Wed Dec 16 02:47:50 UTC 2020 I: starting to build snap-aligner/buster/amd64 on jenkins on '2020-12-16 02:47' Wed Dec 16 02:47:50 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_1/1316/console.log Wed Dec 16 02:47:50 UTC 2020 I: Downloading source for buster/snap-aligner=1.0~beta.18+dfsg-3 --2020-12-16 02:47:50-- http://deb.debian.org/debian/pool/main/s/snap-aligner/snap-aligner_1.0~beta.18+dfsg-3.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2203 (2.2K) Saving to: ‘snap-aligner_1.0~beta.18+dfsg-3.dsc’ 0K .. 100% 148M=0s 2020-12-16 02:47:50 (148 MB/s) - ‘snap-aligner_1.0~beta.18+dfsg-3.dsc’ saved [2203/2203] Wed Dec 16 02:47:50 UTC 2020 I: snap-aligner_1.0~beta.18+dfsg-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: snap-aligner Binary: snap-aligner Architecture: amd64 arm64 mips64el ppc64el alpha kfreebsd-amd64 ppc64 sparc64 Version: 1.0~beta.18+dfsg-3 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: http://snap.cs.berkeley.edu/ Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/snap-aligner Vcs-Git: https://salsa.debian.org/med-team/snap-aligner.git Build-Depends: debhelper (>= 11~), help2man, zlib1g-dev Package-List: snap-aligner deb science optional arch=amd64,arm64,mips64el,ppc64el,alpha,kfreebsd-amd64,ppc64,sparc64 Checksums-Sha1: 619b4c4cc646a385e36c2b03fdf504bbca4c3c16 1975632 snap-aligner_1.0~beta.18+dfsg.orig.tar.xz bed8e1ed7e2392d4b1beb7c50f6bec9153a26e13 7772 snap-aligner_1.0~beta.18+dfsg-3.debian.tar.xz Checksums-Sha256: a5ed636903d9c37cf51f09973003b39d571882ba399d437c263fd7f755f55fdb 1975632 snap-aligner_1.0~beta.18+dfsg.orig.tar.xz bc1bd9c8fb005bb0b68ea2d8be466251756a84c5d80d66f099b2946b360dfa53 7772 snap-aligner_1.0~beta.18+dfsg-3.debian.tar.xz Files: a435cf84e55809d806f569778bf1ed45 1975632 snap-aligner_1.0~beta.18+dfsg.orig.tar.xz 04eecda33add116c4dddc5701ca12c41 7772 snap-aligner_1.0~beta.18+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlxWzVcRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHFHRAAkVHahJQS9ikx33oSTDB+txJiJUGA+AxE 8FwnrkfG1Fnl5MFwBGyCTBpG7sgpeCVGR3rtq4R7KXpNqzJVHmZgCuYWJLHR6REh JZVS8RxMvYRBCvfk2f6yN5h9XNni4KovrDuOe8boWJaugx71gsFLiTucrWe13wLT OHX/7tugovqh0FyYIox4ogrVWbtC035Af7yP19Nad6M3/hfeO2mg3UaWYS9pKtUi B2hi/GxdhJ9qFCILcLLTGfn20M2IA+JdyOoOULzl0meLrpn2gUWeALgHqcO+xq1C twjx6/x23IzeHzAST8+gtE0cVyU2o1ICMNskYHL7Fr6D0okpbDgP8PBPmp4LirzJ LWxB16wiX0a8TjADOzxPenUHQu41LLNlmUfCdWTDXtAZfk1jpS1kFm06jOKCx70h STUlxRAtcVtZXBd9evfKQPKntgqCLlbOAcC6Y45xOEpmW0xOLTw9XLTFaUrbKrud PNNkl8MEXqx/1/n+3XxpWh5RssGtqYPCqsFgc9B4TpqPlE7l1/uCOyedT6Eig1Jt MfAPP4DKgKuHM/3i2zzTkq4gUVOAqY7/KH2bydyelRR1SfEasZ88EyXF3e24Omgm PcWkKDGvF1M5+PEBz8vLYw86Q6O5pgsg/RKDu/3FoGc7T81KidELr8fIQ2x+ayj4 LP1T07A+hbM= =KaP1 -----END PGP SIGNATURE----- Wed Dec 16 02:47:50 UTC 2020 I: Checking whether the package is not for us Wed Dec 16 02:47:50 UTC 2020 I: Starting 1st build on remote node ionos1-amd64.debian.net. Wed Dec 16 02:47:50 UTC 2020 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Wed Dec 16 02:50:59 UTC 2020 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Dec 15 14:47:52 -12 2020 I: pbuilder-time-stamp: 1608086872 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 [snap-aligner_1.0~beta.18+dfsg-3.dsc] I: copying [./snap-aligner_1.0~beta.18+dfsg.orig.tar.xz] I: copying [./snap-aligner_1.0~beta.18+dfsg-3.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 Sat Feb 2 23:15:35 2019 -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 ./snap-aligner_1.0~beta.18+dfsg-3.dsc dpkg-source: info: extracting snap-aligner in snap-aligner-1.0~beta.18+dfsg dpkg-source: info: unpacking snap-aligner_1.0~beta.18+dfsg.orig.tar.xz dpkg-source: info: unpacking snap-aligner_1.0~beta.18+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying non-x86-and-kfreebsd dpkg-source: info: applying drop-msse dpkg-source: info: applying spelling dpkg-source: info: applying finish-rename dpkg-source: info: applying hardening.patch dpkg-source: info: applying add_missing_return.