Tue May 2 20:57:12 UTC 2023 I: starting to build bamtools/bookworm/i386 on jenkins on '2023-05-02 20:56' Tue May 2 20:57:12 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/12854/console.log Tue May 2 20:57:12 UTC 2023 I: Downloading source for bookworm/bamtools=2.5.2+dfsg-4 --2023-05-02 20:57:13-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bamtools/bamtools_2.5.2%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2474 (2.4K) [text/prs.lines.tag] Saving to: ‘bamtools_2.5.2+dfsg-4.dsc’ 0K .. 100% 164M=0s 2023-05-02 20:57:13 (164 MB/s) - ‘bamtools_2.5.2+dfsg-4.dsc’ saved [2474/2474] Tue May 2 20:57:13 UTC 2023 I: bamtools_2.5.2+dfsg-4.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-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 4.6.2 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, pkg-config 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 555c783a9f64b5c3ed8d8522cd7ceecdb0b49948 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Checksums-Sha256: bba4d268cb9457cd836b59c60eac6a9f25e10cd9aea646f03e5deffb82c1c5c1 155732 bamtools_2.5.2+dfsg.orig.tar.xz 03dbebdc47fa8df6f74cc0180ae92ba5fb82a4c68f47057f0cde400c46d0ea09 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Files: a29fafa8a0f930c3029749245032e886 155732 bamtools_2.5.2+dfsg.orig.tar.xz af47d97bec384ea6a5c62b32113efb9c 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Dgit: fee001dee532092f05d7db31157b1fc20e33eec4 debian archive/debian/2.5.2+dfsg-4 https://git.dgit.debian.org/bamtools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOg3ysUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqKMA//WW/p0BGgck2pI5ZBkl85nfntshBJ TmDTHCoBthP/9FdimOTfmdmyiOYf8jcHubyR+9+2xOYne450K6sesnVn/GhdUdLj t9Vytli7g/u0+47ua+43ybfyyMtlnEJWXvCR4bmSgVAUjoQsEmTlWGLjwkZXDqcy 34IPRhV3rucZp5tfB/i9Y/CBkjov9IECOs1ehRFo8RGMoxq5GDlvvnrtmT+HrHFB MciXGcgPioxJ50eWYFvMhJ/pNfI37PASAmMkeV07BYNl4JMM/RomxrN3pFbeiqYG YN+Tz94qURvwvSBqBizw7DfzGaQSxU3USe8F0s/VgDi2xERn1vHDcPGUAjXaUX0I wQxaKFcIJ7qTZPCeWKrKko0PFwMkNZmmnCO1fHQSvuIgfK/21i2BX42bN3xlQ19k bcRbyuGGmkI39lk3ujqGehyynw2jWycT50Ez9SmJznmpsOXzLNHg3PjMgJ00A6AX 1ueGBDjloSbz/4KzIpzF9YJxULx/bBh+51qgDd5++5QLb4biIE5rNdiw1kmQEo+8 LFve7mG+vZNum+DwPaOGK4+/n0QA3HSdz/f4xXXa4fOBfAhVOdRL/nizGgI0xGj7 WRTHWtgOVcHyKupX+h75/vrsD+dQCzZAt0mUc8FrtupkFMY2PY8k6PD+dHUDJwr5 m5aZ+b2W7i23djo= =MYt6 -----END PGP SIGNATURE----- Tue May 2 20:57:13 UTC 2023 I: Checking whether the package is not for us Tue May 2 20:57:13 UTC 2023 I: Starting 1st build on remote node ionos6-i386.debian.net. Tue May 2 20:57:13 UTC 2023 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Tue May 2 20:59:33 UTC 2023 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 3 15:20:17 -12 2024 I: pbuilder-time-stamp: 1717471217 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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-4.dsc] I: copying [./bamtools_2.5.2+dfsg.orig.tar.xz] I: copying [./bamtools_2.5.2+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 19 10:01:15 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bamtools_2.5.2+dfsg-4.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-4.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 I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/40825/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='43632604ee014e1690e68435958cddb0' 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='40825' 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.OqGH3fu3/pbuilderrc_w1vx --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OqGH3fu3/b1 --logfile b1/build.log bamtools_2.5.2+dfsg-4.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos6-i386 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 22 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 22 2023 more -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 22 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/40825/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, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 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 pkg-config; however: Package pkg-config 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} libarchive13{a} libbrotli1{a} libbsd0{a} libclang-cpp14{a} libclang1-14{a} libcurl4{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{a} libldap-2.5-0{a} libllvm14{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libz3-4{a} m4{a} man-db{a} pkg-config{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 92.8 MB of archives. After unpacking 388 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 liblocale-gettext-perl i386 1.07-5 [15.5 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-9 [420 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 d-shlibs all 0.104 [18.6 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 43 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 45 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libz3-4 i386 4.8.12-3.1 [7853 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libllvm14 i386 1:14.0.6-12 [25.0 MB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libclang-cpp14 i386 1:14.0.6-12 [12.7 MB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libclang1-14 i386 1:14.0.6-12 [7086 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 doxygen i386 1.9.4-4 [4836 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 help2man i386 1.49.3 [198 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libjsoncpp-dev i386 1.9.5-4 [26.4 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Fetched 92.8 MB in 2s (42.2 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 ... 19604 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_i386.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_i386.deb ... 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Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../22-libsasl2-modules-db_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../23-libsasl2-2_2.1.28+dfsg-10_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../24-libldap-2.5-0_2.5.13+dfsg-5_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../25-libnghttp2-14_1.52.