Sat Jan 6 16:18:16 UTC 2024 I: starting to build nim-hts/bullseye/i386 on jenkins on '2024-01-06 16:17' Sat Jan 6 16:18:16 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_4/6463/console.log Sat Jan 6 16:18:16 UTC 2024 I: Downloading source for bullseye/nim-hts=0.3.14+ds-1 --2024-01-06 16:18:16-- http://cdn-fastly.deb.debian.org/debian/pool/main/n/nim-hts/nim-hts_0.3.14%2bds-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2241 (2.2K) [text/prs.lines.tag] Saving to: ‘nim-hts_0.3.14+ds-1.dsc’ 0K .. 100% 337M=0s 2024-01-06 16:18:16 (337 MB/s) - ‘nim-hts_0.3.14+ds-1.dsc’ saved [2241/2241] Sat Jan 6 16:18:16 UTC 2024 I: nim-hts_0.3.14+ds-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: nim-hts Binary: nim-hts-dev, nim-hts-examples Architecture: all Version: 0.3.14+ds-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Nilesh Patra , Debian Nim Team Homepage: https://github.com/brentp/hts-nim Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/nim-hts Vcs-Git: https://salsa.debian.org/med-team/nim-hts.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, libhts-dev, libhts3 Build-Depends: debhelper-compat (= 13), nim, libhts-dev, samtools, tabix, bcftools Package-List: nim-hts-dev deb libs optional arch=all nim-hts-examples deb libs optional arch=all Checksums-Sha1: 8ed3ed8e82fcae6728e4e5879425c404d51c8b61 524264 nim-hts_0.3.14+ds.orig.tar.xz 725e3bdd13fe74fee77b99d53980fdf0b887d135 340648 nim-hts_0.3.14+ds-1.debian.tar.xz Checksums-Sha256: 11a5aca6f3d772d5472312293a44a641a6e8dc5d7fe03d9e97573f28698c8497 524264 nim-hts_0.3.14+ds.orig.tar.xz c56f9cbfff7a28e95ee01993879027359cd0c6cb43664fd4715317879a75f28a 340648 nim-hts_0.3.14+ds-1.debian.tar.xz Files: ea153d404aab7b191bbed9e26d217c08 524264 nim-hts_0.3.14+ds.orig.tar.xz 9ede83f4317269a831e0bbf18dc4f951 340648 nim-hts_0.3.14+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAl/ExmcUHG5wYXRyYTk3 NEBnbWFpbC5jb20ACgkQALrnSzQzafFTfw//ax3osjuAoNQnyZuqB34x+6ZUNtvi 2ThO7A9Vr8Hb7T0TEXALJe4OTDbxV9p0dWMM0iwbkarorZcxoKiQ1RZ8xycYVhxB APtolaicbUL59S9ymDwpWbuaqtcmtgl90urvpimkWq3LzDPA1q0RT+MDE5y8c57d np/VwCmv/IQNT3vWoYR6LEFQy/XuXgdVbsoOCi57J9Cx9sCiC92cuwu4IwonsFTa PKJA3qOde3OIfZ2j9tcTqBCNcDP3ZESMpzJMsyD7DZp5oUs/i05I7W6xcj1n/Gx3 2KCpPQ08Ss+3XZK6F2TjAYNOkhOdDYufhgqzncme3Sfd7O3O2sfJY9Qfpy16CJfD oxfTNtHDPFQZtV7tBwe1o9l+48mT7Pu+CuU19M6i6CE/9Jkj/ydIAVvpujbGtNyl ys5v1ubAwOZKexwd1qagv/d6hFBRbJL6tZq3Sk39nMTBkQU/iQr16xNrDL/2FEJL CV277ciYsvunDEXm0NQ6sq5siN0g4EYDCaO3bv2AeH29FZnbO0JVNzx7PI5rSCny pJKpQ2q9w6nX7tPlUzUMF9R33lOErrz+yd2xVveZZD0+cSX8pwx6zsRb7lpSf5Bd /4GfBNo7B5Rfr0q11vvUYypAUFfVY7djm+vOYE31wALMpcx/csTx8JRi/DSD2Cvj b3hlC82eJqrhZ+s= =j/9+ -----END PGP SIGNATURE----- Sat Jan 6 16:18:16 UTC 2024 I: Checking whether the package is not for us Sat Jan 6 16:18:16 UTC 2024 I: Starting 1st build on remote node ionos16-i386.debian.net. Sat Jan 6 16:18:16 UTC 2024 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Sat Jan 6 16:18:53 UTC 2024 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Feb 7 10:41:17 -12 2025 I: pbuilder-time-stamp: 1738968077 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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: using eatmydata during job I: Copying source file I: copying [nim-hts_0.3.14+ds-1.dsc] I: copying [./nim-hts_0.3.14+ds.orig.tar.xz] I: copying [./nim-hts_0.3.14+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.gSkRRSKU/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 30 10:16:07 2020 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./nim-hts_0.3.14+ds-1.dsc dpkg-source: info: extracting nim-hts in nim-hts-0.3.14+ds dpkg-source: info: unpacking nim-hts_0.3.14+ds.orig.tar.xz dpkg-source: info: unpacking nim-hts_0.3.14+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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30620/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,-fixfilepath parallel=16 ' DISTRIBUTION='bullseye' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='2bdc4fecf2354e97b8299963d07324a1' 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='30620' PS1='# ' PS2='> ' 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.dv4XvhNx/pbuilderrc_d34N --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dv4XvhNx/b1 --logfile b1/build.log nim-hts_0.3.14+ds-1.