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/5509/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0f2a0e0688674bb19c7aade9b34e0d00' 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='5509' 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.Ij2OrqpiuM/pbuilderrc_uHCI --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Ij2OrqpiuM/b1 --logfile b1/build.log snap-aligner_1.0~beta.18+dfsg-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 4.19.0-13-amd64 #1 SMP Debian 4.19.160-2 (2020-11-28) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38984 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 38984 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14328 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 43744 Feb 28 2019 cat -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash -rwxr-xr-x 1 root root 109408 Feb 28 2019 date -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd -rwxr-xr-x 1 root root 93744 Feb 28 2019 df -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir -rwxr-xr-x 1 root root 84288 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 39520 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 35424 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 198976 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 98048 Jan 5 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln -rwxr-xr-x 1 root root 56760 Jul 26 2018 login -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 9 2019 more -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138728 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 39616 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Dec 6 20:26 sh -> dash -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty -rwsr-xr-x 1 root root 63568 Jan 9 2019 su -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch -rwxr-xr-x 1 root root 35424 Feb 28 2019 true -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34896 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/5509/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), help2man, 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 ... 19195 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 help2man; however: Package help2man 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} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblocale-gettext-perl{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, 36 newly installed, 0 to remove and 0 not upgraded. Need to get 19.4 MB of archives. After unpacking 70.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u1 [117 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u1 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u2 [1258 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u1 [689 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 19.4 MB in 1s (37.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_amd64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../06-liblocale-gettext-perl_1.07-3+b4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-3+b4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../09-libmagic1_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u1) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.35-4+deb10u1_amd64.deb ... Unpacking file (1:5.35-4+deb10u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../12-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... 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I: Building the package I: Running cd /build/snap-aligner-1.0~beta.18+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package snap-aligner dpkg-buildpackage: info: source version 1.0~beta.18+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/snap-aligner-1.0~beta.18+dfsg' dh_auto_clean make -j15 clean make[2]: Entering directory '/build/snap-aligner-1.0~beta.18+dfsg' rm -f SNAPLib/Util.o SNAPLib/FASTQ.o SNAPLib/DataReader.o SNAPLib/AlignerContext.o SNAPLib/FASTA.o SNAPLib/GenericFile_map.o SNAPLib/SeedSequencer.o SNAPLib/GenericFile.o SNAPLib/BigAlloc.o SNAPLib/CommandProcessor.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/SAM.o SNAPLib/GenericFile_stdio.o SNAPLib/MultiInputReadSupplier.o SNAPLib/AlignerStats.o SNAPLib/mapq.o SNAPLib/ReadWriter.o SNAPLib/ReadSupplierQueue.o SNAPLib/AlignerOptions.o SNAPLib/exit.o SNAPLib/HashTable.o SNAPLib/Bam.o SNAPLib/DataWriter.o SNAPLib/ParallelTask.o SNAPLib/Genome.o SNAPLib/stdafx.o SNAPLib/ProbabilityDistance.o SNAPLib/GenericFile_Blob.o SNAPLib/PairedAligner.o SNAPLib/BaseAligner.