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.52.0-1) ... Selecting previously unselected package libpsl5:i386. Preparing to unpack .../26-libpsl5_0.21.2-1_i386.deb ... Unpacking libpsl5:i386 (0.21.2-1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../27-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:i386. Preparing to unpack .../28-libssh2-1_1.10.0-3+b1_i386.deb ... Unpacking libssh2-1:i386 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:i386. Preparing to unpack .../29-libcurl4_7.88.1-9_i386.deb ... Unpacking libcurl4:i386 (7.88.1-9) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../30-libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:i386. Preparing to unpack .../31-libjsoncpp25_1.9.5-4_i386.deb ... Unpacking libjsoncpp25:i386 (1.9.5-4) ... Selecting previously unselected package librhash0:i386. Preparing to unpack .../32-librhash0_1.4.3-3_i386.deb ... Unpacking librhash0:i386 (1.4.3-3) ... Selecting previously unselected package libuv1:i386. Preparing to unpack .../33-libuv1_1.44.2-1_i386.deb ... Unpacking libuv1:i386 (1.44.2-1) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:i386 (1.0.9-2+b6) ... Setting up libnghttp2-14:i386 (1.52.0-1) ... Setting up libmagic1:i386 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:i386 (4.8.12-3.1) ... Setting up libpkgconf3:i386 (1.8.1-1) ... Setting up libuv1:i386 (1.44.2-1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:i386 (2:4.0.2-3) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:i386 (1.9.5-4) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:i386 (1.4.3-3) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:i386 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libxml2:i386 (2.9.14+dfsg-1.2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libjsoncpp-dev:i386 (1.9.5-4) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:i386 (3.6.2-1) ... Setting up libedit2:i386 (3.1-20221030-2) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up pkgconf:i386 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:i386 (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libllvm14:i386 (1:14.0.6-12) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:i386 (7.88.1-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libclang1-14 (1:14.0.6-12) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp14 (1:14.0.6-12) ... Setting up cmake (3.25.1-1) ... Setting up debhelper (13.11.4) ... Setting up doxygen (1.9.4-4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/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-4_source.changes dpkg-buildpackage: info: source package bamtools dpkg-buildpackage: info: source version 2.5.2+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && 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 .. -- The CXX compiler identification is GNU 12.2.0 -- 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 "1.2.13") -- 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 -- Generating done 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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' 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 files to exclude Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/bam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/index Searching INPUT for files to process... Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/algorithms Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/bam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/index Reading and parsing tag files Parsing files Preprocessing /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/api_global.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/api_global.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAux.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAux.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamReader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamReader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Preprocessing /build/bamtools-2.5.2+d/build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:25: warning: Documentation for undefined enum 'MergeOrder' found. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:187: warning: documented symbol 'bool BamTools::AddTag' was not declared or defined. /build/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/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/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/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/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:559: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. fsg/src/api/SamProgramChain.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Parsing file /build/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... 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... 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 namespace index... 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 module 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... lookup cache used 1133/65536 hits=3617 misses=1174 finished... make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' dh_auto_build -Nlibbamtools-doc cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/bamtools-2.5.2+dfsg -B/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/CMakeFiles /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' cd /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' cd /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/BamTools_static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/build make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o [ 2%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 3%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp [ 4%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o [ 5%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 6%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 7%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o [ 8%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o [ 9%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 10%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o [ 11%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp [ 12%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp [ 13%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 14%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 15%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o [ 