Fri Nov 29 07:22:49 UTC 2024 I: starting to build bamtools/trixie/i386 on jenkins on '2024-11-29 07:22' Fri Nov 29 07:22:49 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_6/46307/console.log Fri Nov 29 07:22:49 UTC 2024 I: Downloading source for trixie/bamtools=2.5.2+dfsg-6 --2024-11-29 07:22:49-- http://deb.debian.org/debian/pool/main/b/bamtools/bamtools_2.5.2%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2387 (2.3K) [text/prs.lines.tag] Saving to: ‘bamtools_2.5.2+dfsg-6.dsc’ 0K .. 100% 334M=0s 2024-11-29 07:22:49 (334 MB/s) - ‘bamtools_2.5.2+dfsg-6.dsc’ saved [2387/2387] Fri Nov 29 07:22:50 UTC 2024 I: bamtools_2.5.2+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bamtools Binary: bamtools, libbamtools-dev, libbamtools2.5.2, libbamtools-doc Architecture: any all Version: 2.5.2+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Étienne Mollier Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bamtools Vcs-Git: https://salsa.debian.org/med-team/bamtools.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkgconf Package-List: bamtools deb science optional arch=any libbamtools-dev deb libdevel optional arch=any libbamtools-doc deb doc optional arch=all libbamtools2.5.2 deb libs optional arch=any Checksums-Sha1: 22affe59a445f08e603c3f9d5378b32d06fbccd7 155732 bamtools_2.5.2+dfsg.orig.tar.xz 7cc3351c7180b79fd41ffb7c49da5260689c9987 11368 bamtools_2.5.2+dfsg-6.debian.tar.xz Checksums-Sha256: bba4d268cb9457cd836b59c60eac6a9f25e10cd9aea646f03e5deffb82c1c5c1 155732 bamtools_2.5.2+dfsg.orig.tar.xz e4c667cb47d93420c0473c6f674d8a138a1e64362aeca55b81341aeb7e353785 11368 bamtools_2.5.2+dfsg-6.debian.tar.xz Files: a29fafa8a0f930c3029749245032e886 155732 bamtools_2.5.2+dfsg.orig.tar.xz c495be9488890186b00051d0a63c21a9 11368 bamtools_2.5.2+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmaRGHQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFLqQ/+OcycIB7F7GyBa40zu1kb1I7EPmqDwpmm 5zxpxM++K8E3kxQbL8LYFmq97whd69kzjnVkAz35FVZ/3oqSUAThRdqe5+Y+NzZC P1szfBrsE7bFUgykd3sWur0yZauja6zQ9Otm/IA+6qcrBY+SXIpxWkFc+RCkRcUj O0tC1ZVRtALgFW8GJneBQyp9LGzoZsJDgZhMAJfl/Tc3tuNhSFTC0vF3IxG3bjJt zgsfGL4rXcmr7LJZFn7lygEIDooVThSPPkHgPvw582m/9Ck4fG7K/G7gDdd7C8Rh X0Ko3UKLHgaebXE+qQXn9aNlwYEO901UdVY3zvtHMoFaZjI9w8s9lor4+azlNPM3 Kjz/ZhntRJOzZ3vsorDTzOiAh4YhY0CYQ7/rsnH27QQrbc4IXsV2ug2l2tWuAC27 HeCxd8m8qfa/lNvS8xRVTTXR+o2e0h+duBtdRLFL/9AGkZjlGp2M5Oss1zCuit+0 +Sv/kqYEKH02yu4mhkeGheXc5Q7YdjsheghWipL3f2yc9uMDDo5j0O62tMrsuVeo yoWuP9mpJ6xOEGrzmvgCbbfO8eU2Y4jR+iv8xXMJ+R2C69Y1rcEU1688qzpHrKLH QGKzLr8ihwnumx5Vukoetn0WTI0RYVczlOzvYi46IdnIMHd1/VyPWRx54gATr4+8 WldzQv42FhU= =fapy -----END PGP SIGNATURE----- Fri Nov 29 07:22:50 UTC 2024 I: Checking whether the package is not for us Fri Nov 29 07:22:50 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Fri Nov 29 07:22:50 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Fri Nov 29 07:23:43 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 1 01:45:51 -12 2026 I: pbuilder-time-stamp: 1767275151 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [bamtools_2.5.2+dfsg-6.dsc] I: copying [./bamtools_2.5.2+dfsg.orig.tar.xz] I: copying [./bamtools_2.5.2+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 12 11:50:12 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bamtools_2.5.2+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting bamtools in bamtools-2.5.2+dfsg dpkg-source: info: unpacking bamtools_2.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking bamtools_2.5.2+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-ignore-thirdparty-and-fix-jsoncpp.patch dpkg-source: info: applying shared_and_static.patch dpkg-source: info: applying typo.patch dpkg-source: info: applying filter_script.patch dpkg-source: info: applying do_not_corrupt_output.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/96601/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='42b9694bdd424bf48138d33b5def04f5' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='96601' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/pbuilderrc_dLTS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/b1 --logfile b1/build.log bamtools_2.5.2+dfsg-6.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/96601/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkgconf dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19952 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libclang-cpp19{a} libclang1-19{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt10{a} libgssapi-krb5-2{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libllvm19{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} libz3-4{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 110 MB of archives. After unpacking 463 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 27 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 28 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 42 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 43 http://deb.debian.org/debian trixie/main i386 d-shlibs all 0.107 [11.0 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 