I: pbuilder: network access will be disabled during build I: Current time: Sat May 13 23:22:54 +14 2023 I: pbuilder-time-stamp: 1683969774 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 [nim-hts_0.3.19+ds-1.dsc] I: copying [./nim-hts_0.3.19+ds.orig.tar.xz] I: copying [./nim-hts_0.3.19+ds-1.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Oct 19 23:36:07 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./nim-hts_0.3.19+ds-1.dsc: no acceptable signature found dpkg-source: info: extracting nim-hts in nim-hts-0.3.19+ds dpkg-source: info: unpacking nim-hts_0.3.19+ds.orig.tar.xz dpkg-source: info: unpacking nim-hts_0.3.19+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying dontDoNestedTests.patch dpkg-source: info: applying disable-test-with-sourceless-file.patch dpkg-source: info: applying fix-version-comparision.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/712377/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 May 13 23:23 /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/712377/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/712377/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]="x86_64-pc-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=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f1067cd672464e909bacfca99c23ea6e LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-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=712377 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.k2Vo3wUm/pbuilderrc_2IbZ --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.k2Vo3wUm/b2 --logfile b2/build.log --extrapackages usrmerge nim-hts_0.3.19+ds-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 13 23:23 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/712377/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: amd64 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), nim, libhts-dev, samtools, tabix, bcftools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 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 nim; however: Package nim is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on tabix; however: Package tabix is not installed. pbuilder-satisfydepends-dummy depends on bcftools; however: Package bcftools 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: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bcftools{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libfile-stripnondeterminism-perl{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} libpcre3{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} nim{a} po-debconf{a} samtools{a} sensible-utils{a} tabix{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl git libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 53 newly installed, 0 to remove and 0 not upgraded. Need to get 30.2 MB of archives. After unpacking 111 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 bcftools amd64 1.16-1 [692 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-9 [481 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 nim amd64 1.6.10-2 [4077 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 tabix amd64 1.16+ds-3 [457 kB] Fetched 30.2 MB in 1s (49.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-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 .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../15-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../16-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../17-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../18-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../19-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../20-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../21-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../22-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../23-libcurl3-gnutls_7.88.1-9_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.88.1-9) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../24-libdeflate0_1.14-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.14-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../25-libhtscodecs2_1.3.0-4_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.3.0-4) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../26-libhts3_1.16+ds-3_amd64.deb ... Unpacking libhts3:amd64 (1.16+ds-3) ... Selecting previously unselected package bcftools. Preparing to unpack .../27-bcftools_1.16-1_amd64.deb ... Unpacking bcftools (1.16-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../28-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../29-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../30-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../31-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 .../32-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 .../33-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 .../34-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../35-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../36-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../37-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../38-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package gettext. Preparing to unpack .../39-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../40-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 .../41-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../42-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../43-libcurl4-gnutls-dev_7.88.1-9_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (7.88.1-9) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../44-libdeflate-dev_1.14-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.14-1) ... Selecting previously unselected package liblzma-dev:amd64. Preparing to unpack .../45-liblzma-dev_5.4.1-0.2_amd64.deb ... Unpacking liblzma-dev:amd64 (5.4.1-0.2) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../46-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Selecting previously unselected package libhts-dev:amd64. Preparing to unpack .../47-libhts-dev_1.16+ds-3_amd64.deb ... Unpacking libhts-dev:amd64 (1.16+ds-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../48-libncurses6_6.4-4_amd64.deb ... Unpacking libncurses6:amd64 (6.4-4) ... Selecting previously unselected package libpcre3:amd64. Preparing to unpack .../49-libpcre3_2%3a8.39-15_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15) ... Selecting previously unselected package nim. Preparing to unpack .../50-nim_1.6.10-2_amd64.deb ... Unpacking nim (1.6.10-2) ... Selecting previously unselected package samtools. Preparing to unpack .../51-samtools_1.16.1-1_amd64.deb ... Unpacking samtools (1.16.1-1) ... Selecting previously unselected package tabix. Preparing to unpack .../52-tabix_1.16+ds-3_amd64.deb ... Unpacking tabix (1.16+ds-3) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up autopoint (0.21-12) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up liblzma-dev:amd64 (5.4.1-0.2) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up nim (1.6.10-2) ... Setting up libdeflate-dev:amd64 (1.14-1) ... Setting up tabix (1.16+ds-3) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... 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 gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-9) ... Setting up libcurl4-gnutls-dev:amd64 (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3:amd64 (1.16+ds-3) ... Setting up bcftools (1.16-1) ... Setting up libhts-dev:amd64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up samtools (1.16.1-1) ... Processing triggers for libc-bin (2.36-9) ... 