Sat Dec 25 21:15:04 UTC 2021 I: starting to build bamtools/bullseye/amd64 on jenkins on '2021-12-25 21:14' Sat Dec 25 21:15:04 UTC 2021 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/93555/console.log Sat Dec 25 21:15:04 UTC 2021 I: Downloading source for bullseye/bamtools=2.5.1+dfsg-9 --2021-12-25 21:15:04-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bamtools/bamtools_2.5.1%2bdfsg-9.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2388 (2.3K) Saving to: ‘bamtools_2.5.1+dfsg-9.dsc’ 0K .. 100% 103M=0s 2021-12-25 21:15:04 (103 MB/s) - ‘bamtools_2.5.1+dfsg-9.dsc’ saved [2388/2388] Sat Dec 25 21:15:04 UTC 2021 I: bamtools_2.5.1+dfsg-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bamtools Binary: bamtools, libbamtools-dev, libbamtools2.5.1, libbamtools-doc Architecture: any all Version: 2.5.1+dfsg-9 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Dominique Belhachemi Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 4.5.1 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 Package-List: bamtools deb science optional arch=any libbamtools-dev deb libdevel optional arch=any libbamtools-doc deb doc optional arch=all libbamtools2.5.1 deb libs optional arch=any Checksums-Sha1: 0274c3250223060da999b74bb3804aad7f62da7e 196644 bamtools_2.5.1+dfsg.orig.tar.gz adbc2defafd41498f4703a89b5604c169739f215 11848 bamtools_2.5.1+dfsg-9.debian.tar.xz Checksums-Sha256: 034873ddc9cbe557af9f081893083c361aff55e079448b22d856a667c50110ef 196644 bamtools_2.5.1+dfsg.orig.tar.gz 09aa1cf457ec64c4a7be912d1692d52e2a0a23a9c03569229ef20e6d89f9d0b6 11848 bamtools_2.5.1+dfsg-9.debian.tar.xz Files: 012e7ec1a1c9bc44b62794ba9c855de0 196644 bamtools_2.5.1+dfsg.orig.tar.gz aeaa4c253ae8060308b3df8bf0788b2b 11848 bamtools_2.5.1+dfsg-9.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmB4mRIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGCMBAAi95gvSr5LSi4fIbnTHsvkKidL8DxWt2+ Ny0eNNMNE8rw0HnN4yoQAzOlkMJSqkh/+QVM0Gt5NnjHCLCrfXHvRlINyjwe/gI3 i3xwzpds6j7MlqRCLubOad+1t0RZCybqbz/ljALKCUe7AU83LrPMKL2z9GdwMdnP eEUM0/XRbv/g0ThV3WTonuZu5YOIhrY8+MZ2qLaKYM7agf/dnbzE/QmLfmvpPP7Y owPd2dAt39Ga1nuAMmqotVmUrBnd+3gusSX4W8pVvRvzPU420V7vncONJcbSS82w Nbp9xfHii844xAqwMgeKPDysN8t5vcNca0KAoE4evKxJgXKUm6yJkDEXKeFouU/F q79C1EPrXu5f78VsI9b6X30yfErR594rxv5huqDV/5xQD1Dog07Y/eA6PE9FB4oN BEwE8LDayfY1lW4gPKQuI92lUeLKckBZLy5Qx/wZ3Cr4b25M2QlunpJ08fiVJDg2 JNlHGfGRhj4UP1V9aiTvp5cIyWHIyWgxb6P4uhl6mWYCqdD566OgNp1tEd6h54PV iaqMD6JhvX8bjS9wnrR5GHZAbPgoeZL1aZ+mpXcU0lXbAMyGZM1gmNHK9B5/e4fv 6mzmyMlDnW0h1P6sDWBdk8rHZASY6mcJWngH4uadU+Id7oRJSmZov4EbQ4y0q+lX k5v8Zd1rK3I= =b58F -----END PGP SIGNATURE----- Sat Dec 25 21:15:04 UTC 2021 I: Checking whether the package is not for us Sat Dec 25 21:15:04 UTC 2021 I: Starting 1st build on remote node ionos15-amd64.debian.net. Sat Dec 25 21:15:04 UTC 2021 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Sat Dec 25 21:16:59 UTC 2021 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Jan 27 15:38:12 -12 2023 I: pbuilder-time-stamp: 1674877092 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bamtools_2.5.1+dfsg-9.dsc] I: copying [./bamtools_2.5.1+dfsg.orig.tar.gz] I: copying [./bamtools_2.5.1+dfsg-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.3_G2D0Hq/trustedkeys.kbx': General error gpgv: Signature made Thu Apr 15 07:50:42 2021 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./bamtools_2.5.1+dfsg-9.dsc dpkg-source: info: extracting bamtools in bamtools-2.5.1+dfsg dpkg-source: info: unpacking bamtools_2.5.1+dfsg.orig.tar.gz dpkg-source: info: unpacking bamtools_2.5.1+dfsg-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying doxygen-tweak dpkg-source: info: applying 0001-ignore-thirdparty-and-fix-jsoncpp.patch dpkg-source: info: applying 0003-remove-custom-ExportHeader-function-use-install-inst.patch dpkg-source: info: applying 0006-Doxygen-reproducibility dpkg-source: info: applying 0008_Cmake_Test.patch dpkg-source: info: applying spelling dpkg-source: info: applying tiddit.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/469913/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=16' DISTRIBUTION='' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='dc814580e42c4a8dbc6f080198474e71' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='469913' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/pbuilderrc_nMFd --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/b1 --logfile b1/build.log bamtools_2.5.1+dfsg-9.dsc' SUDO_GID='111' SUDO_UID='106' 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 ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 23 2020 date -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd -rwxr-xr-x 1 root root 93936 Sep 23 2020 df -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep -rwxr-xr-x 1 root root 39680 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 59632 Jul 28 2021 more -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty -rwsr-xr-x 1 root root 71912 Jul 28 2021 su -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch -rwxr-xr-x 1 root root 39680 Sep 23 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew I: user script /srv/workspace/pbuilder/469913/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19655 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. 