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://85.184.249.68:3128' I: uname -a Linux ionos16-i386 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5776 -rwxr-xr-x 1 root root 1367848 Mar 27 2022 bash -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp -rwxr-xr-x 1 root root 128724 Dec 10 2020 dash -rwxr-xr-x 1 root root 124904 Sep 22 2020 date -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd -rwxr-xr-x 1 root root 100752 Sep 22 2020 df -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir -rwxr-xr-x 1 root root 83644 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 22 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 71928 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 30112 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 210488 Jan 25 2023 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 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Nov 7 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln -rwxr-xr-x 1 root root 55572 Feb 7 2020 login -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls -rwxr-xr-x 1 root root 153124 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp -rwxr-xr-x 1 root root 58920 Jan 20 2022 more -rwsr-xr-x 1 root root 50720 Jan 20 2022 mount -rwxr-xr-x 1 root root 13856 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 8 15:47 sh -> dash -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty -rwsr-xr-x 1 root root 79396 Jan 20 2022 su -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch -rwxr-xr-x 1 root root 34664 Sep 22 2020 true -rwxr-xr-x 1 root root 17768 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 30236 Jan 20 2022 umount -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir -rwxr-xr-x 1 root root 63024 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 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 5898 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 8049 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/30620/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: i386 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 ... 17763 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} libicu67{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{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} sse2-support{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 30.6 MB of archives. After unpacking 100 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-8+deb11u1 [149 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sse2-support i386 6 [8544 B] Get: 7 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3+deb11u1 [273 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3+deb11u1 [135 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3+deb11u1 [69.2 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 14 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 libbrotli1 i386 1.0.9-2+b2 [286 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 libsasl2-modules-db i386 2.1.27+dfsg-2.1+deb11u1 [70.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libsasl2-2 i386 2.1.27+dfsg-2.1+deb11u1 [110 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libldap-2.4-2 i386 2.4.57+dfsg-3+deb11u1 [244 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libnghttp2-14 i386 1.43.0-1 [85.7 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libpsl5 i386 0.21.0-1.2 [57.9 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 libssh2-1 i386 1.9.0-2 [164 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 libcurl3-gnutls i386 7.74.0-1.3+deb11u9 [374 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 libdeflate0 i386 1.7-1 [48.4 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 libhts3 i386 1.11-4 [408 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 bcftools i386 1.11-1 [651 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 37 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7+deb11u4 [728 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libcurl4-gnutls-dev i386 7.74.0-1.3+deb11u9 [477 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 libdeflate-dev i386 1.7-1 [44.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 liblzma-dev i386 5.2.5-2.1~deb11u1 [240 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2+deb11u2 [194 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libhts-dev i386 1.11-4 [3817 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libncurses6 i386 6.2+20201114-2+deb11u2 [110 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 nim i386 1.4.6+really1.4.2-2 [3619 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 samtools i386 1.11-1 [576 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 tabix i386 1.11-4 [369 kB] Fetched 30.6 MB in 1s (48.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 17763 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_i386.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. 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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 I: Building the package I: Running cd /build/reproducible-path/nim-hts-0.3.14+ds/ && 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 > ../nim-hts_0.3.14+ds-1_source.changes dpkg-buildpackage: info: source package nim-hts dpkg-buildpackage: info: source version 0.3.14+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 i386 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/nim-hts-0.3.14+ds' dh_auto_clean install -d /build/reproducible-path/nim-hts-0.3.14\+ds/debian/.debhelper/generated/_source/home # 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/reproducible-path/nim-hts-0.3.14+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/reproducible-path/nim-hts-0.3.14+ds' dh_auto_build