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/712377/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/712377/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/nim-hts-0.3.19+ds/ && 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 > ../nim-hts_0.3.19+ds-1_source.changes dpkg-buildpackage: info: source package nim-hts dpkg-buildpackage: info: source version 0.3.19+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/nim-hts-0.3.19+ds' dh_auto_clean # remnants from testing rm -f ____t.vcf t.gz ti.txt.gz ti.txt.gz.csi rm -f tests/run tests/HG02002.bam.csi tests/auxtest tests/newsample.vcf tests/outmissing.vcf tests/outv.vcf tests/outz.vcf tests/sample.fa.fai tests/all tests/htstest tests/bgzftest tests/bamtest rm -rf tests/nimcache make[1]: Leaving directory '/build/nim-hts-0.3.19+ds' dh_clean rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars debian/files rm -fr -- debian/nim-hts-dev/ debian/tmp/ debian/nim-hts-examples/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a -name autom4te.cache -prune -exec rm -rf {} + \) \) debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_build make[1]: Entering directory '/build/nim-hts-0.3.19+ds' dh_auto_build # Regenerate repacked files cat tests/sa.sam | samtools view -Sb - > tests/sa.bam samtools index tests/sa.bam tests/sa.bam.bai cat debian/missing-sources/HG02002.sam | samtools view -Sb - > tests/HG02002.bam samtools index tests/HG02002.bam tests/HG02002.bam.bai tabix tests/test.vcf.gz bcftools index tests/test.bcf make[1]: Leaving directory '/build/nim-hts-0.3.19+ds' rm -f debian/nim-hts-dev.debhelper.log debian/nim-hts-examples.debhelper.log debian/rules override_dh_auto_test make[1]: Entering directory '/build/nim-hts-0.3.19+ds' nim c --nimcache:/build/nim-hts-0.3.19+ds/tests/nimcache tests/all.nim Hint: used config file '/etc/nim/nim.cfg' [Conf] Hint: used config file '/etc/nim/config.nims' [Conf] Hint: used config file '/build/nim-hts-0.3.19+ds/tests/nim.cfg' [Conf] ............................................................................................................ /build/nim-hts-0.3.19+ds/src/hts/bam/flag.nim(1, 18) Hint: duplicate import of 'hts_concat'; previous import here: /build/nim-hts-0.3.19+ds/src/hts/bam.nim(1, 17) [DuplicateModuleImport] . /build/nim-hts-0.3.19+ds/src/hts/bam/cigar.nim(1, 18) Hint: duplicate import of 'hts_concat'; previous import here: /build/nim-hts-0.3.19+ds/src/hts/bam/flag.nim(1, 18) [DuplicateModuleImport] /build/nim-hts-0.3.19+ds/src/hts/bam/cigar.nim(2, 8) Hint: duplicate import of 'strutils'; previous import here: /build/nim-hts-0.3.19+ds/src/hts/bam.nim(4, 8) [DuplicateModuleImport] /build/nim-hts-0.3.19+ds/src/hts/bam.nim(262, 52) Warning: implicit conversion to 'cstring' from a non-const location: region; this will become a compile time error in the future [CStringConv] /build/nim-hts-0.3.19+ds/src/hts/bam.nim(373, 28) Warning: implicit conversion to 'cstring' from a non-const location: mode; this will become a compile time error in the future [CStringConv] .. /build/nim-hts-0.3.19+ds/src/hts/bam/auxtags.nim(3, 1) Hint: duplicate import of 'strformat'; previous import here: /build/nim-hts-0.3.19+ds/src/hts/bam.nim(3, 8) [DuplicateModuleImport] .... /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(118, 18) Warning: conversion to enum with holes is unsafe: Status(ret) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(119, 16) Warning: conversion to enum with holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(181, 16) Warning: conversion to enum with holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(190, 16) Warning: conversion to enum with holes is unsafe: Status(bcf_hdr_sync(h.hdr)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(288, 18) Warning: conversion to enum with holes is unsafe: Status(int(bcf_update_format(f.v.vcf.header.hdr, f.v.c, cstring(key), nil, 0, cint(htype)))) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(297, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(309, 22) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(320, 22) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(352, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(359, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(366, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(376, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(391, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(405, 20) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(432, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(436, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(441, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(461, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(467, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(527, 23) Warning: conversion to enum with holes is unsafe: BCF_TYPE(fmt.type) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(542, 23) Warning: conversion to enum with holes is unsafe: BCF_TYPE(fld.type) [HoleEnumConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(601, 27) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(603, 31) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(645, 30) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(664, 36) Warning: implicit conversion to 'cstring' from a non-const location: `[]`(region) do: 0 .. pred(cidx, 1); this will become a compile time error in the future [CStringConv] /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(700, 32) Warning: implicit conversion to 'cstring' from a non-const location: v.fname; this will become a compile time error in the future [CStringConv] . /build/nim-hts-0.3.19+ds/src/hts/fai.nim(38, 24) Warning: See corresponding Defect; IndexError is deprecated [Deprecated] ... /build/nim-hts-0.3.19+ds/src/hts/csi.nim(17, 51) Warning: implicit conversion to 'cstring' from a non-const location: base_path & ".csi"; this will become a compile time error in the future [CStringConv] .... /build/nim-hts-0.3.19+ds/tests/vcftest.nim(23, 7) template/generic instantiation of `suite` from here /build/nim-hts-0.3.19+ds/tests/vcftest.nim(46, 8) template/generic instantiation of `test` from here /build/nim-hts-0.3.19+ds/tests/vcftest.nim(63, 13) template/generic instantiation of `check` from here /build/nim-hts-0.3.19+ds/src/hts/vcf.nim(448, 16) Warning: conversion to enum with holes is unsafe: Status(int(ret)) [HoleEnumConv] /build/nim-hts-0.3.19+ds/tests/vcftest.nim(404, 7) Hint: 'current_line' is declared but not used [XDeclaredButNotUsed] /build/nim-hts-0.3.19+ds/tests/vcftest.nim(406, 7) Hint: 'currentBlock' is declared but not used [XDeclaredButNotUsed] /build/nim-hts-0.3.19+ds/tests/vcftest.nim(411, 7) Hint: 'block_pos_i' is declared but not used [XDeclaredButNotUsed] ..... CC: ../../../usr/lib/nim/lib/std/private/digitsutils.nim CC: ../../../usr/lib/nim/lib/system/assertions.nim CC: ../../../usr/lib/nim/lib/system/formatfloat.nim CC: ../../../usr/lib/nim/lib/system/dollars.nim CC: ../../../usr/lib/nim/lib/system/io.nim CC: ../../../usr/lib/nim/lib/system.nim CC: ../../../usr/lib/nim/lib/std/exitprocs.nim CC: ../../../usr/lib/nim/lib/pure/parseutils.nim CC: ../../../usr/lib/nim/lib/pure/math.nim CC: ../../../usr/lib/nim/lib/pure/algorithm.nim CC: ../../../usr/lib/nim/lib/pure/unicode.nim CC: ../../../usr/lib/nim/lib/pure/strutils.nim CC: ../../../usr/lib/nim/lib/pure/streams.nim CC: ../../../usr/lib/nim/lib/pure/times.nim CC: ../../../usr/lib/nim/lib/pure/hashes.nim CC: ../../../usr/lib/nim/lib/pure/collections/sets.nim CC: ../../../usr/lib/nim/lib/pure/os.nim CC: ../../../usr/lib/nim/lib/pure/strformat.nim CC: ../../../usr/lib/nim/lib/pure/terminal.nim CC: ../../../usr/lib/nim/lib/pure/unittest.nim CC: ../src/hts/private/hts_concat.nim CC: ../src/hts/bam/flag.nim CC: flagtest.nim CC: ../src/hts/bam.nim CC: cigartest.nim CC: htstest.nim CC: ../src/hts/vcf.nim CC: ../src/hts/fai.nim CC: ../src/hts/bgzf.nim CC: ../src/hts/csi.nim CC: ../src/hts/bgzf/bgzi.nim CC: ../src/hts/stats.nim CC: ../src/hts.nim CC: bgzftest.nim CC: faitest.nim CC: auxtest.nim CC: vcftest.nim CC: bamtest.nim CC: statstests.nim CC: vcfiso.nim CC: ../src/hts/files.nim CC: test_files.nim CC: all.nim Hint: [Link] Hint: gc: refc; opt: none (DEBUG BUILD, `-d:release` generates faster code) 83553 lines; 5.941s; 144.738MiB peakmem; proj: /build/nim-hts-0.3.19+ds/tests/all.nim; out: /build/nim-hts-0.3.19+ds/tests/all [SuccessX] tests/all [Suite] flag test-suite [OK] test flags [Suite] flag cigar-suite [OK] test op [OK] new cigar [Suite] flag hts-suite [OK] test hts [Suite] bgzf-suite [OK] test-write [OK] test-read [OK] bgzf-iterator [E::bgzf_read_block] Failed to read