to unpack .../48-libldap-2.5-0_2.5.13+dfsg-5+b3_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5+b3) ... Selecting previously unselected package libnghttp2-14:i386. -Preparing to unpack .../43-libnghttp2-14_1.59.0-1_i386.deb ... +Preparing to unpack .../49-libnghttp2-14_1.59.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.59.0-1) ... Selecting previously unselected package libpsl5t64:i386. -Preparing to unpack .../44-libpsl5t64_0.21.2-1.1_i386.deb ... +Preparing to unpack .../50-libpsl5t64_0.21.2-1.1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:i386. -Preparing to unpack .../45-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_i386.deb ... +Preparing to unpack .../51-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:i386. -Preparing to unpack .../46-libssh2-1t64_1.11.0-4.1+b2_i386.deb ... +Preparing to unpack .../52-libssh2-1t64_1.11.0-4.1+b2_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl3t64-gnutls:i386. -Preparing to unpack .../47-libcurl3t64-gnutls_8.7.1-3_i386.deb ... +Preparing to unpack .../53-libcurl3t64-gnutls_8.7.1-3_i386.deb ... Unpacking libcurl3t64-gnutls:i386 (8.7.1-3) ... Selecting previously unselected package libcurl4-gnutls-dev:i386. -Preparing to unpack .../48-libcurl4-gnutls-dev_8.7.1-3_i386.deb ... +Preparing to unpack .../54-libcurl4-gnutls-dev_8.7.1-3_i386.deb ... Unpacking libcurl4-gnutls-dev:i386 (8.7.1-3) ... Selecting previously unselected package libdeflate0:i386. -Preparing to unpack .../49-libdeflate0_1.20-1_i386.deb ... +Preparing to unpack .../55-libdeflate0_1.20-1_i386.deb ... Unpacking libdeflate0:i386 (1.20-1) ... Selecting previously unselected package libdeflate-dev:i386. -Preparing to unpack .../50-libdeflate-dev_1.20-1_i386.deb ... +Preparing to unpack .../56-libdeflate-dev_1.20-1_i386.deb ... Unpacking libdeflate-dev:i386 (1.20-1) ... Selecting previously unselected package libfastahack0:i386. -Preparing to unpack .../51-libfastahack0_1.0.0+dfsg-11+b1_i386.deb ... +Preparing to unpack .../57-libfastahack0_1.0.0+dfsg-11+b1_i386.deb ... Unpacking libfastahack0:i386 (1.0.0+dfsg-11+b1) ... Selecting previously unselected package libfastahack-dev:i386. -Preparing to unpack .../52-libfastahack-dev_1.0.0+dfsg-11+b1_i386.deb ... +Preparing to unpack .../58-libfastahack-dev_1.0.0+dfsg-11+b1_i386.deb ... Unpacking libfastahack-dev:i386 (1.0.0+dfsg-11+b1) ... Selecting previously unselected package libgzstream0:i386. -Preparing to unpack .../53-libgzstream0_1.5+git20171107.9a20658-2_i386.deb ... +Preparing to unpack .../59-libgzstream0_1.5+git20171107.9a20658-2_i386.deb ... Unpacking libgzstream0:i386 (1.5+git20171107.9a20658-2) ... Selecting previously unselected package libgzstream-dev:i386. -Preparing to unpack .../54-libgzstream-dev_1.5+git20171107.9a20658-2_i386.deb ... +Preparing to unpack .../60-libgzstream-dev_1.5+git20171107.9a20658-2_i386.deb ... Unpacking libgzstream-dev:i386 (1.5+git20171107.9a20658-2) ... Selecting previously unselected package libhtscodecs2:i386. -Preparing to unpack .../55-libhtscodecs2_1.6.0-1+b1_i386.deb ... +Preparing to unpack .../61-libhtscodecs2_1.6.0-1+b1_i386.deb ... Unpacking libhtscodecs2:i386 (1.6.0-1+b1) ... Selecting previously unselected package libhts3:i386. -Preparing to unpack .../56-libhts3_1.19+ds-1_i386.deb ... +Preparing to unpack .../62-libhts3_1.19+ds-1_i386.deb ... Unpacking libhts3:i386 (1.19+ds-1) ... Selecting previously unselected package liblzma-dev:i386. -Preparing to unpack .../57-liblzma-dev_5.6.1+really5.4.5-1_i386.deb ... +Preparing to unpack .../63-liblzma-dev_5.6.1+really5.4.5-1_i386.deb ... Unpacking liblzma-dev:i386 (5.6.1+really5.4.5-1) ... Selecting previously unselected package libhts-dev:i386. -Preparing to unpack .../58-libhts-dev_1.19+ds-1_i386.deb ... +Preparing to unpack .../64-libhts-dev_1.19+ds-1_i386.deb ... Unpacking libhts-dev:i386 (1.19+ds-1) ... Selecting previously unselected package libncurses6:i386. -Preparing to unpack .../59-libncurses6_6.4+20240414-1_i386.deb ... +Preparing to unpack .../65-libncurses6_6.4+20240414-1_i386.deb ... Unpacking libncurses6:i386 (6.4+20240414-1) ... Selecting previously unselected package libsqlite3-dev:i386. -Preparing to unpack .../60-libsqlite3-dev_3.45.1-1_i386.deb ... +Preparing to unpack .../66-libsqlite3-dev_3.45.1-1_i386.deb ... Unpacking libsqlite3-dev:i386 (3.45.1-1) ... Selecting previously unselected package libssl-dev:i386. -Preparing to unpack .../61-libssl-dev_3.2.1-3_i386.deb ... +Preparing to unpack .../67-libssl-dev_3.2.1-3_i386.deb ... Unpacking libssl-dev:i386 (3.2.1-3) ... Selecting previously unselected package python3-pysam. -Preparing to unpack .../62-python3-pysam_0.22.0+ds-1+b1_i386.deb ... +Preparing to unpack .../68-python3-pysam_0.22.0+ds-1+b1_i386.deb ... Unpacking python3-pysam (0.22.0+ds-1+b1) ... Selecting previously unselected package samtools. -Preparing to unpack .../63-samtools_1.19.2-1_i386.deb ... +Preparing to unpack .../69-samtools_1.19.2-1_i386.deb ... Unpacking samtools (1.19.2-1) ... Setting up libhtscodecs2:i386 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:i386 (1.5.7-2) ... +Setting up libkeyutils1:i386 (1.6.3-3) ... Setting up libicu72:i386 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6) ... Setting up libmagic-mgc (1:5.45-2+b1) ... @@ -558,16 +620,18 @@ Setting up libdeflate0:i386 (1.20-1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... +Setting up libcom-err2:i386 (1.47.0-2.4) ... Setting up file (1:5.45-2+b1) ... Setting up libfastahack0:i386 (1.0.0+dfsg-11+b1) ... Setting up libelf1t64:i386 (0.191-1+b1) ... +Setting up libkrb5support0:i386 (1.20.1-5+b1) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-4+b1) ... Setting up libfastahack-dev:i386 (1.0.0+dfsg-11+b1) ... Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Apr 29 09:52:21 UTC 2024. -Universal Time is now: Mon Apr 29 09:52:21 UTC 2024. +Local time is now: Sun Jun 1 16:18:09 UTC 2025. +Universal Time is now: Sun Jun 1 16:18:09 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -576,6 +640,7 @@ Setting up libncurses6:i386 (6.4+20240414-1) ... Setting up libssl-dev:i386 (3.2.1-3) ... Setting up autopoint (0.21-14) ... +Setting up libk5crypto3:i386 (1.20.1-5+b1) ... Setting up libbamtools2.5.2:i386 (2.5.2+dfsg-5) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-4+b1) ... Setting up autoconf (2.71-3) ... @@ -587,6 +652,7 @@ Setting up libuchardet0:i386 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up netbase (6.4) ... +Setting up libkrb5-3:i386 (1.20.1-5+b1) ... Setting up libssh2-1t64:i386 (1.11.0-4.1+b2) ... Setting up libdeflate-dev:i386 (1.20-1) ... Setting up readline-common (8.2-4) ... @@ -601,6 +667,7 @@ Setting up libgzstream-dev:i386 (1.5+git20171107.9a20658-2) ... Setting up dh-autoreconf (20) ... Setting up libbamtools-dev:i386 (2.5.2+dfsg-5) ... +Setting up libgssapi-krb5-2:i386 (1.20.1-5+b1) ... Setting up libreadline8t64:i386 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-3+b1) ... @@ -633,7 +700,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lumpy-sv_0.3.1+dfsg-7_source.changes +I: user script /srv/workspace/pbuilder/90725/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/90725/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/lumpy-sv-0.3.1+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 > ../lumpy-sv_0.3.1+dfsg-7_source.changes dpkg-buildpackage: info: source package lumpy-sv dpkg-buildpackage: info: source version 0.3.1+dfsg-7 dpkg-buildpackage: info: source distribution unstable @@ -643,7 +714,7 @@ debian/rules clean dh clean --with python3 dh_auto_clean - make -j11 clean + make -j21 clean make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' Cleaning up. #rm -Rf /lib @@ -658,17 +729,17 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j11 "INSTALL=install --strip-program=true" + make -j21 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lumpy-sv-0.3.1+dfsg' [ -d bin ] || mkdir -p bin [ -d bin ] || mkdir -p bin +[ -d obj ] || mkdir -p obj make --no-print-directory -C src/filter/ cp scripts/lumpyexpress bin/lumpyexpress -cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -[ -d obj ] || mkdir -p obj -> bin/lumpyexpress.config [ -d bin ] || mkdir -p bin +cc -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz Building lumpy: +> bin/lumpyexpress.config ========================================================= #make --no-print-directory --directory= api for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \ @@ -732,10 +803,10 @@ * compiling SV_Pair.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o * compiling SV_Evidence.cpp - * compiling SV_BreakPoint.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o + * compiling SV_BreakPoint.cpp * compiling SV_Bedpe.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o * compiling SV_SplitRead.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o @@ -744,14 +815,21 @@ g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o * compiling SV_BedpeReader.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o * compiling SV_BamReader.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o * compiling SV_InterChromBamReader.cpp + * compiling SV_EvidenceReader.cpp g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o -In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_PairReader.cpp:15: +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o + * compiling SV_Tools.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o + * compiling SV_VcfVariant.