49 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 50 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libedit2 i386 3.1-20240808-1 [98.0 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libz3-4 i386 4.13.3-1 [9211 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libllvm19 i386 1:19.1.3-2 [30.4 MB] Get: 59 http://deb.debian.org/debian trixie/main i386 libclang-cpp19 i386 1:19.1.3-2 [15.5 MB] Get: 60 http://deb.debian.org/debian trixie/main i386 libclang1-19 i386 1:19.1.3-2 [8999 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libfmt10 i386 10.1.1+ds1-4 [134 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 doxygen i386 1.9.8+ds-2+b3 [5225 kB] Get: 63 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libjsoncpp-dev i386 1.9.6-3 [25.0 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Fetched 110 MB in 1s (78.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (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 ... 19952 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../08-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../11-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bamtools-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bamtools_2.5.2+dfsg-6_source.changes dpkg-buildpackage: info: source package bamtools dpkg-buildpackage: info: source version 2.5.2+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' test ! -f docs/Doxyfile.orig || mv docs/Doxyfile.orig docs/Doxyfile make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for one of the modules 'jsoncpp>=1' Found system JsonCpp, not using bundled version -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.3.1") -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done (1.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' cp docs/Doxyfile docs/Doxyfile.orig doxygen -u docs/Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 300 of file 'docs/Doxyfile' has become obsolete. 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Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAux.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAux.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api//build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:25: warning: Documentation for undefined enum 'MergeOrder' found. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:187: warning: documented symbol 'bool BamTools::AddTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:307: warning: documented symbol 'template< typename T > bool BamTools::AddTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:377: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:407: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:434: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:559: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. IBamIODevice.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Sort.h... Generating code for file api_global.h... Generating code for file BamAlgorithms.h... Generating code for file BamAlignment.h... Generating code for file BamAux.h... Generating code for file BamConstants.h... Generating code for file BamIndex.h... Generating code for file BamMultiReader.h... Generating code for file BamReader.h... Generating code for file BamWriter.h... Generating code for file IBamIODevice.h... Generating code for file SamConstants.h... Generating code for file SamHeader.h... Generating code for file SamProgram.h... Generating code for file SamProgramChain.h... Generating code for file SamReadGroup.h... Generating code for file SamReadGroupDictionary.h... Generating code for file SamSequence.h... Generating code for file SamSequenceDictionary.h... Generating file documentation... Generating docs for file Sort.h... Generating docs for file api_global.h... Generating docs for file BamAlgorithms.h... Generating docs for file BamAlignment.cpp... Generating docs for file BamAlignment.h... Generating docs for file BamAux.h... Generating docs for file BamConstants.h... Generating docs for file BamIndex.h... Generating docs for file BamMultiReader.cpp... Generating docs for file BamMultiReader.h... Generating docs for file BamReader.cpp... Generating docs for file BamReader.h... Generating docs for file BamWriter.cpp... Generating docs for file BamWriter.h... Generating docs for file IBamIODevice.h... Generating docs for file SamConstants.h... Generating docs for file SamHeader.cpp... Generating docs for file SamHeader.h... Generating docs for file SamProgram.cpp... Generating docs for file SamProgram.h... Generating docs for file SamProgramChain.cpp... Generating docs for file SamProgramChain.h... Generating docs for file SamReadGroup.cpp... Generating docs for file SamReadGroup.h... Generating docs for file SamReadGroupDictionary.cpp... Generating docs for file SamReadGroupDictionary.h... Generating docs for file SamSequence.cpp... Generating docs for file SamSequence.h... Generating docs for file SamSequenceDictionary.cpp... Generating docs for file SamSequenceDictionary.