Sat Apr 22 10:52:53 UTC 2023 I: starting to build bamtools/bookworm/arm64 on jenkins on '2023-04-22 10:52' Sat Apr 22 10:52:53 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_17/26200/console.log Sat Apr 22 10:52:53 UTC 2023 I: Downloading source for bookworm/bamtools=2.5.2+dfsg-4 --2023-04-22 10:52:53-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bamtools/bamtools_2.5.2%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2474 (2.4K) [text/prs.lines.tag] Saving to: ‘bamtools_2.5.2+dfsg-4.dsc’ 0K .. 100% 129M=0s 2023-04-22 10:52:53 (129 MB/s) - ‘bamtools_2.5.2+dfsg-4.dsc’ saved [2474/2474] Sat Apr 22 10:52:53 UTC 2023 I: bamtools_2.5.2+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bamtools Binary: bamtools, libbamtools-dev, libbamtools2.5.2, libbamtools-doc Architecture: any all Version: 2.5.2+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bamtools Vcs-Git: https://salsa.debian.org/med-team/bamtools.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkg-config Package-List: bamtools deb science optional arch=any libbamtools-dev deb libdevel optional arch=any libbamtools-doc deb doc optional arch=all libbamtools2.5.2 deb libs optional arch=any Checksums-Sha1: 22affe59a445f08e603c3f9d5378b32d06fbccd7 155732 bamtools_2.5.2+dfsg.orig.tar.xz 555c783a9f64b5c3ed8d8522cd7ceecdb0b49948 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Checksums-Sha256: bba4d268cb9457cd836b59c60eac6a9f25e10cd9aea646f03e5deffb82c1c5c1 155732 bamtools_2.5.2+dfsg.orig.tar.xz 03dbebdc47fa8df6f74cc0180ae92ba5fb82a4c68f47057f0cde400c46d0ea09 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Files: a29fafa8a0f930c3029749245032e886 155732 bamtools_2.5.2+dfsg.orig.tar.xz af47d97bec384ea6a5c62b32113efb9c 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Dgit: fee001dee532092f05d7db31157b1fc20e33eec4 debian archive/debian/2.5.2+dfsg-4 https://git.dgit.debian.org/bamtools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOg3ysUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqKMA//WW/p0BGgck2pI5ZBkl85nfntshBJ TmDTHCoBthP/9FdimOTfmdmyiOYf8jcHubyR+9+2xOYne450K6sesnVn/GhdUdLj t9Vytli7g/u0+47ua+43ybfyyMtlnEJWXvCR4bmSgVAUjoQsEmTlWGLjwkZXDqcy 34IPRhV3rucZp5tfB/i9Y/CBkjov9IECOs1ehRFo8RGMoxq5GDlvvnrtmT+HrHFB MciXGcgPioxJ50eWYFvMhJ/pNfI37PASAmMkeV07BYNl4JMM/RomxrN3pFbeiqYG YN+Tz94qURvwvSBqBizw7DfzGaQSxU3USe8F0s/VgDi2xERn1vHDcPGUAjXaUX0I wQxaKFcIJ7qTZPCeWKrKko0PFwMkNZmmnCO1fHQSvuIgfK/21i2BX42bN3xlQ19k bcRbyuGGmkI39lk3ujqGehyynw2jWycT50Ez9SmJznmpsOXzLNHg3PjMgJ00A6AX 1ueGBDjloSbz/4KzIpzF9YJxULx/bBh+51qgDd5++5QLb4biIE5rNdiw1kmQEo+8 LFve7mG+vZNum+DwPaOGK4+/n0QA3HSdz/f4xXXa4fOBfAhVOdRL/nizGgI0xGj7 WRTHWtgOVcHyKupX+h75/vrsD+dQCzZAt0mUc8FrtupkFMY2PY8k6PD+dHUDJwr5 m5aZ+b2W7i23djo= =MYt6 -----END PGP SIGNATURE----- Sat Apr 22 10:52:53 UTC 2023 I: Checking whether the package is not for us Sat Apr 22 10:52:53 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net. Sat Apr 22 10:52:53 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net. Sat Apr 22 10:57:13 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri May 24 05:15:59 -12 2024 I: pbuilder-time-stamp: 1716570959 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bamtools_2.5.2+dfsg-4.dsc] I: copying [./bamtools_2.5.2+dfsg.orig.tar.xz] I: copying [./bamtools_2.5.2+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 19 10:01:15 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bamtools_2.5.2+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting bamtools in bamtools-2.5.2+dfsg dpkg-source: info: unpacking bamtools_2.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking bamtools_2.5.2+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-ignore-thirdparty-and-fix-jsoncpp.patch dpkg-source: info: applying shared_and_static.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15894/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='15894' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/pbuilderrc_VQJF --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/b1 --logfile b1/build.log bamtools_2.5.2+dfsg-4.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 22 04:50 /bin -> usr/bin I: user script /srv/workspace/pbuilder/15894/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: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libclang-cpp14{a} libclang1-14{a} libcurl4{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{a} libldap-2.5-0{a} libllvm14{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libz3-4{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 76.5 MB of archives. After unpacking 349 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 liblocale-gettext-perl arm64 1.07-5 [15.1 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 d-shlibs all 0.104 [18.6 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libllvm14 arm64 1:14.0.6-12 [19.3 MB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libclang-cpp14 arm64 1:14.0.6-12 [9866 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libclang1-14 arm64 1:14.0.6-12 [5465 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 doxygen arm64 1.9.4-4 [4216 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 help2man arm64 1.49.3 [198 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp-dev arm64 1.9.5-4 [26.4 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Fetched 76.5 MB in 2s (40.