Thu Oct 10 17:24:46 UTC 2024 I: starting to build dwgsim/unstable/armhf on jenkins on '2024-10-10 17:24' Thu Oct 10 17:24:46 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_34/11109/console.log Thu Oct 10 17:24:46 UTC 2024 I: Downloading source for unstable/dwgsim=0.1.14-3 --2024-10-10 17:24:46-- http://deb.debian.org/debian/pool/main/d/dwgsim/dwgsim_0.1.14-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2114 (2.1K) [text/prs.lines.tag] Saving to: ‘dwgsim_0.1.14-3.dsc’ 0K .. 100% 233M=0s 2024-10-10 17:24:46 (233 MB/s) - ‘dwgsim_0.1.14-3.dsc’ saved [2114/2114] Thu Oct 10 17:24:46 UTC 2024 I: dwgsim_0.1.14-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: dwgsim Binary: dwgsim Architecture: any Version: 0.1.14-3 Maintainer: Debian Med Packaging Team Uploaders: Kevin Murray Homepage: https://github.com/nh13/DWGSIM/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/dwgsim Vcs-Git: https://salsa.debian.org/med-team/dwgsim.git Testsuite: autopkgtest Testsuite-Triggers: samtools Build-Depends: debhelper-compat (= 13), samtools, zlib1g-dev Package-List: dwgsim deb science optional arch=any Checksums-Sha1: d330122e6299ff51e4107af60b3d6cdc8090cc4c 2206455 dwgsim_0.1.14.orig.tar.gz 5846d1935eaba7867a1bc9d112a0c4037aa9ad69 7704 dwgsim_0.1.14-3.debian.tar.xz Checksums-Sha256: a974a253bf6bcd5a2162f9ebc6c78c56a29c541850f375a45ddb2b649574ce1b 2206455 dwgsim_0.1.14.orig.tar.gz 1d159801db359cadf25ddf361f872b398ef536795fa26a9e7e2f055ff1d43761 7704 dwgsim_0.1.14-3.debian.tar.xz Files: 741f201d279ad66a0dfe490ac7ed7c7f 2206455 dwgsim_0.1.14.orig.tar.gz 356b48f44bcf7ad2bcdefbb86f23b1cb 7704 dwgsim_0.1.14-3.debian.tar.xz Dgit: acc5db7228e949b35832cf8e19f44016ebaab283 debian archive/debian/0.1.14-3 https://git.dgit.debian.org/dwgsim -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmbK5pQUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqY5A//ZuKRLB5/eyPkZ2VOgnwA67PdzA3J XVYix9mO0GAxKbmOjiy3omxMmg1wi6rq3zcKfU9yX7W2ka+feug/K4Hfttc633x2 sAfH33aKA6gGa5pJ8k61NFe3GEgbRys4vw76OJt8Aa3kAHIww/nu0orhwfbjqAT8 hlQiPVr4m+IgMNvNZSDjZd6+GV0O14Ykq2jKW/25N1sPez8X0kWL9F17SgJKa5mI SMVB9p0OiY8m/qR7bENSLZaiflOSVsGl4a6mlfDcW9O5qz0XOOpNFtXyUJg7/BKz Pvzz2poAN6tAQj1qBKKtGE3cIISZQjSn4qBcQKGXS1oOu+ILzy3dR2ucoprVnUDO 6xdlTPmOp+hZoxlClcnnq8OygiVZSISy9U9Wgl02vD+urW/pq5t+2NBpE0hX/tn5 26HcinuJV5zNZgkcDKeRylQecumxd+IBVJYCA717SA1PD8LhBOfp8RW3f+nDuwbp IK7XNLaoRrWycBfIRY3lukafhIni3gmogsARkavhmu6dfwaTraf6OlFDfxyE8zv1 nC2A+LjjooMHOyVTr80eycGnRnOvg3+P81aGmEbeILV2CP07pzqstzTKdydhsZ/q N1zMyfjXtZbdX5qRihMjwV7aNtmVb+I/gRwvtTrjwS96QYHgi+IeXeapWEiahFRD GZFNDvAIMJswWYs= =cOPO -----END PGP SIGNATURE----- Thu Oct 10 17:24:46 UTC 2024 I: Checking whether the package is not for us Thu Oct 10 17:24:46 UTC 2024 I: Starting 1st build on remote node virt32z-armhf-rb.debian.net. Thu Oct 10 17:24:46 UTC 2024 I: Preparing to do remote build '1' on virt32z-armhf-rb.debian.net. Thu Oct 10 17:26:02 UTC 2024 I: Deleting $TMPDIR on virt32z-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Oct 10 05:24:52 -12 2024 I: pbuilder-time-stamp: 1728581092 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [dwgsim_0.1.14-3.dsc] I: copying [./dwgsim_0.1.14.orig.tar.gz] I: copying [./dwgsim_0.1.14-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Aug 25 08:08:52 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./dwgsim_0.1.14-3.dsc: no acceptable signature found dpkg-source: info: extracting dwgsim in dwgsim-0.1.14 dpkg-source: info: unpacking dwgsim_0.1.14.orig.tar.gz dpkg-source: info: unpacking dwgsim_0.1.14-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-Debian-ise-makefile.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying remove-privacy-breach-links.patch dpkg-source: info: applying copy-samtools-test-properly.