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating docs for namespace BamTools Generating docs for compound BamTools::BamAlignment... Generating docs for compound BamTools::BamIndex... Generating docs for compound BamTools::BamMultiReader... Generating docs for compound BamTools::BamReader... Generating docs for compound BamTools::BamRegion... Generating docs for compound BamTools::BamWriter... Generating docs for compound BamTools::CigarOp... Generating docs for compound BamTools::CustomHeaderTag... Generating docs for compound BamTools::IBamIODevice... Generating docs for compound BamTools::RefData... Generating docs for compound BamTools::SamHeader... Generating docs for compound BamTools::SamProgram... Generating docs for compound BamTools::SamProgramChain... Generating docs for compound BamTools::SamReadGroup... Generating docs for compound BamTools::SamReadGroupDictionary... Generating docs for compound BamTools::SamSequence... Generating docs for compound BamTools::SamSequenceDictionary... Generating docs for namespace BamTools::Algorithms Generating docs for compound BamTools::Algorithms::Sort... Generating docs for nested compound BamTools::Algorithms::Sort::ByName... Generating docs for nested compound BamTools::Algorithms::Sort::ByPosition... Generating docs for nested compound BamTools::Algorithms::Sort::ByTag... Generating docs for nested compound BamTools::Algorithms::Sort::Unsorted... Generating docs for namespace BamTools::Constants Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... type lookup cache used 1077/65536 hits=2076 misses=1118 symbol lookup cache used 1050/65536 hits=5949 misses=1050 finished... make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_auto_build -Nlibbamtools-doc cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/bamtools-2.5.2+dfsg -B/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/depend make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/depend make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/BamTools_static.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/build make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/build make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 3%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o [ 3%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o [ 3%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o [ 4%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o [ 7%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o [ 7%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp [ 8%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 8%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o [ 10%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o [ 10%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 12%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o [ 12%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o [ 13%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp [ 14%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp [ 16%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o [ 16%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o [ 17%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 18%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o [ 19%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgram.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp [ 21%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o [ 21%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp [ 22%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 23%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 24%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 25%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 26%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 27%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 28%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 29%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 30%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 31%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 32%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 33%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 34%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o [ 35%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 36%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 37%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd 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/usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamPipe_p.cpp [ 39%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 40%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 41%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 42%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 43%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/ByteArray_p.cpp [ 44%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HostAddress_p.