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-cpp11{a} libclang1-11{a} libcurl4{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libjsoncpp-dev{a} libjsoncpp24{a} libldap-2.4-2{a} libllvm11{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libprocps8{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libz3-4{a} m4{a} man-db{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 libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 73.4 MB of archives. After unpacking 307 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 liblocale-gettext-perl amd64 1.07-4+b1 [19.0 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 cmake-data all 3.18.4-2+deb11u1 [1725 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7 [693 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libarchive13 amd64 3.4.3-2+b1 [343 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u1 [341 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp24 amd64 1.9.4-4 [78.9 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 librhash0 amd64 1.4.1-2 [129 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libuv1 amd64 1.40.0-2 [132 kB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 cmake amd64 3.18.4-2+deb11u1 [5593 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 d-shlibs all 0.98 [17.9 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 46 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 47 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 48 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 49 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 50 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 51 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 53 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 54 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get: 55 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 56 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 57 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 58 http://deb.debian.org/debian bullseye/main amd64 libclang-cpp11 amd64 1:11.0.1-2 [9632 kB] Get: 59 http://deb.debian.org/debian bullseye/main amd64 libclang1-11 amd64 1:11.0.1-2 [5521 kB] Get: 60 http://deb.debian.org/debian bullseye/main amd64 doxygen amd64 1.9.1-1 [4232 kB] Get: 61 http://deb.debian.org/debian bullseye/main amd64 help2man amd64 1.48.1 [190 kB] Get: 62 http://deb.debian.org/debian bullseye/main amd64 libjsoncpp-dev amd64 1.9.4-4 [25.4 kB] Get: 63 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Fetched 73.4 MB in 1s (71.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19655 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8_amd64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../05-liblocale-gettext-perl_1.07-4+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../06-libncurses6_6.2+20201114-2_amd64.deb ... Unpacking libncurses6:amd64 (6.2+20201114-2) ... Selecting previously unselected package libprocps8:amd64. Preparing to unpack .../07-libprocps8_2%3a3.3.17-5_amd64.deb ... Unpacking libprocps8:amd64 (2:3.3.17-5) ... Selecting previously unselected package procps. Preparing to unpack .../08-procps_2%3a3.3.17-5_amd64.deb ... Unpacking procps (2:3.3.17-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../09-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../10-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../11-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../12-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../13-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../14-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. 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Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up bsdextrautils (2.36.1-8) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libz3-4:amd64 (4.8.10-1) ... Setting up libuv1:amd64 (1.40.0-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up d-shlibs (0.98) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up libjsoncpp24:amd64 (1.9.4-4) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up librhash0:amd64 (1.4.1-2) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up cmake-data (3.18.4-2+deb11u1) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libprocps8:amd64 (2:3.3.17-5) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up libjsoncpp-dev:amd64 (1.9.4-4) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libarchive13:amd64 (3.4.3-2+b1) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libclang1-11 (1:11.0.1-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u1) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp11 (1:11.0.1-2) ... Setting up dh-autoreconf (20) ... Setting up doxygen (1.9.1-1) ... Setting up cmake (3.18.4-2+deb11u1) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u2) ... 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-2.5.1+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_2.5.1+dfsg-9_source.changes dpkg-buildpackage: info: source package bamtools dpkg-buildpackage: info: source version 2.5.1+dfsg-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 10.2.1 -- 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 CMake Deprecation Warning at CMakeLists.txt:22 (cmake_policy): The OLD behavior for policy CMP0042 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Checking for one of the modules 'jsoncpp>=1' Did NOT find system JsonCpp, instead using bundled version -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY -- Build files have been written to: /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/bamtools-2.5.1+dfsg' doxygen -u docs/Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 300 of file 'docs/Doxyfile' has become obsolete. 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Configuration file 'docs/Doxyfile' updated. doxygen docs/Doxyfile warning: argument 'a4wide' for option PAPER_TYPE is not a valid enum value Using the default: a4! Doxygen version used: 1.9.1 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/bam Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/index Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/utils Searching INPUT for files to process... Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/algorithms Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/bam Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/index Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.1+dfsg/src/api/internal/utils Reading and parsing tag files Parsing files Preprocessing /build/bamtools-2.5.1+dfsg/src/api/algorithms/Sort.