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/27286/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='1533677d4b0241ea8d1e0a7a38ddae10' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='27286' 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.dry3TJ2S/pbuilderrc_RjpP --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dry3TJ2S/b1 --logfile b1/build.log dwgsim_0.1.14-3.dsc' SUDO_GID='110' SUDO_UID='103' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux virt32z 6.1.0-26-armmp-lpae #1 SMP Debian 6.1.112-1 (2024-09-30) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/27286/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: armhf 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), samtools, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19519 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 samtools; however: Package samtools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev 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} 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} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libpipeline1{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} samtools{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales 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 23.1 MB of archives. After unpacking 78.4 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 2 http://deb.debian.org/debian unstable/main armhf libmagic-mgc armhf 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main armhf libmagic1t64 armhf 1:5.45-3 [98.1 kB] Get: 4 http://deb.debian.org/debian unstable/main armhf file armhf 1:5.45-3 [42.0 kB] Get: 5 http://deb.debian.org/debian unstable/main armhf gettext-base armhf 0.22.5-2 [195 kB] Get: 6 http://deb.debian.org/debian unstable/main armhf libuchardet0 armhf 0.0.8-1+b1 [65.7 kB] Get: 7 http://deb.debian.org/debian unstable/main armhf groff-base armhf 1.23.0-5 [1091 kB] Get: 8 http://deb.debian.org/debian unstable/main armhf bsdextrautils armhf 2.40.2-9 [88.8 kB] Get: 9 http://deb.debian.org/debian unstable/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 10 http://deb.debian.org/debian unstable/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 11 http://deb.debian.org/debian unstable/main armhf m4 armhf 1.4.19-4 [264 kB] Get: 12 http://deb.debian.org/debian unstable/main armhf autoconf all 2.72-3 [493 kB] Get: 13 http://deb.debian.org/debian unstable/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main armhf autopoint all 0.22.5-2 [723 kB] Get: 16 http://deb.debian.org/debian unstable/main armhf libdebhelper-perl all 13.20 [89.7 kB] Get: 17 http://deb.debian.org/debian unstable/main armhf libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main armhf libelf1t64 armhf 0.191-2 [183 kB] Get: 23 http://deb.debian.org/debian unstable/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 24 http://deb.debian.org/debian unstable/main armhf libicu72 armhf 72.1-5 [9075 kB] Get: 25 http://deb.debian.org/debian unstable/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.1 [604 kB] Get: 26 http://deb.debian.org/debian unstable/main armhf gettext armhf 0.22.5-2 [1485 kB] Get: 27 http://deb.debian.org/debian unstable/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main armhf debhelper all 13.20 [915 kB] Get: 30 http://deb.debian.org/debian unstable/main armhf libbrotli1 armhf 1.1.0-2+b4 [293 kB] Get: 31 http://deb.debian.org/debian unstable/main armhf libcom-err2 armhf 1.47.1-1 [22.1 kB] Get: 32 http://deb.debian.org/debian unstable/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 33 http://deb.debian.org/debian unstable/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 34 http://deb.debian.org/debian unstable/main armhf libkeyutils1 armhf 1.6.3-3 [7908 B] Get: 35 http://deb.debian.org/debian unstable/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 36 http://deb.debian.org/debian unstable/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 37 http://deb.debian.org/debian unstable/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8 [18.2 kB] Get: 38 http://deb.debian.org/debian unstable/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8 [50.2 kB] Get: 39 http://deb.debian.org/debian unstable/main armhf libldap-2.5-0 armhf 2.5.18+dfsg-3 [163 kB] Get: 40 http://deb.debian.org/debian unstable/main armhf libnghttp2-14 armhf 1.63.0-1 [62.9 kB] Get: 41 http://deb.debian.org/debian unstable/main armhf libnghttp3-9 armhf 1.4.0-1 [55.1 kB] Get: 42 http://deb.debian.org/debian unstable/main armhf libngtcp2-16 armhf 1.6.0-1 [118 kB] Get: 43 http://deb.debian.org/debian unstable/main armhf libngtcp2-crypto-gnutls8 armhf 1.6.0-1 [17.1 kB] Get: 44 http://deb.debian.org/debian unstable/main armhf libpsl5t64 armhf 0.21.2-1.1 [55.6 kB] Get: 45 http://deb.debian.org/debian unstable/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b4 [53.2 kB] Get: 46 http://deb.debian.org/debian unstable/main armhf libssh2-1t64 armhf 1.11.0-7 [199 kB] Get: 47 http://deb.debian.org/debian unstable/main armhf libcurl3t64-gnutls armhf 8.10.1-1 [308 kB] Get: 48 http://deb.debian.org/debian unstable/main armhf libdeflate0 armhf 1.22-1 [36.3 kB] Get: 49 http://deb.debian.org/debian unstable/main armhf libhtscodecs2 armhf 1.6.1-1 [63.1 kB] Get: 50 http://deb.debian.org/debian unstable/main armhf libhts3t64 armhf 1.20+ds-1 [399 kB] Get: 51 http://deb.debian.org/debian unstable/main armhf libncurses6 armhf 6.5-2 [81.8 kB] Get: 52 http://deb.debian.org/debian unstable/main armhf samtools armhf 1.20-3 [620 kB] Get: 53 http://deb.debian.org/debian unstable/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1 [904 kB] Fetched 23.1 MB in 0s (50.8 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 ... 19519 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_armhf.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.22.5-2_armhf.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-5_armhf.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.2-9_armhf.deb ... Unpacking bsdextrautils (2.40.2-9) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../08-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_armhf.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... 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_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:armhf. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/dwgsim-0.1.14/ && 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 > ../dwgsim_0.1.14-3_source.changes dpkg-buildpackage: info: source package dwgsim dpkg-buildpackage: info: source version 0.1.14-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_auto_clean make -j3 clean make[1]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' rm -vfr gmon.out *.o a.out *.exe *.dSYM razip bgzip dwgsim *~ *.a *.so.* *.so *.dylib; make[1]: Leaving directory '/build/reproducible-path/dwgsim-0.1.14' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' sed -i 's/occour/occur/' src/dwgsim_opt.c sed -i 's/occour/occur/' debian/dwgsim.1 dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/dwgsim_opt.c -o src/dwgsim_opt.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut.c -o src/mut.o In file included from src/dwgsim_opt.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); | ^~~~~~~~~~~~~~~~~~ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/contigs.c -o src/contigs.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/regions_bed.c -o src/regions_bed.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_txt.c -o src/mut_txt.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_bed.c -o src/mut_bed.o In file included from src/mut_txt.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); | ^~~~~~~~~~~~~~~~~~ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ In file included from src/mut_bed.c:33: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); | ^~~~~~~~~~~~~~~~~~ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_vcf.c -o src/mut_vcf.o cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/mut_input.c -o src/mut_input.o In file included from src/mut_vcf.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); | ^~~~~~~~~~~~~~~~~~ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ In file included from src/mut_input.c:36: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); | ^~~~~~~~~~~~~~~~~~ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ cc -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION=\"0.1.14-3\" src/dwgsim.c -o src/dwgsim.o src/dwgsim.c: In function 'dwgsim_core': src/dwgsim.c:864:35: warning: initialization of 'FILE *' from incompatible pointer type 'struct gzFile_s **' [-Wincompatible-pointer-types] 864 | FILE *fpo = (0 == j) ? opt->fp_bwa1: opt->fp_bwa2; | ^ src/dwgsim.c:867:38: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 867 | gzprintf(fpo, "@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d\n", | ^~~ | | | FILE * In file included from src/dwgsim.c:44: /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:875:38: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 875 | gzputc(fpo, "ACGTN"[(int)tmp_seq[j][i]]); | ^~~ | | | FILE * /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:876:38: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 876 | gzprintf(fpo, "\n+\n%s\n", qstr); | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:885:38: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 885 | gzprintf(fpo, "@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d\n", | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:894:38: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 894 | gzputc(fpo, "ACGTN"[(int)tmp_seq[j][i]]); | ^~~ | | | FILE * /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:895:38: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 895 | gzprintf(fpo, "\n+\n"); | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:897:38: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 897 | gzputc(fpo, qstr[i]); | ^~~ | | | FILE * /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:898:38: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 898 | gzprintf(fpo, "\n"); | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:904:39: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 904 | gzprintf(opt->fp_bfast, "@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx\n", | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:912:43: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 912 | gzputc(opt->fp_bfast, "ACGTN"[(int)tmp_seq[j][i]]); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:913:43: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 913 | gzprintf(opt->fp_bfast, "\n+\n%s\n", qstr); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:916:41: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 916 | gzputc(opt->fp_bfast, 'A'); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:918:43: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 918 | gzputc(opt->fp_bfast, "01234"[(int)tmp_seq[j][i]]); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:919:43: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 919 | gzprintf(opt->fp_bfast, "\n+\n"); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:921:43: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 921 | gzputc(opt->fp_bfast, qstr[i]); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:922:43: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 922 | gzprintf(opt->fp_bfast, "\n"); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:972:35: warning: initialization of 'FILE *' from incompatible pointer type 'struct gzFile_s **' [-Wincompatible-pointer-types] 972 | FILE *fpo = (0 == j) ? opt->fp_bwa1: opt->fp_bwa2; | ^ src/dwgsim.c:975:40: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 975 | gzprintf(fpo, "@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d\n", | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:983:40: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 983 | gzputc(fpo, "ACGTN"[(int)tmp_seq[j][i]]); | ^~~ | | | FILE * /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:984:40: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 984 | gzprintf(fpo, "\n+\n%s\n", qstr); | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:993:40: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 993 | gzprintf(fpo, "@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx/%d\n", | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:1002:40: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 1002 | gzputc(fpo, "ACGTN"[(int)tmp_seq[j][i]]); | ^~~ | | | FILE * /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:1003:40: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 1003 | gzprintf(fpo, "\n+\n"); | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:1005:40: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 1005 | gzputc(fpo, qstr[i]); | ^~~ | | | FILE * /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:1006:40: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 1006 | gzprintf(fpo, "\n"); | ^~~ | | | FILE * /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'FILE *' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:1012:39: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 1012 | gzprintf(opt->fp_bfast, "@%s%s%s_%u_%u_%1u_%1u_%1u_%1u_%d:%d:%d_%d:%d:%d_%llx\n", | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:1020:43: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 1020 | gzputc(opt->fp_bfast, "ACGTN"[(int)tmp_seq[j][i]]); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:1021:43: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 1021 | gzprintf(opt->fp_bfast, "\n+\n%s\n", qstr); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:1024:41: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 1024 | gzputc(opt->fp_bfast, 'A'); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:1026:43: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 1026 | gzputc(opt->fp_bfast, "01234"[(int)tmp_seq[j][i]]); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:1027:43: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 1027 | gzprintf(opt->fp_bfast, "\n+\n"); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c:1029:43: warning: passing argument 1 of 'gzputc' from incompatible pointer type [-Wincompatible-pointer-types] 1029 | gzputc(opt->fp_bfast, qstr[i]); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1508:35: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1508 | ZEXTERN int ZEXPORT gzputc(gzFile file, int c); | ~~~~~~~^~~~ src/dwgsim.c:1030:43: warning: passing argument 1 of 'gzprintf' from incompatible pointer type [-Wincompatible-pointer-types] 1030 | gzprintf(opt->fp_bfast, "\n"); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1471:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1471 | ZEXTERN int ZEXPORTVA gzprintf(gzFile file, const char *format, ...); | ~~~~~~~^~~~ src/dwgsim.c: In function 'main': src/dwgsim.c:1088:25: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 1088 | opt->fp_bfast = gzopen(fn_tmp, "w"); | ^ src/dwgsim.c:1092:24: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 1092 | opt->fp_bwa1 = gzopen(fn_tmp, "w"); | ^ src/dwgsim.c:1094:24: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] 1094 | opt->fp_bwa2 = gzopen(fn_tmp, "w"); | ^ src/dwgsim.c:1104:22: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] 1104 | gzclose(opt->fp_bfast); | ~~~^~~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ src/dwgsim.c:1107:22: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] 1107 | gzclose(opt->fp_bwa1); gzclose(opt->fp_bwa2); | ~~~^~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ src/dwgsim.c:1107:45: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] 1107 | gzclose(opt->fp_bwa1); gzclose(opt->fp_bwa2); | ~~~^~~~~~~~~ | | | struct gzFile_s ** /usr/include/zlib.h:1634:39: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' 1634 | ZEXTERN int ZEXPORT gzclose(gzFile file); | ~~~~~~~^~~~ In file included from src/dwgsim.c:46: src/mut.h: At top level: src/mut.h:62:1: warning: inline function 'mut_get_ins_long_n' declared but never defined 62 | mut_get_ins_long_n(uint8_t *ins, uint32_t *n); | ^~~~~~~~~~~~~~~~~~ src/mut.h:59:1: warning: inline function 'mut_get_ins_bytes' declared but never defined 59 | mut_get_ins_bytes(int32_t n); | ^~~~~~~~~~~~~~~~~ cc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/dwgsim-0.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -Wno-error=incompatible-pointer-types -Wall -O3 -I. -Wl,-z,relro -Wl,-z,now -o dwgsim src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o -lm -lz -lpthread make[2]: Leaving directory '/build/reproducible-path/dwgsim-0.1.14' make[1]: Leaving directory '/build/reproducible-path/dwgsim-0.1.14' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' ln -s /usr/share/doc/samtools/examples samtools dh_auto_test make -j3 test make[2]: Entering directory '/build/reproducible-path/dwgsim-0.1.14' if [ -d tmp ]; then rm -r tmp; fi /bin/bash testdata/test.sh /build/reproducible-path/dwgsim-0.1.14/testdata /build/reproducible-path/dwgsim-0.1.14 /build/reproducible-path/dwgsim-0.1.14 [dwgsim_core] seq1 length: 1575 [dwgsim_core] seq2 length: 1584 [dwgsim_core] 2 sequences, total length: 3159 [dwgsim_core] Currently on: 0 [dwgsim_core] 0 [dwgsim_core] 4986 [dwgsim_core] 10000 [dwgsim_core] Complete! make[2]: Leaving directory '/build/reproducible-path/dwgsim-0.1.14' make[1]: Leaving directory '/build/reproducible-path/dwgsim-0.1.14' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/dwgsim/ dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-armhf.so.3 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-armhf.so.3.