16%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/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++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 19%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/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++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 21%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 22%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 23%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 24%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 25%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 26%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 27%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 28%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 29%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 30%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 31%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 32%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 33%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 34%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/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++/12/string:48, from /usr/include/c++/12/stdexcept:39, from /build/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/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++/12/string:48, from /usr/include/c++/12/stdexcept:39, from /build/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/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++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 35%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 36%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 37%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 38%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 39%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 40%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 41%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 42%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 43%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o cd 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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/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 46%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/ByteArray_p.cpp [ 47%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostAddress_p.cpp [ 48%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 50%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 51%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -MF 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src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 54%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE 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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/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 57%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 58%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 59%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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 /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 60%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 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CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 68%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 69%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 70%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 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CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 73%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 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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 /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 78%] Linking CXX static library libbamtools.a cd /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/BamTools_static.dir/cmake_clean_target.cmake cd /build/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 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CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -lz cd /build/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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [ 79%] Built target BamTools make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' cd /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/CMakeFiles/BamTools-utils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make -f src/CMakeFiles/BamTools-utils.dir/build.make 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_revert.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp [ 97%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o [ 98%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_split.cpp cd /build/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/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_stats.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h:15, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:12: /build/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++/12/string:48, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.h:13, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:15: /build/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++/12/string:48, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.h:13, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable bamtools cd /build/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/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/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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' [100%] Built target bamtools_cmd make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' cd obj-* && ln -s src/toolkit/ bin dh_auto_test --arch cd obj-i686-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/bamtools "--help" 1: Working Directory: /build/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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu/src/bamtools "stats" "-in" "/build/bamtools-2.5.2+dfsg/tests/data/sam_spec_example.bam" 2: Working Directory: /build/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 0.02 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 0.03 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.04 sec make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -Nlibbamtools-doc cd obj-i686-linux-gnu && make -j16 install DESTDIR=/build/bamtools-2.5.