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../05-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../08-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../11-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/bamtools-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bamtools_2.5.2+dfsg-4_source.changes dpkg-buildpackage: info: source package bamtools dpkg-buildpackage: info: source version 2.5.2+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. -- The CXX compiler identification is GNU 12.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for one of the modules 'jsoncpp>=1' Found system JsonCpp, not using bundled version -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' doxygen -u docs/Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 300 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'SHOW_DIRECTORIES' at line 500 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'COLS_IN_ALPHA_INDEX' at line 801 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'HTML_ALIGN_MEMBERS' at line 862 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'USE_INLINE_TREES' at line 1032 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'LATEX_SOURCE_CODE' at line 1152 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'XML_SCHEMA' at line 1244 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'XML_DTD' at line 1250 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'PERL_PATH' at line 1411 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'CLASS_DIAGRAMS' at line 1424 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Tag 'MSCGEN_PATH' at line 1433 of file 'docs/Doxyfile' has become obsolete. This tag has been removed. warning: Changing CLASS_GRAPH option to TEXT because obsolete option CLASS_DIAGRAM was found and set to NO. 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: 1.9.4 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-2.5.2+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/index Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/bam Searching INPUT for files to process... Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/index Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/bam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/algorithms Reading and parsing tag files Parsing files Preprocessing /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/api_global.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/api_global.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAux.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAux.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamReader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamReader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Preprocessing /build/bamtools-2.5.2+d/build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:25: warning: Documentation for undefined enum 'MergeOrder' found. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:187: warning: documented symbol 'bool BamTools::AddTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:307: warning: documented symbol 'template< typename T > bool BamTools::AddTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:377: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:407: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:434: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:559: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. fsg/src/api/SamProgramChain.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Sort.h... Generating code for file api_global.h... Generating code for file BamAlgorithms.h... Generating code for file BamAlignment.h... Generating code for file BamAux.h... Generating code for file BamConstants.h... Generating code for file BamIndex.h... Generating code for file BamMultiReader.h... Generating code for file BamReader.h... Generating code for file BamWriter.h... Generating code for file IBamIODevice.h... Generating code for file SamConstants.h... Generating code for file SamHeader.h... Generating code for file SamProgram.h... Generating code for file SamProgramChain.h... Generating code for file SamReadGroup.h... Generating code for file SamReadGroupDictionary.h... Generating code for file SamSequence.h... Generating code for file SamSequenceDictionary.h... Generating file documentation... Generating docs for file Sort.h... Generating docs for file api_global.h... Generating docs for file BamAlgorithms.h... Generating docs for file BamAlignment.cpp... Generating docs for file BamAlignment.h... Generating docs for file BamAux.h... Generating docs for file BamConstants.h... Generating docs for file BamIndex.h... Generating docs for file BamMultiReader.cpp... Generating docs for file BamMultiReader.h... Generating docs for