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/GenericFile_HDFS.o SNAPLib/AlignmentResult.o SNAPLib/GzipDataWriter.o SNAPLib/LandauVishkin.o SNAPLib/Read.o SNAPLib/RangeSplitter.o SNAPLib/GenomeIndex.o SNAPLib/BiasTables.o SNAPLib/Compat.o SNAPLib/PairedReadMatcher.o SNAPLib/Error.o SNAPLib/ReadReader.o SNAPLib/ApproximateCounter.o SNAPLib/Seed.o SNAPLib/BufferedAsync.o SNAPLib/Tables.o SNAPLib/ChimericPairedEndAligner.o apps/snap/Main.o apps/snap/stdafx.o tests/ProbabilityDistanceTest.o tests/LandauVishkinTest.o tests/TestLib.o tests/EventTest.o tests/main.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o snap-aligner unit_tests SNAPCommand snap SNAP make[2]: Leaving directory '/build/snap-aligner-1.0~beta.18+dfsg' rm -f debian/*.1 rm -f */*.d */*/*.d make[1]: Leaving directory '/build/snap-aligner-1.0~beta.18+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/snap-aligner-1.0~beta.18+dfsg' dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/snap-aligner-1.0~beta.18+dfsg' g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Util.o SNAPLib/Util.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTQ.o SNAPLib/FASTQ.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataReader.o SNAPLib/DataReader.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerContext.o SNAPLib/AlignerContext.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/FASTA.o SNAPLib/FASTA.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_map.o SNAPLib/GenericFile_map.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SeedSequencer.o SNAPLib/SeedSequencer.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile.o SNAPLib/GenericFile.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BigAlloc.o SNAPLib/BigAlloc.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/CommandProcessor.o SNAPLib/CommandProcessor.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Histogram.o SNAPLib/Histogram.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/IntersectingPairedEndAligner.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SAM.o SNAPLib/SAM.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_stdio.o SNAPLib/GenericFile_stdio.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/MultiInputReadSupplier.o SNAPLib/MultiInputReadSupplier.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerStats.o SNAPLib/AlignerStats.cpp SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeHeader(const ReaderContext&, char*, size_t, size_t*, bool, int, const char**, const char*, const char*, bool) const': SNAPLib/SAM.cpp:922:97: warning: format '%u' expects argument of type 'unsigned int', but argument 5 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] bytesConsumed += snprintf(header + bytesConsumed, headerBufferSize - bytesConsumed, "@SQ\tSN:%s\tLN:%u\n", contigs[i].name, end - start); ^~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~ SNAPLib/SAM.cpp: In member function 'virtual bool SAMFormat::writeRead(const ReaderContext&, LandauVishkinWithCigar*, char*, size_t, size_t*, size_t, Read*, AlignmentResult, int, GenomeLocation, Direction, bool, int*, bool, bool, Read*, AlignmentResult, GenomeLocation, Direction, bool) const': SNAPLib/SAM.cpp:1252:55: warning: field precision specifier '.*' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] int charsInString = snprintf(buffer, bufferSpace, "%.*s\t%d\t%s\t%u\t%d\t%s\t%s\t%u\t%lld\t%.*s\t%.*s%s%.*s%s%s\tPG:Z:SNAP%s%.*s\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnameLen, read->getId(), ~~~~~~~~ SNAPLib/SAM.cpp:1252:55: warning: format '%u' expects argument of type 'unsigned int', but argument 8 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] SNAPLib/SAM.cpp:1252:55: warning: format '%u' expects argument of type 'unsigned int', but argument 12 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] SNAPLib/SAM.cpp:1252:55: warning: format '%lld' expects argument of type 'long long int', but argument 13 has type '_int64' {aka 'long int'} [-Wformat=] SNAPLib/SAM.cpp: In static member function 'static const char* SAMFormat::computeCigarString(const Genome*, LandauVishkinWithCigar*, char*, int, char*, int, const char*, GenomeDistance, unsigned