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/algorithms/Sort.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/api_global.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/api_global.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamAlgorithms.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamAlgorithms.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamAux.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamAux.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamConstants.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamConstants.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamIndex.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamIndex.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamReader.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamReader.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamReader.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamReader.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamWriter.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamWriter.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/BamWriter.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/BamWriter.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/IBamIODevice.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/IBamIODevice.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamConstants.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamConstants.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamHeader.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamHeader.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamHeader.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamHeader.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamProgram.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamProgram.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamProgram.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamProgram.h... Preprocessing /build/bamtools-2.5.1+d/build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.cpp:25: warning: Documentation for undefined enum 'MergeOrder' found. /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h:188: warning: documented symbol 'bool BamTools::AddTag' was not declared or defined. /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h:304: warning: documented symbol 'template< typename T > bool BamTools::AddTag' was not declared or defined. /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h:369: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h:395: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h:418: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.h:543: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. fsg/src/api/SamProgramChain.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamProgramChain.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamProgramChain.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamProgramChain.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamReadGroup.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamReadGroup.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamReadGroup.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamReadGroup.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamReadGroupDictionary.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamReadGroupDictionary.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamReadGroupDictionary.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamReadGroupDictionary.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamSequence.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamSequence.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamSequence.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamSequence.h... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamSequenceDictionary.cpp... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamSequenceDictionary.cpp... Preprocessing /build/bamtools-2.5.1+dfsg/src/api/SamSequenceDictionary.h... Parsing file /build/bamtools-2.5.1+dfsg/src/api/SamSequenceDictionary.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Computing nesting relations for classes... Associating documentation with classes... 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 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 code for file Sort.h... Generating file documentation... 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 docs for file Sort.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating namespace index... Generating docs for namespace BamTools Generating docs for compound BamTools::BamAlignment... Generating docs for compound BamTools::CigarOp... Generating docs for compound BamTools::RefData... Generating docs for compound BamTools::BamRegion... Generating docs for compound BamTools::CustomHeaderTag... Generating docs for compound BamTools::BamIndex... Generating docs for compound BamTools::BamMultiReader... Generating docs for compound BamTools::BamReader... Generating docs for compound BamTools::BamWriter... Generating docs for compound BamTools::IBamIODevice... 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 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 1173/65536 hits=4513 misses=1214 finished... mv docs/Doxyfile.bak docs/Doxyfile make[1]: Leaving directory '/build/bamtools-2.5.1+dfsg' dh_auto_build -Nlibbamtools-doc cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/bamtools-2.5.1+dfsg -B/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' make -f src/api/CMakeFiles/BamTools_static.dir/build.make src/api/CMakeFiles/BamTools_static.dir/depend make[3]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/depend cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.1+dfsg /build/bamtools-2.5.1+dfsg/src/api /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools_static.