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 46%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o [ 46%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 47%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 48%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 50%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 51%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 52%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o [ 53%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 54%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o [ 55%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatPrinter_p.cpp [ 56%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 57%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamHeaderValidator_p.cpp [ 58%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 59%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 60%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 61%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils/BamException_p.cpp [ 62%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -c 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src/CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 65%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o cd 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-I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 68%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 69%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 70%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 71%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 72%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 73%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o -c 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Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamHeaderValidator_p.cpp [ 76%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils/BamException_p.cpp [ 77%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o cd 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CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -lz cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libbamtools.so.2.5.2 libbamtools.so.2.5.2 libbamtools.so make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 78%] Built target BamTools make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory 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81%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o [ 82%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_pileup_engine.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 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src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_options.cpp [ 83%] Linking CXX static library libbamtools.a cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/BamTools_static.dir/cmake_clean_target.cmake cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools_static.dir/link.txt --verbose=1 /usr/bin/ar qc libbamtools.a CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o /usr/bin/ranlib libbamtools.a make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 83%] Built target BamTools_static [ 84%] Linking CXX static library libBamTools-utils.a cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.dir/link.txt --verbose=1 /usr/bin/ar qc libBamTools-utils.a "CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o" /usr/bin/ranlib libBamTools-utils.a make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 84%] Built target BamTools-utils make -f src/CMakeFiles/bamtools_cmd.dir/build.make src/CMakeFiles/bamtools_cmd.dir/depend make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/bamtools_cmd.dir/build.make src/CMakeFiles/bamtools_cmd.dir/build make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 86%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o [ 86%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o [ 87%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_convert.cpp [ 88%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp [ 89%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && 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src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_random.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_revert.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_coverage.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_merge.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_resolve.cpp [ 95%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o [ 95%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o [ 96%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_stats.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_filter.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_header.cpp [ 97%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o [ 98%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_split.