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'dwgsim' in '../dwgsim_0.1.14-3_armhf.deb'. dpkg-deb: building package 'dwgsim-dbgsym' in '../dwgsim-dbgsym_0.1.14-3_armhf.deb'. dpkg-genbuildinfo --build=binary -O../dwgsim_0.1.14-3_armhf.buildinfo dpkg-genchanges --build=binary -O../dwgsim_0.1.14-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/27286 and its subdirectories I: Current time: Thu Oct 10 05:25:58 -12 2024 I: pbuilder-time-stamp: 1728581158 Thu Oct 10 17:26:05 UTC 2024 I: 1st build successful. Starting 2nd build on remote node virt64a-armhf-rb.debian.net. Thu Oct 10 17:26:05 UTC 2024 I: Preparing to do remote build '2' on virt64a-armhf-rb.debian.net. Thu Oct 10 17:27:39 UTC 2024 I: Deleting $TMPDIR on virt64a-armhf-rb.debian.net. Thu Oct 10 17:27:42 UTC 2024 I: dwgsim_0.1.14-3_armhf.changes: Format: 1.8 Date: Sun, 25 Aug 2024 09:38:11 +0200 Source: dwgsim Binary: dwgsim dwgsim-dbgsym Architecture: armhf Version: 0.1.14-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: dwgsim - short sequencing read simulator Closes: 1044706 1049717 1074926 Changes: dwgsim (0.1.14-3) unstable; urgency=medium . * Team upload. * d/rules: workaround build failure with gcc 14. (Closes: #1074926) * remove-travis-ci-link.patch: remove unused patch. * d/clean: properly cleanup multiple build artifacts. (Closes: #1044706, #1049717) * d/control: declare compliance to standards version 4.7.0. Checksums-Sha1: 43267d3a2dcedd6d2544bbb9a3a1de8a41be0239 79892 dwgsim-dbgsym_0.1.14-3_armhf.deb 6e183a09c9cc4ff41c41b0e326086efbe4500bb0 5642 dwgsim_0.1.14-3_armhf.buildinfo aefcb64135edc58c473e3431b9f3977e17dac2bb 40900 dwgsim_0.1.14-3_armhf.deb Checksums-Sha256: 015e5dcc65c624e99ae0d8de418eda24fd6dd9377e25eabe9c7b7905b0352e72 79892 dwgsim-dbgsym_0.1.14-3_armhf.deb c2627f57d471747c77f6ed58614e1a60df226b3c8d734348653da1c4eda9b6af 5642 dwgsim_0.1.14-3_armhf.buildinfo 2502c8e017a80d7ba936fd0d0000476d8057f9d12cdfaaaabdd1cc119c4a42f2 40900 dwgsim_0.1.14-3_armhf.deb Files: e7cef5a90ddcbc35d20c280c8c6bba3e 79892 debug optional dwgsim-dbgsym_0.1.14-3_armhf.deb 10c1d8f5cdd986bb26690f92aee2bf40 5642 science optional dwgsim_0.1.14-3_armhf.buildinfo 3c6b27dc3e9b1eac1f7b44d2ff375af1 40900 science optional dwgsim_0.1.14-3_armhf.deb Thu Oct 10 17:27:43 UTC 2024 I: diffoscope 279 will be used to compare the two builds: Running as unit: rb-diffoscope-armhf_34-11109.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.dry3TJ2S/dwgsim_0.1.14-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.dry3TJ2S/dwgsim_0.1.14-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.dry3TJ2S/dwgsim_0.1.14-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.dry3TJ2S/b1/dwgsim_0.1.14-3_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.dry3TJ2S/b2/dwgsim_0.1.14-3_armhf.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.392s) 0.392s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.018s) 0.018s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 732ms CPU time consumed: 731ms Thu Oct 10 17:41:11 UTC 2024 I: diffoscope 279 found no differences in the changes files, and a .buildinfo file also exists. Thu Oct 10 17:41:11 UTC 2024 I: dwgsim from unstable built successfully and reproducibly on armhf. Thu Oct 10 17:41:16 UTC 2024 I: Submitting .buildinfo files to external archives: Thu Oct 10 17:41:16 UTC 2024 I: Submitting 8.0K b1/dwgsim_0.1.14-3_armhf.buildinfo.asc Thu Oct 10 17:41:32 UTC 2024 I: Submitting 8.0K b2/dwgsim_0.1.14-3_armhf.buildinfo.asc Thu Oct 10 17:41:52 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Oct 10 17:41:52 UTC 2024 I: Done submitting .buildinfo files. Thu Oct 10 17:41:52 UTC 2024 I: Removing signed dwgsim_0.1.14-3_armhf.buildinfo.asc files: removed './b1/dwgsim_0.1.14-3_armhf.buildinfo.asc' removed './b2/dwgsim_0.1.14-3_armhf.buildinfo.asc'