int, GenomeDistance, unsigned int, unsigned int, unsigned int, GenomeLocation, Direction, bool, int*, int*)': SNAPLib/SAM.cpp:1459:54: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); ^~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp:1462:52: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); ^~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/Util.cpp: In function 'char* FormatUIntWithCommas(_uint64, char*, size_t)': SNAPLib/Util.cpp:164:21: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] sprintf(tempBuf, ",%03lld", x % 1000); ^~~~~~~~~ ~~~~~~~~ SNAPLib/Util.cpp:167:21: warning: format '%d' expects argument of type 'int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] sprintf(tempBuf, "%d", x); ^~~~ ~ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/mapq.o SNAPLib/mapq.cpp SNAPLib/AlignerContext.cpp: In member function 'void AlignerContext::printStats()': SNAPLib/AlignerContext.cpp:346:27: warning: format '%f' expects argument of type 'double', but argument 9 has type '_int64' {aka 'long int'} [-Wformat=] fprintf(perfFile, "%d\t%d\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%0.2f%%\t%lld\t%lld\tt%.0f\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/AlignerContext.cpp:352:17: stats->lvCalls, ~~~~~~~~~~~~~~ SNAPLib/AlignerContext.cpp:346:27: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'double' [-Wformat=] SNAPLib/AlignerContext.cpp:346:27: warning: format '%lld' expects argument of type 'long long int', but argument 11 has type '_int64' {aka 'long int'} [-Wformat=] g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadWriter.o SNAPLib/ReadWriter.cpp SNAPLib/DataReader.cpp: In member function 'char* DecompressDataReader::findPointer(void*)': SNAPLib/DataReader.cpp:1685:29: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] sprintf(result, "compressed #%d @ %lld", i, (char*)p - e->compressed); ^~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/DataReader.cpp:1689:29: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] sprintf(result, "decompressed #%d %lld", i, (char*) p - e->decompressed); ^~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/DataReader.cpp:1693:29: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type 'long int' [-Wformat=] sprintf(result, "extra #%d %lld", i, (char*) p - e->decompressed - extraBytes); ^~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadSupplierQueue.o SNAPLib/ReadSupplierQueue.cpp SNAPLib/DataReader.cpp: In static member function 'static void DecompressDataReader::decompressThread(void*)': SNAPLib/DataReader.cpp:1813:37: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] fprintf(stderr, "error reading BAM file at offset %lld\n", reader->getFileOffset()); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignerOptions.o SNAPLib/AlignerOptions.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/exit.o SNAPLib/exit.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/HashTable.o SNAPLib/HashTable.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Bam.o SNAPLib/Bam.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/DataWriter.o SNAPLib/DataWriter.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ParallelTask.o SNAPLib/ParallelTask.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Genome.o SNAPLib/Genome.cpp SNAPLib/SAM.cpp:1459:54: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] snprintf(clipBefore, sizeof(clipBefore), "%lluS", basesClippedBefore + extraBasesClippedBefore); ^~~~~~~ SNAPLib/SAM.cpp:1459:54: note: directive argument in the range [1, 9223372036854775807] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/fstream:41, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/SAM.cpp:1462:52: warning: '%llu' directive output may be truncated writing between 1 and 19 bytes into a region of size 16 [-Wformat-truncation=] snprintf(clipAfter, sizeof(clipAfter), "%lluS", basesClippedAfter + extraBasesClippedAfter); ^~~~~~~ SNAPLib/SAM.cpp:1462:52: note: directive argument in the range [1, 9223372036854775807] In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/fstream:41, from SNAPLib/stdafx.h:14, from SNAPLib/SAM.cpp:19: /usr/include/x86_64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 3 and 21 bytes into a destination of size 16 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/stdafx.o SNAPLib/stdafx.