Thu Oct 22 04:39:44 UTC 2020 I: starting to build maq/buster/i386 on jenkins on '2020-10-22 04:39' Thu Oct 22 04:39:44 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/15783/console.log Thu Oct 22 04:39:44 UTC 2020 I: Downloading source for buster/maq=0.7.1-8 --2020-10-22 04:39:44-- http://deb.debian.org/debian/pool/main/m/maq/maq_0.7.1-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1943 (1.9K) Saving to: ‘maq_0.7.1-8.dsc’ 0K . 100% 193M=0s 2020-10-22 04:39:44 (193 MB/s) - ‘maq_0.7.1-8.dsc’ saved [1943/1943] Thu Oct 22 04:39:44 UTC 2020 I: maq_0.7.1-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: maq Binary: maq Architecture: any Version: 0.7.1-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Charles Plessy Homepage: http://maq.sourceforge.net/ Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/med-team/maq Vcs-Git: https://salsa.debian.org/med-team/maq.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), zlib1g-dev Package-List: maq deb science optional arch=any Checksums-Sha1: ca51faa2f2a24e81fe7a38d75613a84433c69af8 398368 maq_0.7.1.orig.tar.gz a7b7d738044f36c0bf426ff89862e050283364e7 11148 maq_0.7.1-8.debian.tar.xz Checksums-Sha256: efb8d66ae9319b260db7e56fd17d2f2299f1dee84522848a2205d9f069eb00ba 398368 maq_0.7.1.orig.tar.gz 0bbb5817aa8fef10e838d46c0412265d613c6925ee66a0a3b532402b7980b6da 11148 maq_0.7.1-8.debian.tar.xz Files: 894adf6f73abee5767d55a1fb623004f 398368 maq_0.7.1.orig.tar.gz 57a5027e7264c83facd2bab7ac69bdc0 11148 maq_0.7.1-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltMotMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEZjQ//RJdYROI0LhHdk52SzH0QdaSKdyNX8asd HlxK7SgUNgTRGiuyTHM1ZSmcqfX4q+yU6lBJZ9KKxuuA7rC7LoCMFrWNbs+7k1Ee CTfw9BqRetvekNM3aXnjLdSXSBtLIRck8NWiERPSPhX0H6C2RHMgn7K7ghxbz9rp wqIEAHQl6wtm1xAvBaU239p2XzSkoI268MzweRZKIKYKk15SMpVBlx5LiJn9Ia2N vXKXjrX9o7/xjWsCrm6Ep6g86MRhIfNVod4QZhST/X7y3EO5Joo+D/ZkNarmOI7T NlBDo/v4JNuJly/hZxBATOfo4JiYeevGjm2cmAotBRRPFbiccdC/tzyAkO4Tpi7M B/KSQFE2+XdWC3LVXJ747qrqyO31axYVpOuIeEFxwPQO+pXXM7OJC/+G4U+cF2Pq mRTy50hI1HEizRsowcutT7PwzwZGZ0II7zWdqtuEBvJ7xrWACoXCk+AMzxyz88Lo n04xmJOGWBsPjfcJiVMDxxwsLZ4e70tBSG5ONU/FYluklCIWBINRMcdW4jIlHv83 JVfLQwoetRRKS+ViuTL8vTnKunEVedWSLKoif9fUrLCvlnDUc/W6BeF46+/rw+8a mOLlmJVofxADG+ssS4dDOAWcgQrf6WRlp9Xy1Xc+8Lgjk9QfHHPX4qq6ygMWKCJG W75G85mJHsY= =dCzr -----END PGP SIGNATURE----- Thu Oct 22 04:39:44 UTC 2020 I: Checking whether the package is not for us Thu Oct 22 04:39:44 UTC 2020 I: Starting 1st build on remote node profitbricks-build6-i386.debian.net. Thu Oct 22 04:39:44 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build6-i386.debian.net. Thu Oct 22 04:40:08 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Nov 23 23:02:45 -12 2021 I: pbuilder-time-stamp: 1637751765 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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 [maq_0.7.1-8.dsc] I: copying [./maq_0.7.1.orig.tar.gz] I: copying [./maq_0.7.1-8.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon Jul 16 01:51:15 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./maq_0.7.1-8.dsc dpkg-source: info: extracting maq in maq-0.7.1 dpkg-source: info: unpacking maq_0.7.1.orig.tar.gz dpkg-source: info: unpacking maq_0.7.1-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 10_prevent_-64_option.patch dpkg-source: info: applying gcc-4.7.patch dpkg-source: info: applying mayhem.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/6407/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=18' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='6176ccc55b7c43449c8527d047682f67' 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='6407' 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/tmp.ccOYU9ExSG/pbuilderrc_hy7N --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ccOYU9ExSG/b1 --logfile b1/build.log maq_0.7.1-8.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 profitbricks-build6-i386 4.19.0-12-amd64 #1 SMP Debian 4.19.152-1 (2020-10-18) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Nov 23 02:47 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/6407/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 (>= 11~), 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 ... 