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h:15, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:12: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:10: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:15: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:10: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable bamtools cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -o bamtools -Wl,-rpath,/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src: libBamTools-utils.a -L/usr/lib/i386-linux-gnu -ljsoncpp libbamtools.so.2.5.2 make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [100%] Built target bamtools_cmd make[2]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' cd obj-* && ln -s src/toolkit/ bin dh_auto_test --arch cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22 make[2]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j22 UpdateCTestConfiguration from :/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: bamtools_help 1: Test command: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/bamtools "--help" 1: Working Directory: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/tests 1: Test timeout computed to be: 1500 test 2 Start 2: bamtools_stats 2: Test command: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/bamtools "stats" "-in" "/build/reproducible-path/bamtools-2.5.2+dfsg/tests/data/sam_spec_example.bam" 2: Working Directory: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/tests 2: Test timeout computed to be: 1500 1: 1: usage: bamtools [--help] COMMAND [ARGS] 1: 1: Available bamtools commands: 1: convert Converts between BAM and a number of other formats 1: count Prints number of alignments in BAM file(s) 1: coverage Prints coverage statistics from the input BAM file 1: filter Filters BAM file(s) by user-specified criteria 1: header Prints BAM header information 1: index Generates index for BAM file 1: merge Merge multiple BAM files into single file 1: random Select random alignments from existing BAM file(s), intended more as a testing tool. 1: resolve Resolves paired-end reads (marking the IsProperPair flag as needed) 1: revert Removes duplicate marks and restores original base qualities 1: sort Sorts the BAM file according to some criteria 1: split Splits a BAM file on user-specified property, creating a new BAM output file for each value found 1: stats Prints some basic statistics from input BAM file(s) 1: 1: See 'bamtools help COMMAND' for more information on a specific command. 1: 1/2 Test #1: bamtools_help .................... Passed 0.00 sec 2: 2: ********************************************** 2: Stats for BAM file(s): 2: ********************************************** 2: 2: Total reads: 6 2: Mapped reads: 6 (100%) 2: Forward strand: 4 (66.6667%) 2: Reverse strand: 2 (33.3333%) 2: Failed QC: 0 (0%) 2: Duplicates: 0 (0%) 2: Paired-end reads: 2 (33.3333%) 2: 'Proper-pairs': 2 (100%) 2: Both pairs mapped: 2 (100%) 2: Read 1: 1 2: Read 2: 1 2: Singletons: 0 (0%) 2: 2/2 Test #2: bamtools_stats ................... Passed 0.00 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.01 sec make[2]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -Nlibbamtools-doc cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/bamtools-2.5.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/bamtools-2.5.2+dfsg -B/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.so.2.5.2 -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.so -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.a -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools -- Set non-toolchain portion of runtime path of "/build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools" to "" -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/bamtools_api_export.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig/bamtools-1.pc make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_install --arch d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/i386-linux-gnu/pkgconfig \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libbamtools-dev/usr/lib/i386-linux-gnu install -d -m 755 debian/libbamtools2.5.2/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libbamtools.a debian/libbamtools-dev/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libbamtools.so debian/libbamtools-dev/usr/lib/i386-linux-gnu mv /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.so.2.5.2 debian/libbamtools2.5.2/usr/lib/i386-linux-gnu PKGDEV=libbamtools-dev PKGSHL=libbamtools2.5.2 install -d -m 755 debian/libbamtools-dev/usr/include mv debian/tmp/usr/include/bamtools debian/libbamtools-dev/usr/include install -d -m 755 debian/libbamtools-dev/usr/lib/i386-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libbamtools-dev/usr/lib/i386-linux-gnu/pkgconfig make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_install --indep rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bamtools' in '../bamtools_2.5.2+dfsg-6_i386.deb'. dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.5.2+dfsg-6_i386.deb'. dpkg-deb: building package 'libbamtools-dev' in '../libbamtools-dev_2.5.2+dfsg-6_i386.deb'. dpkg-deb: building package 'libbamtools2.5.2' in '../libbamtools2.5.2_2.5.2+dfsg-6_i386.deb'. dpkg-deb: building package 'libbamtools2.5.2-dbgsym' in '../libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_i386.deb'. dpkg-deb: building package 'libbamtools-doc' in '../libbamtools-doc_2.5.2+dfsg-6_all.deb'. dpkg-genbuildinfo --build=binary -O../bamtools_2.5.2+dfsg-6_i386.buildinfo dpkg-genchanges --build=binary -O../bamtools_2.5.2+dfsg-6_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/96601 and its subdirectories I: Current time: Thu Jan 1 01:46:42 -12 2026 I: pbuilder-time-stamp: 1767275202 Fri Nov 29 07:23:44 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos12-i386.debian.net. Fri Nov 29 07:23:44 UTC 2024 I: Preparing to do remote build '2' on ionos12-i386.debian.net. Fri Nov 29 07:25:20 UTC 2024 I: Deleting $TMPDIR on ionos12-i386.debian.net. Fri Nov 29 07:25:21 UTC 2024 I: bamtools_2.5.2+dfsg-6_i386.changes: Format: 1.8 Date: Fri, 12 Jul 2024 13:46:23 +0200 Source: bamtools Binary: bamtools bamtools-dbgsym libbamtools-dev libbamtools-doc libbamtools2.5.2 libbamtools2.5.2-dbgsym Architecture: i386 all Version: 2.5.2+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dynamic library for manipulating BAM (genome alignment) libbamtools2.5.2 - dynamic library for manipulating BAM (genome alignment) files Closes: 1075990 Changes: bamtools (2.5.2+dfsg-6) unstable; urgency=medium . * Fix output data on bigendian architectures (Thanks a lot for the patch from Vladimir Petko !) Closes: #1075990 * Standards-Version: 4.7.0 (routine-update) * Build-Depends: s/pkg-config/pkgconf/ Checksums-Sha1: b58be58e671b65b781bbccbed95311cfcfebec7d 3499432 bamtools-dbgsym_2.5.2+dfsg-6_i386.deb c01fb7ea5134cb60b0d859e4150e24078e016b5a 7947 bamtools_2.5.2+dfsg-6_i386.buildinfo 58bc2709b59f5bf74551365caa047877430231a0 218756 bamtools_2.5.2+dfsg-6_i386.deb 7de5890c27534a05ab955ee5105c86a0067863a8 241784 libbamtools-dev_2.5.2+dfsg-6_i386.deb f9306a30d994e5f269e8a175e05ecb9ca55ba63f 161144 libbamtools-doc_2.5.2+dfsg-6_all.deb 902d6e7c46158b2e27059c703a733a7d039de4ac 2700952 libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_i386.deb 21e005acf38e6d43d0d02555053bef6e8489c3f6 177696 libbamtools2.5.2_2.5.2+dfsg-6_i386.deb Checksums-Sha256: 8822b92226f1c6dab32ad13cbd729aa3e63f6a3de2d75670f1bcda87cfbe3dff 3499432 bamtools-dbgsym_2.5.2+dfsg-6_i386.deb d360d20aa5d715113abec50096b0842cc7b587958ec3b039a8aaad1bf0c5dfe5 7947 bamtools_2.5.2+dfsg-6_i386.buildinfo 4f8f61f87e07601f3a460fe4885606f5dfdcd5250f489284ba64db6200fbe8ab 218756 bamtools_2.5.2+dfsg-6_i386.deb 5e7acff7c43f43d56ca0528c5323c4d9b2e5adec6218ecd7fff433dd8841736b 241784 libbamtools-dev_2.5.2+dfsg-6_i386.deb 192d96bc78fff3165af2b7c4377f2178ba57a1704bbee04443305bdd8eb966c7 161144 libbamtools-doc_2.5.2+dfsg-6_all.deb c856e615ac98366f05e1c773eb37bb526f994b9fd11b94d1de101719314bac38 2700952 libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_i386.deb d1fc42c37c26aca665e129ceae6672500293a5bde59250a0da8d78ec25285115 177696 libbamtools2.5.2_2.5.2+dfsg-6_i386.deb Files: dd3b0a161c71066b1f374cd9f68b32c7 3499432 debug optional bamtools-dbgsym_2.5.2+dfsg-6_i386.deb 659f39abfac84a0232d24cc7f0f8bbca 7947 science optional bamtools_2.5.2+dfsg-6_i386.buildinfo a39bc8b5dc6acefd08ff003297637c2e 218756 science optional bamtools_2.5.2+dfsg-6_i386.deb da49795728e984056281f7f1faff6b72 241784 libdevel optional libbamtools-dev_2.5.2+dfsg-6_i386.deb b1dcbc565d1eb5900a7057ba1431feb5 161144 doc optional libbamtools-doc_2.5.2+dfsg-6_all.deb ee556df2de7680b9d00a6c4c5a34c266 2700952 debug optional libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_i386.deb e94f0ec791f458fbbe8c8ebdc167d6d6 177696 libs optional libbamtools2.5.2_2.5.2+dfsg-6_i386.deb Fri Nov 29 07:25:23 UTC 2024 I: diffoscope 283 will be used to compare the two builds: Running as unit: rb-diffoscope-i386_6-46307.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/bamtools_2.5.2+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/bamtools_2.5.2+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/bamtools_2.5.2+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/b1/bamtools_2.5.2+dfsg-6_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.Plvc46aX/b2/bamtools_2.5.2+dfsg-6_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.430s) 0.430s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.116s) 0.116s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 729ms CPU time consumed: 691ms Fri Nov 29 07:27:59 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 29 07:27:59 UTC 2024 I: bamtools from trixie built successfully and reproducibly on i386. Fri Nov 29 07:28:01 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 29 07:28:01 UTC 2024 I: Submitting 12K b1/bamtools_2.5.2+dfsg-6_i386.buildinfo.asc Fri Nov 29 07:28:11 UTC 2024 I: Submitting 12K b2/bamtools_2.5.2+dfsg-6_i386.buildinfo.asc Fri Nov 29 07:28:24 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 29 07:28:24 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 29 07:28:24 UTC 2024 I: Removing signed bamtools_2.5.2+dfsg-6_i386.buildinfo.asc files: removed './b1/bamtools_2.5.2+dfsg-6_i386.buildinfo.asc' removed './b2/bamtools_2.5.2+dfsg-6_i386.buildinfo.asc'