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/bamtools-2.5.2+dfsg -B/build/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/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.so.2.5.2 -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.so -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libbamtools.a -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools -- Set runtime path of "/build/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools" to "" -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/bamtools_api_export.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/i386-linux-gnu/pkgconfig/bamtools-1.pc make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/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/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/bamtools-2.5.2+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/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/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 'libbamtools-dev' in '../libbamtools-dev_2.5.2+dfsg-4_i386.deb'. dpkg-deb: building package 'libbamtools-doc' in '../libbamtools-doc_2.5.2+dfsg-4_all.deb'. dpkg-deb: building package 'bamtools' in '../bamtools_2.5.2+dfsg-4_i386.deb'. dpkg-deb: building package 'libbamtools2.5.2' in '../libbamtools2.5.2_2.5.2+dfsg-4_i386.deb'. dpkg-deb: building package 'libbamtools2.5.2-dbgsym' in '../libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_i386.deb'. dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.5.2+dfsg-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../bamtools_2.5.2+dfsg-4_i386.buildinfo dpkg-genchanges --build=binary -O../bamtools_2.5.2+dfsg-4_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/40825 and its subdirectories I: Current time: Mon Jun 3 15:22:31 -12 2024 I: pbuilder-time-stamp: 1717471351 Tue May 2 20:59:33 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Tue May 2 20:59:33 UTC 2023 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Tue May 2 21:07:18 UTC 2023 I: Deleting $TMPDIR on ionos2-i386.debian.net. Tue May 2 21:07:19 UTC 2023 I: bamtools_2.5.2+dfsg-4_i386.changes: Format: 1.8 Date: Mon, 19 Dec 2022 22:45:16 +0100 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-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier 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: 988848 Changes: bamtools (2.5.2+dfsg-4) unstable; urgency=medium . * Team upload. * d/control: libbamtools-doc depends on libjs-jquery. Thanks to Andreas Beckmann (Closes: #988848) * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: f2379895a4742176d2a1a4604e9e8b41a7379f65 3624864 bamtools-dbgsym_2.5.2+dfsg-4_i386.deb 2fddcddb4dfd180dbf37fdf3929332b8e313e07e 7758 bamtools_2.5.2+dfsg-4_i386.buildinfo 35264aff81f5c1567cad8855fbfa0acb0410a886 207004 bamtools_2.5.2+dfsg-4_i386.deb 53be34a0ddfb66b690621b1233637918073b6448 232916 libbamtools-dev_2.5.2+dfsg-4_i386.deb e56466023933d7854010c5bf0f5fb74417156b96 160752 libbamtools-doc_2.5.2+dfsg-4_all.deb 62d8363d04d7dd695c03655df65b86aefc7031b4 2754684 libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_i386.deb bb7f5fcda93bcfc7a48a3fd44a3ad7d0c69d463b 164744 libbamtools2.5.2_2.5.2+dfsg-4_i386.deb Checksums-Sha256: 8825de922e52a20a73a88f03628a922a67283f7dcd36fe05c1cbbc16857d647f 3624864 bamtools-dbgsym_2.5.2+dfsg-4_i386.deb 286d298ca4c613ac3c8547337c522fc6f08b0f2390b0424012cf726f57a7270a 7758 bamtools_2.5.2+dfsg-4_i386.buildinfo e0a6285bb3ab356fb77a162680a9f48d29c49700df5527ab41a098f562c6f91b 207004 bamtools_2.5.2+dfsg-4_i386.deb 7a55284542e5c613ca83f26999d0526adc9aaa4146eec5b8ce4b9a697fe204fb 232916 libbamtools-dev_2.5.2+dfsg-4_i386.deb ba25a3543338262fe9722acb5ed17fb6fe3f5635c0ebf8cf29138e0c864b54af 160752 libbamtools-doc_2.5.2+dfsg-4_all.deb c9740a7c167196c96575e3b117802990d2e56332573bfd7dfed3baad91fe49e3 2754684 libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_i386.deb dbb22bd0426ce0f4d9bb9c77b3dab0891670d8c8f06363569dbff2c434bfe3e5 164744 libbamtools2.5.2_2.5.2+dfsg-4_i386.deb Files: 67804178da75fb626a18932af688a710 3624864 debug optional bamtools-dbgsym_2.5.2+dfsg-4_i386.deb 4142f87abc8c7232f841af16e0c8a78c 7758 science optional bamtools_2.5.2+dfsg-4_i386.buildinfo e27750e0efec2f72fe1764158cc02af5 207004 science optional bamtools_2.5.2+dfsg-4_i386.deb 3595fa751c673c9b630c09f699462726 232916 libdevel optional libbamtools-dev_2.5.2+dfsg-4_i386.deb 5b204fe0fceccbf208e3830fd8b00f37 160752 doc optional libbamtools-doc_2.5.2+dfsg-4_all.deb bca11ef7ad434e2ab7f74450c889c02d 2754684 debug optional libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_i386.deb f13519431c3c5647fbf858fbc1603d76 164744 libs optional libbamtools2.5.2_2.5.2+dfsg-4_i386.deb Tue May 2 21:07:20 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.OqGH3fu3/bamtools_2.5.2+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.OqGH3fu3/bamtools_2.5.2+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.OqGH3fu3/bamtools_2.5.2+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.OqGH3fu3/b1/bamtools_2.5.2+dfsg-4_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.OqGH3fu3/b2/bamtools_2.5.2+dfsg-4_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: 0.439s) 0.439s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.109s) 0.109s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Tue May 2 21:07:21 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Tue May 2 21:07:21 UTC 2023 I: bamtools from bookworm built successfully and reproducibly on i386. Tue May 2 21:07:23 UTC 2023 I: Submitting .buildinfo files to external archives: Tue May 2 21:07:23 UTC 2023 I: Submitting 12K b1/bamtools_2.5.2+dfsg-4_i386.buildinfo.asc Tue May 2 21:07:24 UTC 2023 I: Submitting 12K b2/bamtools_2.5.2+dfsg-4_i386.buildinfo.asc Tue May 2 21:07:25 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 2 21:07:25 UTC 2023 I: Done submitting .buildinfo files. Tue May 2 21:07:25 UTC 2023 I: Removing signed bamtools_2.5.2+dfsg-4_i386.buildinfo.asc files: removed './b1/bamtools_2.5.2+dfsg-4_i386.buildinfo.asc' removed './b2/bamtools_2.5.2+dfsg-4_i386.buildinfo.asc'