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ProbabilityDistance.o SNAPLib/ProbabilityDistance.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_Blob.o SNAPLib/GenericFile_Blob.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedAligner.o SNAPLib/PairedAligner.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BaseAligner.o SNAPLib/BaseAligner.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SingleAligner.o SNAPLib/SingleAligner.cpp SNAPLib/Genome.cpp: In member function 'bool Genome::saveToFile(const char*) const': SNAPLib/Genome.cpp:143:22: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'GenomeDistance' {aka 'long int'} [-Wformat=] fprintf(saveFile,"%lld %d\n",nBases, nContigs); ^~~~~~~~~~~ ~~~~~~ SNAPLib/Genome.cpp:151:26: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'GenomeLocation' {aka 'long int'} [-Wformat=] fprintf(saveFile,"%lld %s\n",contigs[i].beginningLocation, contigs[i].name); ^~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/Genome.cpp: In static member function 'static const Genome* Genome::loadFromFile(const char*, unsigned int, GenomeLocation, GenomeDistance, bool)': SNAPLib/Genome.cpp:239:39: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type '_int64*' {aka 'long int*'} [-Wformat=] if (1 != sscanf(contigNameBuffer, "%lld", &contigStart)) { ^~~~~~ ~~~~~~~~~~~~ SNAPLib/Genome.cpp: In static member function 'static bool Genome::openFileAndGetSizes(const char*, GenericFile**, GenomeDistance*, unsigned int*, bool)': SNAPLib/Genome.cpp:323:47: warning: format '%lld' expects argument of type 'long long int*', but argument 3 has type 'GenomeDistance*' {aka 'long int*'} [-Wformat=] if (NULL == retval || 2 != sscanf(linebuf,"%lld %d\n", nBases, nContigs)) { ^~~~~~~~~~~ ~~~~~~ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/SortedDataWriter.o SNAPLib/SortedDataWriter.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenericFile_HDFS.o SNAPLib/GenericFile_HDFS.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/AlignmentResult.o SNAPLib/AlignmentResult.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GzipDataWriter.o SNAPLib/GzipDataWriter.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/LandauVishkin.o SNAPLib/LandauVishkin.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Read.o SNAPLib/Read.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/RangeSplitter.o SNAPLib/RangeSplitter.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/GenomeIndex.o SNAPLib/GenomeIndex.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BiasTables.o SNAPLib/BiasTables.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Compat.o SNAPLib/Compat.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/PairedReadMatcher.o SNAPLib/PairedReadMatcher.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Error.o SNAPLib/Error.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ReadReader.o SNAPLib/ReadReader.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ApproximateCounter.o SNAPLib/ApproximateCounter.cpp SNAPLib/GenomeIndex.cpp: In static member function 'static bool GenomeIndex::BuildIndexToDirectory(const Genome*, int, double, bool, const char*, unsigned int, unsigned int, bool, unsigned int, bool, const char*, unsigned int, bool)': SNAPLib/GenomeIndex.cpp:291:17: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type '_int64' {aka 'long int'} [-Wformat=] fprintf(stderr,"%llds\n", (timeInMillis() + 500 - start) / 1000); ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/GenomeIndex.cpp:679:32: warning: format '%d' expects argument of type 'int', but argument 3 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] fprintf(histogramFile, "%d larger than %d with %d total genome locations, largest seed %d\n", countOfTooBigForHistogram, maxHistogramEntry, sumOfTooBigForHistogram, largestSeed); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/GenomeIndex.cpp:679:32: warning: format '%d' expects argument of type 'int', but argument 5 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] SNAPLib/GenomeIndex.cpp:679:32: warning: format '%d' expects argument of type 'int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] SNAPLib/GenomeIndex.cpp:731:23: warning: format '%lld' expects argument of type 'long long int', but argument 6 has type '_uint64' {aka 'long unsigned int'} [-Wformat=] fprintf(indexFile,"%d %d %d %lld %d %d %d %lld %d %d", GenomeIndexFormatMajorVersion, GenomeIndexFormatMinorVersion, index->nHashTables, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ index->overflowTableSize, seedLen, chromosomePaddingSize, hashTableKeySize, totalBytesWritten, large ? 