install -d /build/reproducible-path/nim-hts-0.3.14\+ds/debian/.debhelper/generated/_source/home # 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/reproducible-path/nim-hts-0.3.14+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/reproducible-path/nim-hts-0.3.14+ds' nim c --nimcache:/build/reproducible-path/nim-hts-0.3.14+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/reproducible-path/nim-hts-0.3.14+ds/tests/nim.cfg' [Conf] ......................................... /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/fai.nim(38, 24) Warning: See corresponding Defect; IndexError is deprecated [Deprecated] ............CC: stdlib_assertions.nim CC: stdlib_dollars.nim CC: stdlib_formatfloat.nim CC: stdlib_io.nim CC: stdlib_system.nim CC: stdlib_exitprocs.nim CC: stdlib_parseutils.nim CC: stdlib_math.nim CC: stdlib_unicode.nim CC: stdlib_strutils.nim CC: stdlib_streams.nim CC: stdlib_times.nim CC: stdlib_hashes.nim CC: stdlib_sets.nim CC: stdlib_os.nim CC: stdlib_strformat.nim CC: stdlib_terminal.nim CC: stdlib_unittest.nim CC: ../src/hts/private/hts_concat.nim CC: ../src/hts/bam/flag.nim CC: flagtest.nim CC: ../src/hts/simpleoption.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: 78838 lines; 3.620s; 76.449MiB peakmem; Debug build; proj: /build/reproducible-path/nim-hts-0.3.14+ds/tests/all.nim; out: /build/reproducible-path/nim-hts-0.3.14+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 /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(8) bgzftest /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/bgzf.nim(21) write_line /usr/lib/nim/system/fatal.nim(49) sysFatal Unhandled exception: value out of range: 6226997452944179205 notin -2147483648 .. 2147483647 [RangeDefect] [FAILED] test-write /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(24, 25): Check failed: b.read_line(p) >= 0 b.read_line(p) was -1 /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(25, 18): Check failed: $kstr.s == "a\t1\t2" $kstr.s was /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(26, 25): Check failed: b.read_line(p) >= 0 b.read_line(p) was -1 /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(27, 18): Check failed: $kstr.s == "b\t10\t20" $kstr.s was /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(29, 18): Check failed: $kstr.s == "b\t10\t20" $kstr.s was /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(30, 24): Check failed: int(b.tell()) > 0 int(b.tell()) was 0 [FAILED] test-read /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(45, 19): Check failed: nb_lines == 2 nb_lines was 0 [FAILED] 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 /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(59) bgzftest /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/bgzf/bgzi.nim(89) write_interval /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/bgzf.nim(21) write_line /usr/lib/nim/system/fatal.nim(49) sysFatal Unhandled exception: value out of range: 6227011106645213192 notin -2147483648 .. 2147483647 [RangeDefect] [FAILED] write-with-index [E::hts_idx_load3] Could not load local index file 'ti.txt.gz.csi' /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(67, 14): Check failed: open(c, "ti.txt.gz") /usr/lib/nim/pure/unittest.nim(654) bgzftest /usr/lib/nim/system/fatal.nim(49) sysFatal Unhandled exception: index out of bounds, the container is empty [IndexDefect] [FAILED] read-new-index [E::hts_idx_load3] Could not load local index file 'ti.txt.gz.csi' /build/reproducible-path/nim-hts-0.3.14+ds/tests/bgzftest.nim(85) bgzftest /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/bgzf/bgzi.nim(38) open Unhandled exception: hts: error opening index for ti.txt.gz [IOError] [FAILED] 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 /build/reproducible-path/nim-hts-0.3.14+ds/tests/vcftest.nim(65) vcftest /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/vcf.nim(424) delete /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/vcf.nim(272) bcf_hdr_id2type /usr/lib/nim/system/fatal.nim(49) sysFatal Unhandled exception: value out of range [RangeDefect] [FAILED] test writer [OK] vcf write missing format values /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/vcf.nim(538) vcftest /build/reproducible-path/nim-hts-0.3.14+ds/src/hts/vcf.nim(415) bcf_hdr_id2number /usr/lib/nim/system/fatal.nim(49) sysFatal Unhandled exception: value out of range [RangeDefect] [FAILED] 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 [Suite] speed tests 312078 in .. 10.163592403 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 0.09873714670538826 0.00222143377322929 0.00222143377322929 [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]: *** [debian/rules:21: override_dh_auto_test] Error 1 make[1]: Leaving directory '/build/reproducible-path/nim-hts-0.3.14+ds' make: *** [debian/rules:6: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/30620 and its subdirectories Sat Jan 6 16:19:03 UTC 2024 W: No second build log, what happened?