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.1+dfsg /build/bamtools-2.5.1+dfsg/src/api /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake --color= Dependee "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools_static.dir/DependInfo.cmake" is newer than depender "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools_static.dir/depend.internal". Dependee "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools_static.dir/depend.internal". Dependee "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools.dir/DependInfo.cmake" is newer than depender "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools.dir/depend.internal". Dependee "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api/CMakeFiles/BamTools.dir/depend.internal". Scanning dependencies of target BamTools_static make[3]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' make -f src/api/CMakeFiles/BamTools_static.dir/build.make src/api/CMakeFiles/BamTools_static.dir/build make[3]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' Scanning dependencies of target BamTools make[3]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' [ 1%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/BamAlignment.cpp.o make -f src/api/CMakeFiles/BamTools.dir/build.make src/api/CMakeFiles/BamTools.dir/build make[3]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/BamAlignment.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.cpp [ 2%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/BamMultiReader.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/BamMultiReader.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.cpp [ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamAlignment.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/BamAlignment.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamAlignment.cpp [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamMultiReader.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/BamMultiReader.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamMultiReader.cpp [ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamReader.cpp.o [ 6%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/BamReader.cpp.o [ 7%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/BamWriter.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/BamReader.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamReader.cpp cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/BamReader.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamReader.cpp [ 8%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamHeader.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/BamWriter.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamWriter.cpp cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamHeader.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamHeader.cpp [ 9%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamProgram.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamProgram.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamProgram.cpp [ 10%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o [ 11%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/BamWriter.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/BamWriter.cpp [ 12%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamHeader.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamHeader.cpp [ 13%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamProgram.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamProgram.cpp [ 14%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o [ 15%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamProgramChain.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamProgramChain.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamProgramChain.cpp cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamProgramChain.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamProgramChain.cpp cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamReadGroup.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamReadGroup.cpp [ 16%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamReadGroup.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamReadGroup.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamReadGroup.cpp [ 17%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamReadGroupDictionary.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamReadGroupDictionary.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamReadGroupDictionary.cpp [ 18%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamSequence.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamSequence.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamSequence.cpp [ 19%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamReadGroupDictionary.cpp [ 20%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequence.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamSequence.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamSequence.cpp [ 21%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/SamSequenceDictionary.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/SamSequenceDictionary.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamSequenceDictionary.cpp [ 22%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/SamSequenceDictionary.