0 : 1, locationSize); ~~~~~~~~~~~~~~~~~~~~~~~~ SNAPLib/GenomeIndex.cpp:731:23: warning: format '%lld' expects argument of type 'long long int', but argument 10 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] SNAPLib/GenomeIndex.cpp: In static member function 'static GenomeIndex* GenomeIndex::loadFromDirectory(char*, bool, bool)': SNAPLib/GenomeIndex.cpp:1625:44: warning: format '%lld' expects argument of type 'long long int*', but argument 6 has type '_int64*' {aka 'long int*'} [-Wformat=] if (10 != (nRead = sscanf(indexFileBuf,"%d %d %d %lld %d %d %d %lld %d %d", &majorVersion, &minorVersion, &nHashTables, &overflowTableSize, &seedLen, &chromosomePadding, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~ SNAPLib/GenomeIndex.cpp:1625:44: warning: format '%lld' expects argument of type 'long long int*', but argument 10 has type 'size_t*' {aka 'long unsigned int*'} [-Wformat=] g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Seed.o SNAPLib/Seed.cpp SNAPLib/Error.cpp: In function 'void WriteProgressCounter(const char*, _int64)': SNAPLib/Error.cpp:87:20: warning: format '%lld' expects argument of type 'long long int', but argument 4 has type '_int64' {aka 'long int'} [-Wformat=] fprintf(stderr,"reporter:counter:SNAP,%s,%lld\n", counterName, increment); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/BufferedAsync.o SNAPLib/BufferedAsync.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/Tables.o SNAPLib/Tables.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o SNAPLib/ChimericPairedEndAligner.o SNAPLib/ChimericPairedEndAligner.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/Main.o apps/snap/Main.cpp SNAPLib/ReadReader.cpp: In member function 'virtual bool SimpleReadReader::getNextRead(Read*, AlignmentResult*, unsigned int*, bool*, unsigned int*, unsigned int*, const char**)': SNAPLib/ReadReader.cpp:44:5: warning: no return statement in function returning non-void [-Wreturn-type] } ^ g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/snap/stdafx.o apps/snap/stdafx.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/ProbabilityDistanceTest.o tests/ProbabilityDistanceTest.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/LandauVishkinTest.o tests/LandauVishkinTest.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/TestLib.o tests/TestLib.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/EventTest.o tests/EventTest.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o tests/main.o tests/main.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/SNAPCommand.cpp g++ -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o apps/SNAPCommand/stdafx.o apps/SNAPCommand/stdafx.cpp g++ -o snap-aligner -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/Util.o SNAPLib/FASTQ.o SNAPLib/DataReader.o SNAPLib/AlignerContext.o SNAPLib/FASTA.o SNAPLib/GenericFile_map.o SNAPLib/SeedSequencer.o SNAPLib/GenericFile.o SNAPLib/BigAlloc.o SNAPLib/CommandProcessor.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/SAM.o SNAPLib/GenericFile_stdio.o SNAPLib/MultiInputReadSupplier.o SNAPLib/AlignerStats.o SNAPLib/mapq.o SNAPLib/ReadWriter.o SNAPLib/ReadSupplierQueue.o SNAPLib/AlignerOptions.o SNAPLib/exit.o SNAPLib/HashTable.o SNAPLib/Bam.o SNAPLib/DataWriter.o SNAPLib/ParallelTask.o SNAPLib/Genome.o SNAPLib/stdafx.o SNAPLib/ProbabilityDistance.o SNAPLib/GenericFile_Blob.o SNAPLib/PairedAligner.o SNAPLib/BaseAligner.