file BamReader.cpp... Generating docs for file BamReader.h... Generating docs for file BamWriter.cpp... Generating docs for file BamWriter.h... Generating docs for file IBamIODevice.h... Generating docs for file SamConstants.h... Generating docs for file SamHeader.cpp... Generating docs for file SamHeader.h... Generating docs for file SamProgram.cpp... Generating docs for file SamProgram.h... Generating docs for file SamProgramChain.cpp... Generating docs for file SamProgramChain.h... Generating docs for file SamReadGroup.cpp... Generating docs for file SamReadGroup.h... Generating docs for file SamReadGroupDictionary.cpp... Generating docs for file SamReadGroupDictionary.h... Generating docs for file SamSequence.cpp... Generating docs for file SamSequence.h... Generating docs for file SamSequenceDictionary.cpp... Generating docs for file SamSequenceDictionary.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating concept documentation... Generating namespace index... Generating docs for namespace BamTools Generating docs for compound BamTools::BamAlignment... Generating docs for compound BamTools::BamIndex... Generating docs for compound BamTools::BamMultiReader... Generating docs for compound BamTools::BamReader... Generating docs for compound BamTools::BamRegion... Generating docs for compound BamTools::BamWriter... Generating docs for compound BamTools::CigarOp... Generating docs for compound BamTools::CustomHeaderTag... Generating docs for compound BamTools::IBamIODevice... Generating docs for compound BamTools::RefData... Generating docs for compound BamTools::SamHeader... Generating docs for compound BamTools::SamProgram... Generating docs for compound BamTools::SamProgramChain... Generating docs for compound BamTools::SamReadGroup... Generating docs for compound BamTools::SamReadGroupDictionary... Generating docs for compound BamTools::SamSequence... Generating docs for compound BamTools::SamSequenceDictionary... Generating docs for namespace BamTools::Algorithms Generating docs for compound BamTools::Algorithms::Sort... Generating docs for nested compound BamTools::Algorithms::Sort::ByName... Generating docs for nested compound BamTools::Algorithms::Sort::ByPosition... Generating docs for nested compound BamTools::Algorithms::Sort::ByTag... Generating docs for nested compound BamTools::Algorithms::Sort::Unsorted... Generating docs for namespace BamTools::Constants Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... lookup cache used 1133/65536 hits=3617 misses=1174 finished... make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' dh_auto_build -Nlibbamtools-doc cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/bamtools-2.5.2+dfsg -B/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/depend cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/BamTools_static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/build make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/build make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 2%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o [ 3%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o [ 4%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 6%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o [ 5%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp [ 7%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o [ 8%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 9%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 10%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp [ 11%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp [ 12%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS 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-D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 14%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 15%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp [ 16%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp [ 17%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic 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/build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp [ 19%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 20%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 21%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 22%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 23%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 24%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 25%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 26%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/stdexcept:39, from /build/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/stdexcept:39, from /build/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 27%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 28%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 29%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 30%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic 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CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 