19234 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 (>= 11~); however: Package debhelper 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} bsdmainutils{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} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After unpacking 70.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Fetched 19.6 MB in 0s (80.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_i386.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_i386.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:i386. Preparing to unpack .../11-libsigsegv2_2.12-2_i386.deb ... Unpacking libsigsegv2:i386 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_i386.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:i386. Preparing to unpack .../22-libelf1_0.176-1.1_i386.deb ... Unpacking libelf1:i386 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.12-3_i386.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:i386. Preparing to unpack .../24-libglib2.0-0_2.58.3-2+deb10u2_i386.deb ... Unpacking libglib2.0-0:i386 (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:i386. Preparing to unpack .../25-libicu63_63.1-6+deb10u1_i386.deb ... Unpacking libicu63:i386 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../26-libxml2_2.9.4+dfsg1-7+b3_i386.deb ... Unpacking libxml2:i386 (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:i386. Preparing to unpack .../27-libcroco3_0.6.12-3_i386.deb ... Unpacking libcroco3:i386 (0.6.12-3) ... 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Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/maq-0.7.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package maq dpkg-buildpackage: info: source version 0.7.1-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf configure.ac:6: installing './compile' dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h configure: WARNING: unrecognized options: --disable-maintainer-mode, --disable-dependency-tracking dh_auto_build make -j18 make[1]: Entering directory '/build/maq-0.7.1' make all-am make[2]: Entering directory '/build/maq-0.7.1' gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o const.o const.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o seq.o seq.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bfa.o bfa.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o read.o read.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta2bfa.o fasta2bfa.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fastq2bfq.o fastq2bfq.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o merge.o merge.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match_aux.o match_aux.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o match.o match.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_mapping.o sort_mapping.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assemble.o assemble.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pileup.o pileup.cc g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o mapcheck.o mapcheck.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o get_pos.o get_pos.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assopt.o assopt.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o aux_utils.o aux_utils.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rbcc.o rbcc.cc bfa.c: In function 'nst_load_bfa1': bfa.c:31:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(bfa1->name, sizeof(char), len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:32:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&bfa1->ori_len, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:33:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&bfa1->len, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:35:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(bfa1->seq, sizeof(bit64_t), bfa1->len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:37:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(bfa1->mask, sizeof(bit64_t), bfa1->len, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c: In function 