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/GenericFile_HDFS.o SNAPLib/AlignmentResult.o SNAPLib/GzipDataWriter.o SNAPLib/LandauVishkin.o SNAPLib/Read.o SNAPLib/RangeSplitter.o SNAPLib/GenomeIndex.o SNAPLib/BiasTables.o SNAPLib/Compat.o SNAPLib/PairedReadMatcher.o SNAPLib/Error.o SNAPLib/ReadReader.o SNAPLib/ApproximateCounter.o SNAPLib/Seed.o SNAPLib/BufferedAsync.o SNAPLib/Tables.o SNAPLib/ChimericPairedEndAligner.o apps/snap/Main.o apps/snap/stdafx.o -lrt -lz g++ -o unit_tests -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Itests -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/Util.o SNAPLib/FASTQ.o SNAPLib/DataReader.o SNAPLib/AlignerContext.o SNAPLib/FASTA.o SNAPLib/GenericFile_map.o SNAPLib/SeedSequencer.o SNAPLib/GenericFile.o SNAPLib/BigAlloc.o SNAPLib/CommandProcessor.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/SAM.o SNAPLib/GenericFile_stdio.o SNAPLib/MultiInputReadSupplier.o SNAPLib/AlignerStats.o SNAPLib/mapq.o SNAPLib/ReadWriter.o SNAPLib/ReadSupplierQueue.o SNAPLib/AlignerOptions.o SNAPLib/exit.o SNAPLib/HashTable.o SNAPLib/Bam.o SNAPLib/DataWriter.o SNAPLib/ParallelTask.o SNAPLib/Genome.o SNAPLib/stdafx.o SNAPLib/ProbabilityDistance.o SNAPLib/GenericFile_Blob.o SNAPLib/PairedAligner.o SNAPLib/BaseAligner.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/GenericFile_HDFS.o SNAPLib/AlignmentResult.o SNAPLib/GzipDataWriter.o SNAPLib/LandauVishkin.o SNAPLib/Read.o SNAPLib/RangeSplitter.o SNAPLib/GenomeIndex.o SNAPLib/BiasTables.o SNAPLib/Compat.o SNAPLib/PairedReadMatcher.o SNAPLib/Error.o SNAPLib/ReadReader.o SNAPLib/ApproximateCounter.o SNAPLib/Seed.o SNAPLib/BufferedAsync.o SNAPLib/Tables.o SNAPLib/ChimericPairedEndAligner.o tests/ProbabilityDistanceTest.o tests/LandauVishkinTest.o tests/TestLib.o tests/EventTest.o tests/main.o -lrt -lz echo SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o SNAPCOMMAND_OBJ is apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o echo SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o SNAP_OBJ is apps/snap/Main.o apps/snap/stdafx.o g++ -o SNAPCommand -std=gnu++98 -MMD -ISNAPLib -g -O2 -ffile-prefix-map=/build/snap-aligner-1.0~beta.18+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -pthread SNAPLib/Util.o SNAPLib/FASTQ.o SNAPLib/DataReader.o SNAPLib/AlignerContext.o SNAPLib/FASTA.o SNAPLib/GenericFile_map.o SNAPLib/SeedSequencer.o SNAPLib/GenericFile.o SNAPLib/BigAlloc.o SNAPLib/CommandProcessor.o SNAPLib/Histogram.o SNAPLib/IntersectingPairedEndAligner.o SNAPLib/SAM.o SNAPLib/GenericFile_stdio.o SNAPLib/MultiInputReadSupplier.o SNAPLib/AlignerStats.o SNAPLib/mapq.o SNAPLib/ReadWriter.o SNAPLib/ReadSupplierQueue.o SNAPLib/AlignerOptions.o SNAPLib/exit.o SNAPLib/HashTable.o SNAPLib/Bam.o SNAPLib/DataWriter.o SNAPLib/ParallelTask.o SNAPLib/Genome.o SNAPLib/stdafx.o SNAPLib/ProbabilityDistance.o SNAPLib/GenericFile_Blob.o SNAPLib/PairedAligner.o SNAPLib/BaseAligner.o SNAPLib/SingleAligner.o SNAPLib/SortedDataWriter.o SNAPLib/GenericFile_HDFS.o SNAPLib/AlignmentResult.o SNAPLib/GzipDataWriter.o SNAPLib/LandauVishkin.o SNAPLib/Read.o SNAPLib/RangeSplitter.o SNAPLib/GenomeIndex.o SNAPLib/BiasTables.o SNAPLib/Compat.o SNAPLib/PairedReadMatcher.o SNAPLib/Error.o SNAPLib/ReadReader.o SNAPLib/ApproximateCounter.o SNAPLib/Seed.o SNAPLib/BufferedAsync.o SNAPLib/Tables.o SNAPLib/ChimericPairedEndAligner.o apps/SNAPCommand/SNAPCommand.o apps/SNAPCommand/stdafx.o -lrt -lz make[2]: Leaving directory '/build/snap-aligner-1.0~beta.18+dfsg' help2man --no-discard-stderr --no-info --version-string="1.0~beta.18" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./snap-aligner > debian/snap-aligner.1 for option in index single paired; do help2man \ --no-discard-stderr --no-info --version-string="1.0~beta.18" \ --include=debian/snap-aligner-${option}-man-include \ --help-option=" " "./snap-aligner ${option}" > \ debian/snap-aligner-${option}.1; done help2man --no-discard-stderr --no-info --version-string="1.0~beta.18" \ --name "scalable nucleotide alignment program" \ --help-option=" " ./SNAPCommand > debian/SNAPCommand.1 make[1]: Leaving directory '/build/snap-aligner-1.0~beta.18+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/snap-aligner-1.0~beta.18+dfsg' dh_auto_test ./unit_tests ProbabilityDistanceTest: - basic probabilities: [OK] - indels: [OK] LandauVishkinTest: - equal strings: [OK] - prefixes: [OK] - non-equal strings: [OK] - overly distant strings: [OK] - CIGAR strings: [OK] EventTest: - many waiters: [OK] - single waiters: [OK] 9 / 9 tests passed. make[1]: Leaving directory '/build/snap-aligner-1.0~beta.18+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'snap-aligner' in '../snap-aligner_1.0~beta.18+dfsg-3_amd64.deb'. dpkg-deb: building package 'snap-aligner-dbgsym' in '../snap-aligner-dbgsym_1.0~beta.18+dfsg-3_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snap-aligner_1.0~beta.18+dfsg-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/5509 and its subdirectories I: Current time: Tue Dec 15 14:50:58 -12 2020 I: pbuilder-time-stamp: 1608087058 Wed Dec 16 02:50:59 UTC 2020 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Wed Dec 16 02:50:59 UTC 2020 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Wed Dec 16 02:52:45 UTC 2020 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Wed Dec 16 02:52:45 UTC 2020 I: snap-aligner_1.0~beta.18+dfsg-3_amd64.changes: Format: 1.8 Date: Sun, 03 Feb 2019 12:11:59 +0100 Source: snap-aligner Binary: snap-aligner snap-aligner-dbgsym Architecture: amd64 Version: 1.0~beta.18+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: snap-aligner - Scalable Nucleotide Alignment Program Changes: snap-aligner (1.0~beta.18+dfsg-3) unstable; urgency=medium . [ Andreas Tille ] * Team upload. * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.3.0 * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target * Install NOTICE.txt of Apache licensed files * Propagate hardening options . [ Liubov Chuprikova ] * Add missing return in a non-void function Checksums-Sha1: c0c626207216233eb6790b6b3f034bf95d6004d8 2335824 snap-aligner-dbgsym_1.0~beta.18+dfsg-3_amd64.deb a2090a729f13f444a6d497f096d7c4c04ccfad62 4855 snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo b62fb6ecb73372620cd042ee26a0f1d5fe3d3b18 1649252 snap-aligner_1.0~beta.18+dfsg-3_amd64.deb Checksums-Sha256: b150566c372447bd98bf99d4848dd5f6fc114b480012ddc8e0ca8416b12edb96 2335824 snap-aligner-dbgsym_1.0~beta.18+dfsg-3_amd64.deb 206af781006225145b8fff8a6258080d031f5bc24f3a5f7398b9747965798685 4855 snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo 4a75657aba972daf44cb0ce02eb941bfa58e203dd1fce83e354d5068b13dc581 1649252 snap-aligner_1.0~beta.18+dfsg-3_amd64.deb Files: dcc8415b7c5a0d0a1b1951c384b21aa5 2335824 debug optional snap-aligner-dbgsym_1.0~beta.18+dfsg-3_amd64.deb 056632a3f809f3f93bf20405827ba91a 4855 science optional snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo defb64127ff6029be416d6cbbb2b72bf 1649252 science optional snap-aligner_1.0~beta.18+dfsg-3_amd64.deb Wed Dec 16 02:52:47 UTC 2020 I: diffoscope 162 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.Ij2OrqpiuM/snap-aligner_1.0~beta.18+dfsg-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.Ij2OrqpiuM/snap-aligner_1.0~beta.18+dfsg-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.Ij2OrqpiuM/snap-aligner_1.0~beta.18+dfsg-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.Ij2OrqpiuM/b1/snap-aligner_1.0~beta.18+dfsg-3_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.Ij2OrqpiuM/b2/snap-aligner_1.0~beta.18+dfsg-3_amd64.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: 0.335s) 0.335s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.073s) 0.072s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Dec 16 02:52:49 UTC 2020 I: diffoscope 162 found no differences in the changes files, and a .buildinfo file also exists. Wed Dec 16 02:52:49 UTC 2020 I: snap-aligner from buster built successfully and reproducibly on amd64. Wed Dec 16 02:52:50 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Dec 16 02:52:50 UTC 2020 I: Submitting 8.0K b1/snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo.asc Wed Dec 16 02:52:52 UTC 2020 I: Submitting 8.0K b2/snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo.asc Wed Dec 16 02:52:52 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Dec 16 02:52:52 UTC 2020 I: Done submitting .buildinfo files. Wed Dec 16 02:52:52 UTC 2020 I: Removing signed snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo.asc files: removed './b1/snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo.asc' removed './b2/snap-aligner_1.0~beta.18+dfsg-3_amd64.buildinfo.asc'