32%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 33%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 34%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 35%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 36%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 37%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 38%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 39%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 40%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 41%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 43%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 44%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 45%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamPipe_p.cpp [ 46%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 47%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 48%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o -c 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&& /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostAddress_p.cpp [ 52%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 53%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 54%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamPipe_p.cpp [ 55%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 56%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o cd 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-I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 58%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/ByteArray_p.cpp [ 59%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 60%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostAddress_p.cpp [ 61%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 62%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 63%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 65%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 66%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatPrinter_p.cpp [ 67%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 68%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamHeaderValidator_p.cpp [ 69%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT 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/build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 71%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 72%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/utils/BamException_p.cpp [ 73%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 74%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat 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/build/bamtools-2.5.2+dfsg/src/api/internal/utils/BamException_p.cpp [ 77%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 78%] Linking CXX static library libbamtools.a cd 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CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -lz cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libbamtools.so.2.5.2 libbamtools.so.2.5.2 libbamtools.so make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 79%] Built target BamTools make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/BamTools-utils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/build make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 80%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o [ 81%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -c /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -c /build/bamtools-2.5.2+dfsg/src/utils/bamtools_pileup_engine.cpp [ 82%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o.d -o 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BamTools::Fasta::FastaPrivate::CreateIndex(const std::string&)': /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp:161:15: warning: comparison is always true due to limited range of data type [-Wtype-limits] 161 | while ((c >= 0) && (c != '\n')) { | ~~^~~~ [ 84%] Linking CXX static library libBamTools-utils.a cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.dir/link.txt --verbose=1 /usr/bin/ar qc libBamTools-utils.a "CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o" /usr/bin/ranlib libBamTools-utils.a make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 84%] 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CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 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CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_header.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_index.cpp cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_merge.