BGZF block data at offset 0 expected 24944 bytes; hread returned 982 [OK] bgzf-iterator-err [OK] write-with-index [OK] read-new-index [OK] csi-iterator [Suite] fai-suite [OK] fai-read [OK] fai chrom_len [OK] fai indexing [OK] issue26 [OK] close [Suite] aux-test [OK] test aux [OK] tag [OK] drop tag [Suite] vcf suite [E::bcf_hdr_read] Input is not detected as bcf or vcf format [OK] empty file rasies [OK] filter [OK] test writer [OK] vcf write missing format values [OK] iterating over info fields [OK] that adding a new sample and setting values works. [OK] format fields [OK] test empty format [OK] test format setting [OK] add string to header [OK] add info to header [OK] add and set Flag [OK] remove info from header [OK] add format to header [OK] remove format from header [OK] set qual [OK] set id [OK] new from string [Suite] genotypes suite [OK] test alts [OK] unknown alts [OK] contig names [Suite] header record [OK] info test [OK] format test [Suite] vcf alleles [OK] update alleles with low-level setters works [OK] update alleles with high-level setters works [Suite] bug suite [OK] csq reader [OK] re-use same header issue 77 [Suite] speed tests 312078 in .. 11.183339971 seconds [OK] standard format getter [Suite] bam-suite [OK] xam_index [OK] test sa sam [OK] test sa bam [OK] cram writing [OK] set aux [OK] set qname [OK] test from string [Suite] stats suite [OK] test fisher 0.09873714670538818 0.002221433773229274 0.002221433773229274 [OK] binomial [Suite] bugs [OK] vcf/bcf subset alts [Suite] test files [OK] that iteration works [OK] file types [E::hts_open_format] Failed to open file "tests/sadfasdfasdfasdf" : No such file or directory [OK] that bad path gives reasonable error message [OK] readLine make[1]: Leaving directory '/build/nim-hts-0.3.19+ds' create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/nim-hts-dev.substvars debian/nim-hts-examples.substvars rm -fr -- debian/.debhelper/generated/nim-hts-dev/ debian/nim-hts-dev/ debian/tmp/ debian/.debhelper/generated/nim-hts-examples/ debian/nim-hts-examples/ dh_install install -m0755 -d debian/nim-hts-dev/usr/share/nimble/hts/ cp --reflink=auto -a ./src/hts ./src/hts.nim debian/nim-hts-dev/usr/share/nimble/hts// install -m0755 -d debian/nim-hts-examples/usr/share/doc/nim-hts-examples cp --reflink=auto -a ./debian/missing-sources/HG02002.sam ./debian/tests/run-unit-test ./debian/tests/test1.nim ./debian/tests/test2.nim ./tests/HG02002.bam ./tests/HG02002.bam.bai ./tests/HG02002.bam.csi ./tests/aa.fa ./tests/aa.fa.fai ./tests/all.nim ./tests/auxtest.nim ./tests/bamtest.nim ./tests/bgzftest.nim ./tests/cigartest.nim ./tests/decomposed.vcf ./tests/faitest.nim ./tests/flagtest.nim ./tests/htstest.nim ./tests/newsample.vcf ./tests/outmissing.vcf ./tests/outz.vcf ./tests/run.nim ./tests/sa.bam ./tests/sa.bam.bai ./tests/sa.sam ./tests/sample.fa ./tests/sample.fa.fai ./tests/statstests.nim ./tests/test.bcf ./tests/test.bcf.csi ./tests/test_files ./tests/test_files.nim ./tests/test_readme.nim ./tests/unknown-alts.vcf ./tests/vcfiso.nim ./tests/vcftest.nim debian/nim-hts-examples/usr/share/doc/nim-hts-examples/ dh_installdocs install -m0755 -d debian/nim-hts-dev/usr/share/doc/nim-hts-dev install -p -m0644 debian/copyright debian/nim-hts-dev/usr/share/doc/nim-hts-dev/copyright install -p -m0644 debian/copyright debian/nim-hts-examples/usr/share/doc/nim-hts-examples/copyright dh_installchangelogs install -m0755 -d debian/nim-hts-dev/usr/share/doc/nim-hts-dev install -p -m0644 debian/.debhelper/generated/nim-hts-dev/dh_installchangelogs.dch.trimmed debian/nim-hts-dev/usr/share/doc/nim-hts-dev/changelog.Debian install -p -m0644 ./CHANGES.md debian/nim-hts-dev/usr/share/doc/nim-hts-dev/changelog install -m0755 -d debian/nim-hts-examples/usr/share/doc/nim-hts-examples install -p -m0644 debian/.debhelper/generated/nim-hts-examples/dh_installchangelogs.dch.trimmed debian/nim-hts-examples/usr/share/doc/nim-hts-examples/changelog.Debian install -p -m0644 ./CHANGES.md debian/nim-hts-examples/usr/share/doc/nim-hts-examples/changelog dh_perl