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o + * compiling log_space.cpp +g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o +In file included from SV_EvidenceReader.h:20, + from SV_EvidenceReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { @@ -763,25 +841,6 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_Pair.cpp:15: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ -In file included from SV_BreakPoint.h:19, - from SV_Evidence.h:22, - from SV_Evidence.cpp:15: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, - from SV_Bedpe.cpp:14: -../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: -../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 321 | for (register short i = 0; i < _binLevels; ++i) { - | ^ In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_InterChromBamReader.cpp:15: @@ -790,34 +849,31 @@ 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from SV_BreakPoint.h:19, - from SV_BreakPoint.cpp:16: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -In file included from SV_BreakPoint.h:19, - from SV_Evidence.h:22, - from SV_Bedpe.h:18, - from SV_BedpeReader.cpp:15: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -In file included from SV_BreakPoint.h:19, from SV_PairReader.h:22, from SV_BamReader.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from SV_BreakPoint.h:19, - from SV_PairReader.h:22, - from SV_Pair.cpp:19: +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_Bedpe.cpp:14: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ +In file included from SV_Tools.h:19, + from SV_Tools.cpp:24: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, + from SV_Pair.cpp:15: +../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: +../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 321 | for (register short i = 0; i < _binLevels; ++i) { + | ^ +In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from lumpy.cpp:20: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] @@ -829,6 +885,13 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ +In file included from SV_BreakPoint.h:19, + from SV_PairReader.h:22, + from SV_Pair.cpp:19: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12, from SV_SplitRead.cpp:15: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: @@ -842,38 +905,25 @@ ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from SV_BreakPoint.h:19, - from SV_SplitReadReader.h:22, - from SV_SplitRead.cpp:19: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: -SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] - 81 | for (j = 0; j < size; ++j) { - | ~~^~~~~~ -SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: -SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] - 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; - | ^~~~~~~~~~~~~~ -SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] - 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; - | ^~~~~~~~~~~~~~ In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_BedpeReader.h:23, - from SV_Bedpe.h:19: + from SV_SplitRead.h:27, + from SV_SplitReadReader.cpp:16: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -In file included from ../utils//bedFilePE/bedFilePE.h:12, - from SV_SplitRead.h:27, - from SV_SplitReadReader.cpp:16: +In file included from SV_Tools.cpp:27: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ +In file included from SV_BreakPoint.h:19, + from SV_SplitReadReader.h:22, + from SV_SplitRead.cpp:19: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_InterChromBamReader.cpp:19: @@ -881,6 +931,13 @@ ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ +In file included from SV_BreakPoint.h:19, + from SV_Evidence.h:22, + from SV_Evidence.cpp:15: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ In file included from ../utils//bedFilePE/bedFilePE.h:12, from SV_SplitRead.h:27, from SV_BamReader.cpp:19: @@ -888,45 +945,79 @@ ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ -SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: -SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] - 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: -SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long long unsigned int’} [-Wsign-compare] - 208 | ( bam.Position < pos ) ) { - | ~~~~~~~~~~~~~^~~~~ -../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long long unsigned int]’: -../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long long unsigned int]’ -SV_BreakPoint.cpp:1286:14: required from here +In file included from SV_BreakPoint.h:19, + from SV_PairReader.h:22, + from SV_PairReader.cpp:15: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ - * compiling SV_EvidenceReader.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o - * compiling SV_Tools.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o - * compiling SV_VcfVariant.