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/SamSequenceDictionary.cpp [ 23%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/bam/BamHeader_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 24%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/bam/BamHeader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/bam/BamHeader_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 25%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/bam/BamMultiReader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 26%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/bam/BamMultiReader_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 27%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 28%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 29%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/bam/BamReader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat 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-D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/bam/BamWriter_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 33%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/index/BamIndexFactory_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 35%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/index/BamStandardIndex_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/index/BamStandardIndex_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY 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/build/bamtools-2.5.1+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 38%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/BamDeviceFactory_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/BamDeviceFactory_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 39%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/BamFile_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamFile_p.cpp cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/BamFtp_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamFtp_p.cpp [ 44%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/BamHttp_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/BamHttp_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamHttp_p.cpp [ 45%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamFtp_p.cpp [ 46%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamHttp_p.cpp [ 47%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/BamPipe_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/BamPipe_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamPipe_p.cpp [ 48%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BamPipe_p.cpp [ 50%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/BgzfStream_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/BgzfStream_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 51%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 52%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/ByteArray_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/ByteArray_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/ByteArray_p.cpp [ 53%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/ByteArray_p.cpp [ 54%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/HostAddress_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/HostAddress_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp [ 55%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp: In member function 'void BamTools::Internal::HostAddress::Clear()': /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp:273:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess] 273 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); | ^ In file included from /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp:10: /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.h:31:8: note: 'struct BamTools::Internal::IPv6Address' declared here 31 | struct IPv6Address | ^~~~~~~~~~~ [ 56%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/HostInfo_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/HostInfo_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostInfo_p.cpp [ 57%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/HttpHeader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/HttpHeader_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/HttpHeader_p.cpp /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp: In member function 'void BamTools::Internal::HostAddress::Clear()': /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp:273:49: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'struct BamTools::Internal::IPv6Address'; use assignment or value-initialization instead [-Wclass-memaccess] 273 | memset(&m_ip6Address, 0, sizeof(IPv6Address)); | ^ In file included from /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.cpp:10: /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostAddress_p.h:31:8: note: 'struct BamTools::Internal::IPv6Address' declared here 31 | struct IPv6Address | ^~~~~~~~~~~ [ 58%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/HostInfo_p.cpp [ 59%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 60%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 61%] Building CXX object src/api/CMakeFiles/BamTools_static.dir/internal/io/ILocalIODevice_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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src/api/CMakeFiles/BamTools_static.dir/internal/io/TcpSocketEngine_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/BamTools_static.dir/internal/io/TcpSocketEngine_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 66%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/bamtools-2.5.1+dfsg/src/api/internal/sam/SamFormatPrinter_p.cpp [ 75%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o -c /build/bamtools-2.5.1+dfsg/src/api/internal/sam/SamHeaderValidator_p.cpp [ 76%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/c++ -DBAMTOOLS_API_LIBRARY -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -g 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CMakeFiles/BamTools.