'nst_bfa_len': bfa.c:46:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&len, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bfa.c:48:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&len, sizeof(int), 1, fp); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o subsnp.o subsnp.cc fastq2bfq.c: In function 'fastq2bfq': fastq2bfq.c:30:5: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] fp = gzopen(str, "w"); ^ fastq2bfq.c:36:7: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] fp = gzopen(str, "w"); ^ fastq2bfq.c:47:11: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] gzwrite(fp, &i, sizeof(int)); ^~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzwrite OF((gzFile file, ^~ fastq2bfq.c:48:11: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] gzwrite(fp, name, sizeof(char) * i); ^~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzwrite OF((gzFile file, ^~ fastq2bfq.c:49:11: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] gzwrite(fp, &l, sizeof(int)); ^~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzwrite OF((gzFile file, ^~ fastq2bfq.c:50:11: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] gzwrite(fp, seq.s, sizeof(char) * l); ^~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzwrite OF((gzFile file, ^~ fastq2bfq.c:53:12: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] gzclose(fp); ^~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~ fastq2bfq.c:62:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] gzclose(fp); ^~ In file included from /usr/include/zlib.h:34, from fastq2bfq.c:1: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~ sort_mapping.cc: In function 'int ma_make_pair(const match_aux_t*, const match_info_t*, const match_info_t*, pair_info_t*)': sort_mapping.cc:59:61: warning: suggest parentheses around arithmetic in operand of '^' [-Wparentheses] p->i1 = (((m1->i1>>24)+(m2->i1>>24))<<24) | (m1->i1^m2->i1&0xffffff); ~~~~~~^~~~~~~~~ assemble.cc: In function 'base_call_aux_t* assemble_cns_collect(assemble_pos_t*, const assemble_aux_t*)': assemble.cc:106:63: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; ~~~~^~~~~~~~~ match.cc: In function 'int alt_cal_mm(bit64_t)': match.cc:58:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; ~~^~~~~~~~~~ match.cc:61:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] x = x + (x >> 32) & 0x0000007F; ~~^~~~~~~~~~~ match.cc: In function 'int alt_cal_err(bit64_t, bit64_t)': match.cc:67:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] x = x + (x >> 4) & 0x0F0F0F0F0F0F0F0FLLU; ~~^~~~~~~~~~ match.cc:70:8: warning: suggest parentheses around '+' in operand of '&' [-Wparentheses] x = x + (x >> 32) & 0x0000007F; ~~^~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o pair_stat.o pair_stat.cc match.cc: In function 'void process_candidate(const required_option_t*, int, bit64_t, match_data_t*, ref_canlist_t*)': match.cc:284:39: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct ref_canlist_t'; use assignment or value-initialization instead [-Wclass-memaccess] memset(list, 0, sizeof(ref_canlist_t)); ^ match.cc:49:16: note: 'struct ref_canlist_t' declared here typedef struct { ^ match.cc: In function 'void match_search(const match_aux_t*, match_data_t*, const nst_bfa1_t*, int, ref_canlist_t*)': match.cc:292:10: warning: variable 'n_reads' set but not used [-Wunused-but-set-variable] bit32_t n_reads; ^~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_soa.o indel_soa.cc match.cc: In function 'int ma_match(int, char**)': match.cc:525:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(tmpfp, "%s", adaptor); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ mapcheck.cc: In function 'int ma_mapcheck(int, char**)': mapcheck.cc:60:17: warning: variable 'fpout' set but not used [-Wunused-but-set-variable] FILE *fp_bfa, *fpout; ^~~~~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap.o maqmap.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o maqmap_conv.o maqmap_conv.