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o -In file included from SV_Tools.h:19, - from SV_Tools.cpp:24: +In file included from SV_BreakPoint.h:19, + from SV_VcfVariant.h:18, + from SV_VcfVariant.cpp:15: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ - * compiling log_space.cpp -g++ -g -c -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o -In file included from SV_EvidenceReader.h:20, - from SV_EvidenceReader.cpp:15: +In file included from SV_BreakPoint.h:19, + from SV_BreakPoint.cpp:16: ../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: ../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 253 | for (register short i = 0; i < kBinLevels; ++i) { | ^ -In file included from SV_Tools.cpp:27: +In file included from SV_BreakPoint.h:19, + from SV_Evidence.h:22, + from SV_Bedpe.h:18, + from SV_BedpeReader.cpp:15: +../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins&)’: +SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long long unsigned int’} [-Wsign-compare] + 208 | ( bam.Position < pos ) ) { + | ~~~~~~~~~~~~~^~~~~ +SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’: +SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] + 538 | if ( min_mapping_quality < reader->min_mapping_threshold ) + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long long unsigned int]’: +../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long long unsigned int]’ +SV_Tools.cpp:541:32: required from here +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’: +SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] + 81 | for (j = 0; j < size; ++j) { + | ~~^~~~~~ +In file included from ../utils//bedFilePE/bedFilePE.h:12, + from SV_BedpeReader.h:23, + from SV_Bedpe.h:19: ../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’: ../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 321 | for (register short i = 0; i < _binLevels; ++i) { | ^ +SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’: +SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable] + 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; + | ^~~~~~~~~~~~~~ +SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable] + 266 | struct breakpoint_interval *a_overlap_intr, *b_overlap_intr; + | ^~~~~~~~~~~~~~ +../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long long unsigned int]’: +../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string; CHR_POS = long long unsigned int]’ +SV_BreakPoint.cpp:1286:14: required from here +../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] + 253 | for (register short i = 0; i < kBinLevels; ++i) { + | ^ +SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: +SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] + 156 | *end = last; + | ~~~~~^~~~~~ +SV_Tools.cpp:143:13: note: ‘last’ was declared here + 143 | int last; + | ^~~~ SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’: SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized] 704 | if ((l == r) && (l == max_i)) @@ -947,19 +1038,6 @@ SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here 1643 | unsigned int i, l_max_i, r_max_i; | ^~~~~~~ -In file included from SV_BreakPoint.h:19, - from SV_VcfVariant.h:18, - from SV_VcfVariant.cpp:15: -../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS)’: -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ -../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long long unsigned int]’: -../utils//UCSCBins/ucsc_bins.hpp:238:18: required from ‘void UCSCBins::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string; CHR_POS = long long unsigned int]’ -SV_Tools.cpp:541:32: required from here -../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] - 253 | for (register short i = 0; i < kBinLevels; ++i) { - | ^ SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map, BamTools::BamAlignment>&, UCSCBins&, int, int, SV_SplitReadReader*)’: SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 653 | free(new_split_read); @@ -967,13 +1045,6 @@ SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’ 641 | _reader); | ^ -SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’: -SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized] - 156 | *end = last; - | ~~~~~^~~~~~ -SV_Tools.cpp:143:13: note: ‘last’ was declared here - 143 | int last; - | ^~~~ * linking lumpy g++ -Wl,-z,relro -Wl,-z,now -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \ -L../utils//BamTools/lib/ -lbamtools \ @@ -1028,8 +1099,8 @@ dh_md5sums dh_builddeb dpkg-deb: building package 'lumpy-sv' in '../lumpy-sv_0.3.1+dfsg-7_i386.deb'. -dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-7_all.deb'. dpkg-deb: building package 'lumpy-sv-dbgsym' in '../lumpy-sv-dbgsym_0.3.1+dfsg-7_i386.deb'. +dpkg-deb: building package 'lumpy-sv-examples' in '../lumpy-sv-examples_0.3.1+dfsg-7_all.deb'. dpkg-genbuildinfo --build=binary -O../lumpy-sv_0.3.1+dfsg-7_i386.buildinfo dpkg-genchanges --build=binary -O../lumpy-sv_0.3.1+dfsg-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1037,12 +1108,14 @@ 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/90725/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/90725/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/24406 and its subdirectories -I: Current time: Sun Apr 28 21:54:31 -12 2024 -I: pbuilder-time-stamp: 1714384471 +I: removing directory /srv/workspace/pbuilder/90725 and its subdirectories +I: Current time: Mon Jun 2 06:19:04 +14 2025 +I: pbuilder-time-stamp: 1748794744