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h:15, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:12: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.h:13, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 93%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_resolve.cpp [ 95%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -MF 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src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_split.cpp [ 98%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_stats.cpp In file included from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:15: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.h:13, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable bamtools cd /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -o bamtools -Wl,-rpath,/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src: libBamTools-utils.a -L/usr/lib/aarch64-linux-gnu -ljsoncpp libbamtools.so.2.5.2 make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [100%] Built target bamtools_cmd make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' cd obj-* && ln -s src/toolkit/ bin dh_auto_test --arch cd obj-aarch64-linux-gnu && make -j8 test ARGS\+=--verbose ARGS\+=-j8 make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j8 UpdateCTestConfiguration from :/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: bamtools_help 1: Test command: /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/bamtools "--help" 1: Working Directory: /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/tests 1: Test timeout computed to be: 1500 test 2 Start 2: bamtools_stats 2: Test command: /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/bamtools "stats" "-in" "/build/bamtools-2.5.2+dfsg/tests/data/sam_spec_example.bam" 2: Working Directory: /build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/tests 2: Test timeout computed to be: 1500 1: 1: usage: bamtools [--help] COMMAND [ARGS] 1: 1: Available bamtools commands: 1: convert Converts between BAM and a number of other formats 1: count Prints number of alignments in BAM file(s) 1: coverage Prints coverage statistics from the input BAM file 1: filter Filters BAM file(s) by user-specified criteria 1: header Prints BAM header information 1: index Generates index for BAM file 1: merge Merge multiple BAM files into single file 1: random Select random alignments from existing BAM file(s), intended more as a testing tool. 1: resolve Resolves paired-end reads (marking the IsProperPair flag as needed) 1: revert Removes duplicate marks and restores original base qualities 1: sort Sorts the BAM file according to some criteria 1: split Splits a BAM file on user-specified property, creating a new BAM output file for each value found 1: stats Prints some basic statistics from input BAM file(s) 1: 1: See 'bamtools help COMMAND' for more information on a specific command. 1: 1/2 Test #1: bamtools_help .................... Passed 0.02 sec 2: 2: ********************************************** 2: Stats for BAM file(s): 2: ********************************************** 2: 2: Total reads: 6 2: Mapped reads: 6 (100%) 2: Forward strand: 4 (66.6667%) 2: Reverse strand: 2 (33.3333%) 2: Failed QC: 0 (0%) 2: Duplicates: 0 (0%) 2: Paired-end reads: 2 (33.3333%) 2: 'Proper-pairs': 2 (100%) 2: Both pairs mapped: 2 (100%) 2: Read 1: 1 2: Read 2: 1 2: Singletons: 0 (0%) 2: 2/2 Test #2: bamtools_stats ................... Passed 0.02 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.03 sec make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -Nlibbamtools-doc cd obj-aarch64-linux-gnu && make -j8 install DESTDIR=/build/bamtools-2.5.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/bamtools-2.5.2+dfsg -B/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.so.2.5.2 -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.so -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.a -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools -- Set runtime path of "/build/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools" to "" -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/bamtools_api_export.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/bamtools-1.pc make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' dh_install --arch d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/aarch64-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/aarch64-linux-gnu install -d -m 755 debian/libbamtools2.5.2/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.a debian/libbamtools-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.so debian/libbamtools-dev/usr/lib/aarch64-linux-gnu mv /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.so.2.5.2 debian/libbamtools2.5.2/usr/lib/aarch64-linux-gnu PKGDEV=libbamtools-dev PKGSHL=libbamtools2.5.2 install -d -m 755 debian/libbamtools-dev/usr/include mv debian/tmp/usr/include/bamtools debian/libbamtools-dev/usr/include install -d -m 755 debian/libbamtools-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libbamtools-dev/usr/lib/aarch64-linux-gnu/pkgconfig make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' dh_install --indep rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbamtools2.5.2' in '../libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'bamtools' in '../bamtools_2.5.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'libbamtools2.5.2-dbgsym' in '../libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'libbamtools-dev' in '../libbamtools-dev_2.5.