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o -lz [ 79%] Linking CXX static library libbamtools.a cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/cmake -P CMakeFiles/BamTools_static.dir/cmake_clean_target.cmake cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /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/BamAlignment.cpp.o CMakeFiles/BamTools_static.dir/BamMultiReader.cpp.o CMakeFiles/BamTools_static.dir/BamReader.cpp.o CMakeFiles/BamTools_static.dir/BamWriter.cpp.o CMakeFiles/BamTools_static.dir/SamHeader.cpp.o CMakeFiles/BamTools_static.dir/SamProgram.cpp.o CMakeFiles/BamTools_static.dir/SamProgramChain.cpp.o CMakeFiles/BamTools_static.dir/SamReadGroup.cpp.o CMakeFiles/BamTools_static.dir/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools_static.dir/SamSequence.cpp.o CMakeFiles/BamTools_static.dir/SamSequenceDictionary.cpp.o CMakeFiles/BamTools_static.dir/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools_static.dir/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools_static.dir/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools_static.dir/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools_static.dir/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools_static.dir/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools_static.dir/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools_static.dir/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools_static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o CMakeFiles/BamTools_static.dir/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools_static.dir/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools_static.dir/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools_static.dir/internal/utils/BamException_p.cpp.o /usr/bin/ranlib libbamtools.a make[3]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' [ 79%] Built target BamTools_static cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api && /usr/bin/cmake -E cmake_symlink_library libbamtools.so.2.5.1 libbamtools.so.2.5.1 libbamtools.so make[3]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' [ 79%] Built target BamTools make -f src/utils/CMakeFiles/BamTools-utils.dir/build.make src/utils/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.1+dfsg 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src/toolkit/CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -I/build/bamtools-2.5.1+dfsg/src/api -I/build/bamtools-2.5.1+dfsg/src/utils -I/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/toolkit -I/build/bamtools-2.5.1+dfsg/src/third_party/jsoncpp -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o -c /build/bamtools-2.5.1+dfsg/src/toolkit/bamtools_revert.cpp cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/toolkit && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -I/build/bamtools-2.5.1+dfsg/src/api -I/build/bamtools-2.5.1+dfsg/src/utils 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-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.1+dfsg/src -I/build/bamtools-2.5.1+dfsg/src/api -I/build/bamtools-2.5.1+dfsg/src/utils -I/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/toolkit -I/build/bamtools-2.5.1+dfsg/src/third_party/jsoncpp -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -c /build/bamtools-2.5.1+dfsg/src/toolkit/bamtools.cpp [100%] Linking CXX executable bamtools cd /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/toolkit && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/bamtools-2.5.1+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/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools_stats.cpp.o CMakeFiles/bamtools_cmd.dir/bamtools.cpp.o -o bamtools -Wl,-rpath,/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/src/api: ../utils/libbamtools-utils.a -ljsoncpp ../api/libbamtools.so.2.5.1 make[3]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' [100%] Built target bamtools_cmd make[2]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/bamtools-2.5.1+dfsg' cd obj-* && ln -s src/toolkit/ bin dh_auto_test --arch cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=-j16 make[2]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process -j16 Test project /build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu Start 1: bamtools_help Start 2: bamtools_stats 1/2 Test #1: bamtools_help .................... Passed 0.01 sec 2/2 Test #2: bamtools_stats ................... Passed 0.01 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.01 sec make[2]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/bamtools-2.5.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -Nlibbamtools-doc cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/bamtools-2.5.1\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/bamtools-2.5.1+dfsg -B/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/bamtools-1.pc -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libbamtools.so.2.5.1 -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libbamtools.so -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libbamtools.a -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /build/bamtools-2.5.1+dfsg/debian/tmp/usr/bin/bamtools -- Set runtime path of "/build/bamtools-2.5.1+dfsg/debian/tmp/usr/bin/bamtools" to "" make[1]: Leaving directory '/build/bamtools-2.5.1+dfsg/obj-x86_64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/bamtools-2.5.1+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/x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libbamtools2.5.1/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libbamtools.a debian/libbamtools-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libbamtools.so debian/libbamtools-dev/usr/lib/x86_64-linux-gnu mv /build/bamtools-2.5.1+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/libbamtools.so.2.5.1 debian/libbamtools2.5.1/usr/lib/x86_64-linux-gnu PKGDEV=libbamtools-dev