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o altchr.o altchr.cc indel_soa.cc: In function 'void fill_counter(bit32_t*, int, nst_bfa1_t*, gzFile)': indel_soa.cc:42:40: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; ~~^~ indel_soa.cc:56:40: warning: suggest parentheses around '-' inside '<<' [-Wparentheses] if (int(m1->seq[k]>>6) == int(s>>(31-j<<1)&3)) ++score; ~~^~ gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o submap.o submap.c subsnp.cc: In function 'hash_map_char* ma_load_snp(FILE*)': subsnp.cc:20:16: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(key, "%s.%d", name, pos); ^~~~~~~ In file included from /usr/include/stdio.h:873, from subsnp.cc:2: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rbcc.cc: In function 'hash_map_char* cns_load_dbSNP(FILE*)': rbcc.cc:21:17: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(str1, "%s.%d", name, pos); ^~~~~~~ In file included from /usr/include/stdio.h:873, from rbcc.cc:7: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o rmdup.o rmdup.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o simulate.o simulate.c gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o genran.o genran.c g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_pe.o indel_pe.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o stdaln.o stdaln.c simulate.c: In function 'maq_simutrain': simulate.c:83:8: warning: assignment to 'struct gzFile_s **' from incompatible pointer type 'gzFile' {aka 'struct gzFile_s *'} [-Wincompatible-pointer-types] fpout = gzopen(argv[1], "w"); ^ simulate.c:86:10: warning: passing argument 1 of 'gzwrite' from incompatible pointer type [-Wincompatible-pointer-types] gzwrite(fpout, fqc, sizeof(fqc_t)); ^~~~~ In file included from /usr/include/zlib.h:34, from simulate.c:6: /usr/include/zlib.h:1446:29: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzwrite OF((gzFile file, ^~ simulate.c:87:10: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types] gzclose(fpout); ^~~~~ In file included from /usr/include/zlib.h:34, from simulate.c:6: /usr/include/zlib.h:1630:32: note: expected 'gzFile' {aka 'struct gzFile_s *'} but argument is of type 'struct gzFile_s **' ZEXTERN int ZEXPORT gzclose OF((gzFile file)); ^~ subsnp.cc: In function 'hash_set_char* ma_load_snp_set(FILE*)': subsnp.cc:35:16: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(key, "%s.%d", name, pos); ^~~~~~~ In file included from /usr/include/stdio.h:873, from subsnp.cc:2: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o indel_call.o indel_call.cc In file included from /usr/include/string.h:494, from maqmap.h:23, from simulate.c:11: In function 'memset', inlined from 'simustat_core' at simulate.c:386:2: /usr/include/i386-linux-gnu/bits/string_fortified.h:71:10: warning: '__builtin___memset_chk' writing 16 bytes into a region of size 0 overflows the destination [-Wstringop-overflow=] return __builtin___memset_chk (__dest, __ch, __len, __bos0 (__dest)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o eland2maq.o eland2maq.cc stdaln.c: In function 'aln_local_core': stdaln.c:534:25: warning: variable 'b' set but not used [-Wunused-but-set-variable] int gap_open, gap_ext, b; ^ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o csmap2ntmap.o csmap2ntmap.cc gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o break_pair.o break_pair.c In file included from break_pair.c:2: break_pair.c: In function 'breakpair': break_pair.c:16:9: warning: suggest parentheses around assignment used as truth value [-Wparentheses] assert(fp = gzopen(str, "r")); ^~ g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o glfgen.o glfgen.cc eland2maq.cc: In function 'void eland2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:88:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp_eland, "%s", str); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ eland2maq.cc:96:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp_eland, "%s", str); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ eland2maq.cc:99:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp_eland, "%u%u%u%s%u%s", tmp, tmp+1, tmp+2, str, tmp+3, str2); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ eland2maq.cc: In function 'hash_map_char* read_list(FILE*)': eland2maq.cc:33:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(fp, "%s", str); ~~~~~~^~~~~~~~~~~~~~~ eland2maq.cc: In function 'void novo2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:323:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fgets( str2, 4096, fp_novo ); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ indel_call.cc: In function 'int maq_indelpe(int, char**)': indel_call.cc:68:17: warning: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_ungap' may be used uninitialized in this function [-Wmaybe-uninitialized] for (i = 0; i != ii->indelpos.n_ungap; ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~ indel_call.cc:86:21: note: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_ungap' was declared here indel_info_t curr, last; ^~~~ indel_call.cc:22:2: warning: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_types' may be used uninitialized in this function [-Wmaybe-uninitialized] if (ii->indelpos.n_types == 0) return; ^~ indel_call.cc:86:21: note: 'last.indel_info_t::indelpos.assemble_indelpos_t::n_types' was declared here indel_info_t curr, last; ^~~~ indel_call.cc:30:34: warning: 'last.indel_info_t::coor' may be used uninitialized in this function [-Wmaybe-uninitialized] for (j = 0, i = (ii->coor > 32)? ii->coor - 32 : 0; i < ii->coor; ++i) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ indel_call.cc:86:21: note: 'last.indel_info_t::coor' was declared here indel_info_t curr, last; ^~~~ subsnp.cc: In function 'void maq_simucns_core(FILE*, gzFile, FILE*)': subsnp.cc:190:17: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(key, "%s.%d", name, pos); ^~~~~~~ In file included from /usr/include/stdio.h:873, from subsnp.cc:2: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ subsnp.cc:186:18: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(key, "%s.%d", name, i); ^~~~~~~ In file included from /usr/include/stdio.h:873, from subsnp.cc:2: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 3 and 268 bytes into a destination of size 256 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ glfgen.cc: In function 'glf1_t* glfgen1_core(assemble_pos_t*, const assemble_aux_t*, bit8_t)': glfgen.cc:43:63: warning: suggest parentheses around arithmetic in operand of '|' [-Wparentheses] if (info>>24 < 4 && (info>>8&0x3f) != 0) info = 4<<24 | info&0xffffff; ~~~~^~~~~~~~~ eland2maq.cc: In function 'void export2maq_core(FILE*, FILE*, gzFile)': eland2maq.cc:563:17: warning: '%d' directive writing between 1 and 11 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] sprintf(str2, "%s_%d:%d:%d:%d:%d", str, ti[0], ti[1], ti[2], ti[3], ti[4]); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from eland2maq.cc:9: /usr/include/i386-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 11 and 1084 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wall -D_FILE_OFFSET_BITS=64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -ffile-prefix-map=/build/maq-0.7.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o maq main.o const.o seq.o bfa.o read.o fasta2bfa.o fastq2bfq.o merge.o match_aux.o match.o sort_mapping.o assemble.o pileup.o mapcheck.o get_pos.o assopt.o aux_utils.o rbcc.o subsnp.o pair_stat.o indel_soa.o maqmap.o maqmap_conv.o altchr.o submap.o rmdup.o simulate.o genran.o indel_pe.o stdaln.o indel_call.o eland2maq.o csmap2ntmap.o break_pair.o glfgen.o -lm -lz make[2]: Leaving directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' dh_auto_test make -j18 check VERBOSE=1 make[1]: Entering directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j18 install DESTDIR=/build/maq-0.7.1/debian/maq AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/maq-0.7.1' make[2]: Entering directory '/build/maq-0.7.1' make[2]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' /bin/mkdir -p '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c maq '/build/maq-0.7.1/debian/maq/usr/bin' /usr/bin/install -c scripts/maq.pl scripts/farm-run.pl scripts/maq_plot.pl scripts/maq_eval.pl '/build/maq-0.7.1/debian/maq/usr/bin' make[2]: Leaving directory '/build/maq-0.7.1' make[1]: Leaving directory '/build/maq-0.7.1' dh_install dh_installdocs dh_installchangelogs