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.5.2+dfsg-4_arm64.deb'. dpkg-deb: building package 'libbamtools-doc' in '../libbamtools-doc_2.5.2+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../bamtools_2.5.2+dfsg-4_arm64.buildinfo dpkg-genchanges --build=binary -O../bamtools_2.5.2+dfsg-4_arm64.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/15894 and its subdirectories I: Current time: Fri May 24 05:20:12 -12 2024 I: pbuilder-time-stamp: 1716571212 Sat Apr 22 10:57:14 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink10-arm64.debian.net. Sat Apr 22 10:57:14 UTC 2023 I: Preparing to do remote build '2' on codethink10-arm64.debian.net. Sat Apr 22 11:02:46 UTC 2023 I: Deleting $TMPDIR on codethink10-arm64.debian.net. Sat Apr 22 11:02:47 UTC 2023 I: bamtools_2.5.2+dfsg-4_arm64.changes: Format: 1.8 Date: Mon, 19 Dec 2022 22:45:16 +0100 Source: bamtools Binary: bamtools bamtools-dbgsym libbamtools-dev libbamtools-doc libbamtools2.5.2 libbamtools2.5.2-dbgsym Architecture: arm64 all Version: 2.5.2+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dynamic library for manipulating BAM (genome alignment) libbamtools2.5.2 - dynamic library for manipulating BAM (genome alignment) files Closes: 988848 Changes: bamtools (2.5.2+dfsg-4) unstable; urgency=medium . * Team upload. * d/control: libbamtools-doc depends on libjs-jquery. Thanks to Andreas Beckmann (Closes: #988848) * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 2689ca53d085d45e4c2cbf8897a828da04b45e95 3531640 bamtools-dbgsym_2.5.2+dfsg-4_arm64.deb 3d9e0a94f630b88bdc2decc01cd1cb8aa9d348ef 7821 bamtools_2.5.2+dfsg-4_arm64.buildinfo 9e7e37ffa10eb2f580a937d82277a2f459860d09 168256 bamtools_2.5.2+dfsg-4_arm64.deb d1bdcd20ee2587113833bc21de46f5860805d8c0 204272 libbamtools-dev_2.5.2+dfsg-4_arm64.deb e56466023933d7854010c5bf0f5fb74417156b96 160752 libbamtools-doc_2.5.2+dfsg-4_all.deb 9a8066e81c84c94166351abe127b4cf29a1397a0 2735380 libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_arm64.deb 350a6fd7d68d63a6a337d658d2b54cd2edba21c6 134100 libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb Checksums-Sha256: 2c1b8518ddeff141953f6f70097b143c1cd98ea90ff755c4c29dabf533e659cf 3531640 bamtools-dbgsym_2.5.2+dfsg-4_arm64.deb fd658efd3e5cdbb3f5b051fa03dabb4c5f66a6b317f8bee8f5b7a11200e6905c 7821 bamtools_2.5.2+dfsg-4_arm64.buildinfo eb6f80d7da297b403fff93df024000e8d312033a7e526563259b2ed7974d1aa2 168256 bamtools_2.5.2+dfsg-4_arm64.deb db6d625e76eb9beae463ad36c8f0f49d7e0b424f1ea71919e1c44ff7f62afe4d 204272 libbamtools-dev_2.5.2+dfsg-4_arm64.deb ba25a3543338262fe9722acb5ed17fb6fe3f5635c0ebf8cf29138e0c864b54af 160752 libbamtools-doc_2.5.2+dfsg-4_all.deb 3d0995ca76afb0ada200d40ac7eb7cfae3dea4753f3625c1eed42fb217523d61 2735380 libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_arm64.deb a7480f8d87c6aa5098a8c0b0b8a40f94d5fe3c0b30df4b5033a08873f55a519e 134100 libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb Files: 156351337d56b83fb3ffabe3c7c33415 3531640 debug optional bamtools-dbgsym_2.5.2+dfsg-4_arm64.deb 36fad251e07a861e3b1b46cba8dad7ce 7821 science optional bamtools_2.5.2+dfsg-4_arm64.buildinfo 616711dd5f776ba5d2a58e15fa9c4f69 168256 science optional bamtools_2.5.2+dfsg-4_arm64.deb 02dd35816970a71841bf98f0b14c8f32 204272 libdevel optional libbamtools-dev_2.5.2+dfsg-4_arm64.deb 5b204fe0fceccbf208e3830fd8b00f37 160752 doc optional libbamtools-doc_2.5.2+dfsg-4_all.deb 19b3503580c8cb38740ed80247b89ee3 2735380 debug optional libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_arm64.deb b6c8c11a58754a9c82cb66da404ec542 134100 libs optional libbamtools2.5.2_2.5.2+dfsg-4_arm64.deb Sat Apr 22 11:02:49 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/bamtools_2.5.2+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/bamtools_2.5.2+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/bamtools_2.5.2+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/b1/bamtools_2.5.2+dfsg-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.cFI9STDd/b2/bamtools_2.5.2+dfsg-4_arm64.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: 0.521s) 0.521s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.102s) 0.102s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sat Apr 22 11:02:50 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Sat Apr 22 11:02:50 UTC 2023 I: bamtools from bookworm built successfully and reproducibly on arm64. Sat Apr 22 11:02:52 UTC 2023 I: Submitting .buildinfo files to external archives: Sat Apr 22 11:02:52 UTC 2023 I: Submitting 12K b1/bamtools_2.5.2+dfsg-4_arm64.buildinfo.asc Sat Apr 22 11:02:54 UTC 2023 I: Submitting 12K b2/bamtools_2.5.2+dfsg-4_arm64.buildinfo.asc Sat Apr 22 11:02:55 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 22 11:02:55 UTC 2023 I: Done submitting .buildinfo files. Sat Apr 22 11:02:55 UTC 2023 I: Removing signed bamtools_2.5.2+dfsg-4_arm64.buildinfo.asc files: removed './b1/bamtools_2.5.2+dfsg-4_arm64.buildinfo.asc' removed './b2/bamtools_2.5.2+dfsg-4_arm64.buildinfo.asc'