Tue Jun 2 07:18:51 UTC 2020 I: starting to build maq/buster/armhf on jenkins on '2020-06-02 07:18' Tue Jun 2 07:18:51 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_7/3374/console.log Tue Jun 2 07:18:51 UTC 2020 I: Downloading source for buster/maq=0.7.1-8 --2020-06-02 07:18:51-- 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% 20.5M=0s 2020-06-02 07:18:51 (20.5 MB/s) - ‘maq_0.7.1-8.dsc’ saved [1943/1943] Tue Jun 2 07:18:51 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----- Tue Jun 2 07:18:51 UTC 2020 I: Checking whether the package is not for us Tue Jun 2 07:18:51 UTC 2020 I: Starting 1st build on remote node ff4a-armhf-rb.debian.net. Tue Jun 2 07:18:51 UTC 2020 I: Preparing to do remote build '1' on ff4a-armhf-rb.debian.net. Tue Jun 2 07:22:28 UTC 2020 I: Deleting $TMPDIR on ff4a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 1 19:19:00 -12 2020 I: pbuilder-time-stamp: 1591082340 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: 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/15343/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='4c83c6685fb24a35b8a5ab6e3e4068d0' 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='15343' 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.fWgZPK5CdA/pbuilderrc_lKNN --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.fWgZPK5CdA/b1 --logfile b1/build.log maq_0.7.1-8.dsc' SUDO_GID='111' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux ff4a 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 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 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 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 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 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 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 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 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 May 31 20:25 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 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/15343/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 (>= 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 ... 18932 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 18.4 MB of archives. After unpacking 63.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 10 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 11 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 12 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 13 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 14 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 30 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 31 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [207 kB] Fetched 18.4 MB in 2s (9266 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_armhf.deb ... Unpacking libmagic1:armhf (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u1_armhf.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_armhf.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:armhf. Preparing to unpack .../11-libsigsegv2_2.12-2_armhf.deb ... Unpacking libsigsegv2:armhf (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_armhf.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. 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Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... 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 armhf 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=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --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... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 -j3 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 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 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 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)); ^~ 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 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; ~~^~~~~~~~~~~ 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; ^~~~~~~ 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); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 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 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); ~~~~~~^~~~~~~~~ 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 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; ~~~~^~~~~~~~~ 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 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 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 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 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/arm-linux-gnueabihf/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: 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/arm-linux-gnueabihf/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 pair_stat.o pair_stat.cc 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/arm-linux-gnueabihf/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_soa.o indel_soa.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; ~~^~ 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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/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 ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 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 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)); ^~ 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/arm-linux-gnueabihf/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)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 indel_call.o indel_call.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 eland2maq.o eland2maq.cc 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; ^~~~ 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 ); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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 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/arm-linux-gnueabihf/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 -j3 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 -j3 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-dbgsym' in '../maq-dbgsym_0.7.1-8_armhf.deb'. dpkg-deb: building package 'maq' in '../maq_0.7.1-8_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../maq_0.7.1-8_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) 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/15343 and its subdirectories I: Current time: Mon Jun 1 19:22:22 -12 2020 I: pbuilder-time-stamp: 1591082542 Tue Jun 2 07:22:30 UTC 2020 I: 1st build successful. Starting 2nd build on remote node cbxi4b-armhf-rb.debian.net. Tue Jun 2 07:22:30 UTC 2020 I: Preparing to do remote build '2' on cbxi4b-armhf-rb.debian.net. Tue Jun 2 07:27:06 UTC 2020 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net. Tue Jun 2 07:27:09 UTC 2020 I: maq_0.7.1-8_armhf.changes: Format: 1.8 Date: Mon, 16 Jul 2018 15:42:20 +0200 Source: maq Binary: maq maq-dbgsym Architecture: armhf 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: 279a1e6ba9ed7142ace3189178788c89d8659cb0 418824 maq-dbgsym_0.7.1-8_armhf.deb 7602a9843cebea91573ef778cde283c05ce8f6df 4471 maq_0.7.1-8_armhf.buildinfo 118c7ea50efcd7750f2e5c12bc69ddb991578f99 304808 maq_0.7.1-8_armhf.deb Checksums-Sha256: 702a592d3fc5d795ae14d746427816da32dd48059da4bd4a07cc0719a237a843 418824 maq-dbgsym_0.7.1-8_armhf.deb 4b37f21809afd2911be3c348952fef034d37a9acda7e1f6f4ffac853e241c586 4471 maq_0.7.1-8_armhf.buildinfo d1e86a7d0ace4da65fb529b2a2a9590297ab2332fb2ca1e8b470280523702956 304808 maq_0.7.1-8_armhf.deb Files: b9889390460c3afbe140dcd7ce86d319 418824 debug optional maq-dbgsym_0.7.1-8_armhf.deb 974bde2aacbfefe7220bdc3ac1ec77a0 4471 science optional maq_0.7.1-8_armhf.buildinfo a5c904ac0f0596530ec5c316fb5e338b 304808 science optional maq_0.7.1-8_armhf.deb Tue Jun 2 07:27:10 UTC 2020 I: diffoscope 146 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.fWgZPK5CdA/maq_0.7.1-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.fWgZPK5CdA/maq_0.7.1-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.fWgZPK5CdA/maq_0.7.1-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.fWgZPK5CdA/b1/maq_0.7.1-8_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.fWgZPK5CdA/b2/maq_0.7.1-8_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: 0.377s) 0.377s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.056s) 0.056s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jun 2 07:27:13 UTC 2020 I: diffoscope 146 found no differences in the changes files, and a .buildinfo file also exists. Tue Jun 2 07:27:13 UTC 2020 I: maq from buster built successfully and reproducibly on armhf. Tue Jun 2 07:27:15 UTC 2020 I: Submitting .buildinfo files to external archives: Tue Jun 2 07:27:15 UTC 2020 I: Submitting 8.0K b1/maq_0.7.1-8_armhf.buildinfo.asc Tue Jun 2 07:27:15 UTC 2020 I: Submitting 8.0K b2/maq_0.7.1-8_armhf.buildinfo.asc Tue Jun 2 07:27:18 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jun 2 07:27:18 UTC 2020 I: Done submitting .buildinfo files. Tue Jun 2 07:27:18 UTC 2020 I: Removing signed maq_0.7.1-8_armhf.buildinfo.asc files: removed './b1/maq_0.7.1-8_armhf.buildinfo.asc' removed './b2/maq_0.7.1-8_armhf.buildinfo.asc'