dh_installexamples debian/rules override_dh_installman make[1]: Entering directory '/build/maq-0.7.1' dh_installman # when installing via debian/manpages the .pl is stripped and the # files will end up in /usr/share/man/pl/man1 cp -a debian/mans/*.1 debian/maq/usr/share/man/man1 make[1]: Leaving directory '/build/maq-0.7.1' dh_lintian dh_perl dh_link dh_strip_nondeterminism debian/rules override_dh_compress make[1]: Entering directory '/build/maq-0.7.1' dh_compress --exclude=.pdf make[1]: Leaving directory '/build/maq-0.7.1' dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package maq: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'maq' in '../maq_0.7.1-8_i386.deb'. dpkg-deb: building package 'maq-dbgsym' in '../maq-dbgsym_0.7.1-8_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../maq_0.7.1-8_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/6407 and its subdirectories I: Current time: Tue Nov 23 23:03:08 -12 2021 I: pbuilder-time-stamp: 1637751788 Thu Oct 22 04:40:09 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build2-i386.debian.net. Thu Oct 22 04:40:09 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build2-i386.debian.net. Thu Oct 22 04:43:53 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. Thu Oct 22 04:43:53 UTC 2020 I: maq_0.7.1-8_i386.changes: Format: 1.8 Date: Mon, 16 Jul 2018 15:42:20 +0200 Source: maq Binary: maq maq-dbgsym Architecture: i386 Version: 0.7.1-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: maq - maps short fixed-length polymorphic DNA sequence reads to referen Changes: maq (0.7.1-8) unstable; urgency=medium . [ Steffen Moeller ] * debian/upstream/metadata: - Added references to OMICtools, SciCrunch, bio.tools - yamllint cleanliness . [ Andreas Tille ] * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.5 * Lintian should not warn about script-with-language-extension see https://lists.debian.org/debian-med/2018/06/msg00043.html Checksums-Sha1: 15a1120ef87a1cf6b9d2cf1b6c0ddbe5645f7d39 420400 maq-dbgsym_0.7.1-8_i386.deb 86ed402d1f3974070991ce626828006160437bdb 4599 maq_0.7.1-8_i386.buildinfo eb44884ae5cb6487ecafc0028b331b6dccdb789d 327444 maq_0.7.1-8_i386.deb Checksums-Sha256: 44e5a26913573b19713e0d55c2145c2029aaebd9d4c0caf7fef77b96d6f48e5f 420400 maq-dbgsym_0.7.1-8_i386.deb 178c735e1e799cdceb4316d6822f9b8e0ce72f2a038d6e60ac6e43747525d2c6 4599 maq_0.7.1-8_i386.buildinfo 78fe7db021c4845ed258794bdba35caffb88917931797e20752d5e7f517cf508 327444 maq_0.7.1-8_i386.deb Files: 6b6361e963769c0119cf22338ad45fae 420400 debug optional maq-dbgsym_0.7.1-8_i386.deb c0e4bd9dae54d8c30de7a3b14092cef1 4599 science optional maq_0.7.1-8_i386.buildinfo 31fb8a5e8ed99c63285c82a92b9e2b54 327444 science optional maq_0.7.1-8_i386.deb Thu Oct 22 04:43:54 UTC 2020 I: diffoscope 161 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ccOYU9ExSG/maq_0.7.1-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ccOYU9ExSG/maq_0.7.1-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ccOYU9ExSG/maq_0.7.1-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ccOYU9ExSG/b1/maq_0.7.1-8_i386.changes /srv/reproducible-results/rbuild-debian/tmp.ccOYU9ExSG/b2/maq_0.7.1-8_i386.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: 0.209s) 0.209s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.026s) 0.026s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Thu Oct 22 04:43:55 UTC 2020 I: diffoscope 161 found no differences in the changes files, and a .buildinfo file also exists. Thu Oct 22 04:43:55 UTC 2020 I: maq from buster built successfully and reproducibly on i386. Thu Oct 22 04:43:56 UTC 2020 I: Submitting .buildinfo files to external archives: Thu Oct 22 04:43:56 UTC 2020 I: Submitting 8.0K b1/maq_0.7.1-8_i386.buildinfo.asc Thu Oct 22 04:43:57 UTC 2020 I: Submitting 8.0K b2/maq_0.7.1-8_i386.buildinfo.asc Thu Oct 22 04:43:58 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Oct 22 04:43:58 UTC 2020 I: Done submitting .buildinfo files. Thu Oct 22 04:43:58 UTC 2020 I: Removing signed maq_0.7.1-8_i386.buildinfo.asc files: removed './b1/maq_0.7.1-8_i386.buildinfo.asc' removed './b2/maq_0.7.1-8_i386.buildinfo.asc'