dh_link dh_strip_nondeterminism dh_compress cd debian/nim-hts-dev cd debian/nim-hts-examples chmod a-x usr/share/doc/nim-hts-dev/changelog usr/share/doc/nim-hts-dev/changelog.Debian chmod a-x usr/share/doc/nim-hts-examples/HG02002.bam usr/share/doc/nim-hts-examples/HG02002.bam.bai usr/share/doc/nim-hts-examples/HG02002.sam usr/share/doc/nim-hts-examples/changelog usr/share/doc/nim-hts-examples/changelog.Debian usr/share/doc/nim-hts-examples/newsample.vcf usr/share/doc/nim-hts-examples/outmissing.vcf usr/share/doc/nim-hts-examples/outz.vcf usr/share/doc/nim-hts-examples/sa.bam usr/share/doc/nim-hts-examples/sa.bam.bai usr/share/doc/nim-hts-examples/sa.sam usr/share/doc/nim-hts-examples/test.bcf usr/share/doc/nim-hts-examples/unknown-alts.vcf usr/share/doc/nim-hts-examples/vcftest.nim gzip -9nf usr/share/doc/nim-hts-dev/changelog usr/share/doc/nim-hts-dev/changelog.Debian gzip -9nf usr/share/doc/nim-hts-examples/HG02002.bam usr/share/doc/nim-hts-examples/HG02002.bam.bai usr/share/doc/nim-hts-examples/HG02002.sam usr/share/doc/nim-hts-examples/changelog usr/share/doc/nim-hts-examples/changelog.Debian usr/share/doc/nim-hts-examples/newsample.vcf usr/share/doc/nim-hts-examples/outmissing.vcf usr/share/doc/nim-hts-examples/outz.vcf usr/share/doc/nim-hts-examples/sa.bam usr/share/doc/nim-hts-examples/sa.bam.bai usr/share/doc/nim-hts-examples/sa.sam usr/share/doc/nim-hts-examples/test.bcf usr/share/doc/nim-hts-examples/unknown-alts.vcf usr/share/doc/nim-hts-examples/vcftest.nim cd '/build/nim-hts-0.3.19+ds' cd '/build/nim-hts-0.3.19+ds' dh_fixperms find debian/nim-hts-dev ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/nim-hts-examples ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/nim-hts-dev/usr/share/doc -type f -a -true -a ! -regex 'debian/nim-hts-dev/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nim-hts-examples/usr/share/doc -type f -a -true -a ! -regex 'debian/nim-hts-examples/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nim-hts-dev/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/nim-hts-examples/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/nim-hts-dev -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/nim-hts-examples -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 dh_missing dh_installdeb install -m0755 -d debian/nim-hts-dev/DEBIAN install -m0755 -d debian/nim-hts-examples/DEBIAN dh_gencontrol install -m0755 -d debian/nim-hts-dev/DEBIAN echo misc:Depends= >> debian/nim-hts-dev.substvars echo misc:Pre-Depends= >> debian/nim-hts-dev.substvars dpkg-gencontrol -pnim-hts-dev -ldebian/changelog -Tdebian/nim-hts-dev.substvars -Pdebian/nim-hts-dev install -m0755 -d debian/nim-hts-examples/DEBIAN echo misc:Depends= >> debian/nim-hts-examples.substvars echo misc:Pre-Depends= >> debian/nim-hts-examples.substvars dpkg-gencontrol -pnim-hts-examples -ldebian/changelog -Tdebian/nim-hts-examples.substvars -Pdebian/nim-hts-examples chmod 0644 -- debian/nim-hts-examples/DEBIAN/control chmod 0644 -- debian/nim-hts-dev/DEBIAN/control dh_md5sums install -m0755 -d debian/nim-hts-dev/DEBIAN install -m0755 -d debian/nim-hts-examples/DEBIAN cd debian/nim-hts-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/nim-hts-examples >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/nim-hts-dev/DEBIAN/md5sums chmod 0644 -- debian/nim-hts-examples/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/nim-hts-dev .. dpkg-deb --root-owner-group --build debian/nim-hts-examples .. dpkg-deb: building package 'nim-hts-dev' in '../nim-hts-dev_0.3.19+ds-1_all.deb'. dpkg-deb: building package 'nim-hts-examples' in '../nim-hts-examples_0.3.19+ds-1_all.deb'. dpkg-genbuildinfo --build=binary -O../nim-hts_0.3.19+ds-1_amd64.buildinfo dpkg-genchanges --build=binary -O../nim-hts_0.3.19+ds-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/712377/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/712377/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/712377 and its subdirectories I: Current time: Sat May 13 23:23:45 +14 2023 I: pbuilder-time-stamp: 1683969825