PKGSHL=libbamtools2.5.1 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/x86_64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libbamtools-dev/usr/lib/x86_64-linux-gnu/pkgconfig make[1]: Leaving directory '/build/bamtools-2.5.1+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/bamtools-2.5.1+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-2.5.1+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_lintian 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 dpkg-gencontrol: warning: package libbamtools-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libbamtools2.5.1-dbgsym' in '../libbamtools2.5.1-dbgsym_2.5.1+dfsg-9_amd64.deb'. dpkg-deb: building package 'libbamtools-doc' in '../libbamtools-doc_2.5.1+dfsg-9_all.deb'. dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.5.1+dfsg-9_amd64.deb'. dpkg-deb: building package 'libbamtools2.5.1' in '../libbamtools2.5.1_2.5.1+dfsg-9_amd64.deb'. dpkg-deb: building package 'libbamtools-dev' in '../libbamtools-dev_2.5.1+dfsg-9_amd64.deb'. dpkg-deb: building package 'bamtools' in '../bamtools_2.5.1+dfsg-9_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../bamtools_2.5.1+dfsg-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/469913 and its subdirectories I: Current time: Fri Jan 27 15:40:05 -12 2023 I: pbuilder-time-stamp: 1674877205 Sat Dec 25 21:17:00 UTC 2021 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Sat Dec 25 21:17:00 UTC 2021 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Sat Dec 25 21:24:58 UTC 2021 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Sat Dec 25 21:24:58 UTC 2021 I: bamtools_2.5.1+dfsg-9_amd64.changes: Format: 1.8 Date: Thu, 15 Apr 2021 21:28:36 +0200 Source: bamtools Binary: bamtools bamtools-dbgsym libbamtools-dev libbamtools-doc libbamtools2.5.1 libbamtools2.5.1-dbgsym Architecture: amd64 all Version: 2.5.1+dfsg-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dynamic library for manipulating BAM (genome alignment) libbamtools2.5.1 - dynamic library for manipulating BAM (genome alignment) files Closes: 987023 Changes: bamtools (2.5.1+dfsg-9) unstable; urgency=medium . [ Steffen Möller ] * Update metadata - indent and ref to guix . [ Andreas Tille ] * Extend means to prevent timeouts from amd64 also to armhf and s390x Closes: #987023 Checksums-Sha1: 47702652302492d2d5b80d4338190fa61b86dd04 3131572 bamtools-dbgsym_2.5.1+dfsg-9_amd64.deb 40acf92358817950324e3a1f1fae51e027df466e 7700 bamtools_2.5.1+dfsg-9_amd64.buildinfo e3bba66ed32dd2827fe8b04691cdb150ef117497 182868 bamtools_2.5.1+dfsg-9_amd64.deb 148dd35edfa9eb6f434eb88a3ae23a033e59c3f1 207692 libbamtools-dev_2.5.1+dfsg-9_amd64.deb 46abbd47ec79a21c40eff540389b662a82932b81 162472 libbamtools-doc_2.5.1+dfsg-9_all.deb fbbf5e1d269799dac394133a10d99c3a1601e2b7 2277572 libbamtools2.5.1-dbgsym_2.5.1+dfsg-9_amd64.deb b3875c2954a070263580455b0b7801ba583ed186 158304 libbamtools2.5.1_2.5.1+dfsg-9_amd64.deb Checksums-Sha256: 1a59c6d3bd206f84f7ae5c86da0ff0eff7d17d7c370f7e11db99cf5da8c7daf6 3131572 bamtools-dbgsym_2.5.1+dfsg-9_amd64.deb 2ba83583ec55c0cde4289c8d476ca73d9e35f7e6ffc65116a4b0ad3dcbd1ffbe 7700 bamtools_2.5.1+dfsg-9_amd64.buildinfo a8e42eb7a5e20722d33205cd60429d7685135019400c54e6513f6ff1b026ef33 182868 bamtools_2.5.1+dfsg-9_amd64.deb e7d4d6404fb26ad4d69325e19669ddd724df0734762fb614a33f36802b694726 207692 libbamtools-dev_2.5.1+dfsg-9_amd64.deb 564283bb1072b36294ee792239ce13cb1e7c320ee512eaec9eff0e96f9912709 162472 libbamtools-doc_2.5.1+dfsg-9_all.deb 0e167c71a334f4c875513c1a35311e2408c8c40586d683769f0f427e8af7f2e1 2277572 libbamtools2.5.1-dbgsym_2.5.1+dfsg-9_amd64.deb 59d36d6afb7881a168289b1306a844ffc3c3e9dba1638d4c52fbeb502bc13805 158304 libbamtools2.5.1_2.5.1+dfsg-9_amd64.deb Files: 6853c1e6fe00cfbed19cd19af2c6d07a 3131572 debug optional bamtools-dbgsym_2.5.1+dfsg-9_amd64.deb 34f8cce4cedca000b795c3ef55582deb 7700 science optional bamtools_2.5.1+dfsg-9_amd64.buildinfo 195411171d381a234adb48c1d6a4e15f 182868 science optional bamtools_2.5.1+dfsg-9_amd64.deb 924ed97815b48c328f5c92900614a047 207692 libdevel optional libbamtools-dev_2.5.1+dfsg-9_amd64.deb 0da807584769800983ac06ba81296603 162472 doc optional libbamtools-doc_2.5.1+dfsg-9_all.deb e903192ec971cf85e6f536f6b674392e 2277572 debug optional libbamtools2.5.1-dbgsym_2.5.1+dfsg-9_amd64.deb f341ef61fcb8dfd4defaf83fdbc45c05 158304 libs optional libbamtools2.5.1_2.5.1+dfsg-9_amd64.deb Sat Dec 25 21:24:59 UTC 2021 I: will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/bamtools_2.5.1+dfsg-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/bamtools_2.5.1+dfsg-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/bamtools_2.5.1+dfsg-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/b1/bamtools_2.5.1+dfsg-9_amd64.changes /srv/reproducible-results/rbuild-debian/tmp.ZjhpGxh8De/b2/bamtools_2.5.1+dfsg-9_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.338s) 0.338s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.090s) 0.090s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Dec 25 21:25:00 UTC 2021 I: found no differences in the changes files, and a .buildinfo file also exists. Sat Dec 25 21:25:00 UTC 2021 I: bamtools from bullseye built successfully and reproducibly on amd64. Sat Dec 25 21:25:02 UTC 2021 I: Submitting .buildinfo files to external archives: Sat Dec 25 21:25:02 UTC 2021 I: Submitting 12K b1/bamtools_2.5.1+dfsg-9_amd64.buildinfo.asc Sat Dec 25 21:25:03 UTC 2021 I: Submitting 12K b2/bamtools_2.5.1+dfsg-9_amd64.buildinfo.asc Sat Dec 25 21:25:03 UTC 2021 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Dec 25 21:25:03 UTC 2021 I: Done submitting .buildinfo files. Sat Dec 25 21:25:03 UTC 2021 I: Removing signed bamtools_2.5.1+dfsg-9_amd64.buildinfo.asc files: removed './b1/bamtools_2.5.1+dfsg-9_amd64.buildinfo.asc' removed './b2/bamtools_2.5.1+dfsg-9_amd64.buildinfo.asc'