Fri Sep 6 11:44:29 UTC 2024 I: starting to build bamtools/unstable/arm64 on jenkins on '2024-09-06 11:44' Fri Sep 6 11:44:29 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/35855/console.log Fri Sep 6 11:44:29 UTC 2024 I: Downloading source for unstable/bamtools=2.5.2+dfsg-6 --2024-09-06 11:44:29-- http://deb.debian.org/debian/pool/main/b/bamtools/bamtools_2.5.2%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2387 (2.3K) [text/prs.lines.tag] Saving to: ‘bamtools_2.5.2+dfsg-6.dsc’ 0K .. 100% 273M=0s 2024-09-06 11:44:29 (273 MB/s) - ‘bamtools_2.5.2+dfsg-6.dsc’ saved [2387/2387] Fri Sep 6 11:44:29 UTC 2024 I: bamtools_2.5.2+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bamtools Binary: bamtools, libbamtools-dev, libbamtools2.5.2, libbamtools-doc Architecture: any all Version: 2.5.2+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Étienne Mollier Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/bamtools Vcs-Git: https://salsa.debian.org/med-team/bamtools.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkgconf Package-List: bamtools deb science optional arch=any libbamtools-dev deb libdevel optional arch=any libbamtools-doc deb doc optional arch=all libbamtools2.5.2 deb libs optional arch=any Checksums-Sha1: 22affe59a445f08e603c3f9d5378b32d06fbccd7 155732 bamtools_2.5.2+dfsg.orig.tar.xz 7cc3351c7180b79fd41ffb7c49da5260689c9987 11368 bamtools_2.5.2+dfsg-6.debian.tar.xz Checksums-Sha256: bba4d268cb9457cd836b59c60eac6a9f25e10cd9aea646f03e5deffb82c1c5c1 155732 bamtools_2.5.2+dfsg.orig.tar.xz e4c667cb47d93420c0473c6f674d8a138a1e64362aeca55b81341aeb7e353785 11368 bamtools_2.5.2+dfsg-6.debian.tar.xz Files: a29fafa8a0f930c3029749245032e886 155732 bamtools_2.5.2+dfsg.orig.tar.xz c495be9488890186b00051d0a63c21a9 11368 bamtools_2.5.2+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmaRGHQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFLqQ/+OcycIB7F7GyBa40zu1kb1I7EPmqDwpmm 5zxpxM++K8E3kxQbL8LYFmq97whd69kzjnVkAz35FVZ/3oqSUAThRdqe5+Y+NzZC P1szfBrsE7bFUgykd3sWur0yZauja6zQ9Otm/IA+6qcrBY+SXIpxWkFc+RCkRcUj O0tC1ZVRtALgFW8GJneBQyp9LGzoZsJDgZhMAJfl/Tc3tuNhSFTC0vF3IxG3bjJt zgsfGL4rXcmr7LJZFn7lygEIDooVThSPPkHgPvw582m/9Ck4fG7K/G7gDdd7C8Rh X0Ko3UKLHgaebXE+qQXn9aNlwYEO901UdVY3zvtHMoFaZjI9w8s9lor4+azlNPM3 Kjz/ZhntRJOzZ3vsorDTzOiAh4YhY0CYQ7/rsnH27QQrbc4IXsV2ug2l2tWuAC27 HeCxd8m8qfa/lNvS8xRVTTXR+o2e0h+duBtdRLFL/9AGkZjlGp2M5Oss1zCuit+0 +Sv/kqYEKH02yu4mhkeGheXc5Q7YdjsheghWipL3f2yc9uMDDo5j0O62tMrsuVeo yoWuP9mpJ6xOEGrzmvgCbbfO8eU2Y4jR+iv8xXMJ+R2C69Y1rcEU1688qzpHrKLH QGKzLr8ihwnumx5Vukoetn0WTI0RYVczlOzvYi46IdnIMHd1/VyPWRx54gATr4+8 WldzQv42FhU= =fapy -----END PGP SIGNATURE----- Fri Sep 6 11:44:29 UTC 2024 I: Checking whether the package is not for us Fri Sep 6 11:44:29 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri Sep 6 11:44:29 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri Sep 6 11:46:35 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Sep 5 23:44:31 -12 2024 I: pbuilder-time-stamp: 1725623071 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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-6.dsc] I: copying [./bamtools_2.5.2+dfsg.orig.tar.xz] I: copying [./bamtools_2.5.2+dfsg-6.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jul 12 11:50:12 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bamtools_2.5.2+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting bamtools in bamtools-2.5.2+dfsg dpkg-source: info: unpacking bamtools_2.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking bamtools_2.5.2+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-ignore-thirdparty-and-fix-jsoncpp.patch dpkg-source: info: applying shared_and_static.patch dpkg-source: info: applying typo.patch dpkg-source: info: applying filter_script.patch dpkg-source: info: applying do_not_corrupt_output.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2103394/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='46c7bec59adb441b99ff1cfaf94c3ddf' 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='2103394' 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.iPpFhUcy/pbuilderrc_ch55 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.iPpFhUcy/b1 --logfile b1/build.log bamtools_2.5.2+dfsg-6.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 6.1.0-25-cloud-arm64 #1 SMP Debian 6.1.106-3 (2024-08-26) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2103394/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, pkgconf dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19879 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libclang-cpp16t64{a} libclang1-16t64{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfmt9{a} libgssapi-krb5-2{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libllvm16t64{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} libz3-4{a} m4{a} man-db{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 68 newly installed, 0 to remove and 0 not upgraded. Need to get 84.3 MB of archives. After unpacking 396 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-5 [61.3 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-5 [868 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.22.5-2 [198 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-5 [1129 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.2-7 [96.5 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.22.5-2 [723 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-5 [9224 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg-3+b1 [609 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1 [323 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b4 [292 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-3 [32.1 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1-1 [22.8 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-3 [80.8 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-3 [310 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-3 [126 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8 [20.0 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8 [55.4 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.18+dfsg-3 [174 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.63.0-1 [71.2 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-7 [208 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.9.1-2 [434 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.3-1 [90.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 librhash0 arm64 1.4.3-3+b1 [127 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-6 [142 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.30.3-1 [2221 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.30.3-1 [9398 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.106 [10.9 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.20 [89.7 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 50 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-2 [188 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.22.5-2 [1532 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.20 [915 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libedit2 arm64 3.1-20240808-1 [89.2 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libz3-4 arm64 4.8.12-3.1+b2 [6508 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libllvm16t64 arm64 1:16.0.6-27+b1 [20.7 MB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libclang-cpp16t64 arm64 1:16.0.6-27+b1 [10.5 MB] Get: 60 http://deb.debian.org/debian unstable/main arm64 libclang1-16t64 arm64 1:16.0.6-27+b1 [5923 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libfmt9 arm64 9.1.0+ds1-2 [107 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 doxygen arm64 1.9.8+ds-2+b1 [4484 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libjsoncpp-dev arm64 1.9.5-6+b2 [24.8 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-3 [35.3 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-3 [29.4 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-3 [26.0 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Fetched 84.3 MB in 1s (106 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 ... 19879 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-5_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-5) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-5_arm64.deb ... Unpacking procps (2:4.0.4-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.22.5-2_arm64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-5_arm64.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40.2-7_arm64.deb ... Unpacking bsdextrautils (2.40.2-7) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../11-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bamtools-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bamtools_2.5.2+dfsg-6_source.changes dpkg-buildpackage: info: source package bamtools dpkg-buildpackage: info: source version 2.5.2+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' test ! -f docs/Doxyfile.orig || mv docs/Doxyfile.orig docs/Doxyfile make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for one of the modules 'jsoncpp>=1' Found system JsonCpp, not using bundled version -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.3.1") -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done (3.1s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' cp docs/Doxyfile docs/Doxyfile.orig doxygen -u docs/Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 300 of file 'docs/Doxyfile' has become obsolete. 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Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam Searching for files in directory /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms Reading and parsing tag files Parsing files Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAux.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAux.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api//build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:25: warning: Documentation for undefined enum 'MergeOrder' found. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:187: warning: documented symbol 'bool BamTools::AddTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:307: warning: documented symbol 'template< typename T > bool BamTools::AddTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:377: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:407: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:434: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:559: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. IBamIODevice.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Preprocessing /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Parsing file /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Sort.h... Generating code for file api_global.h... Generating code for file BamAlgorithms.h... Generating code for file BamAlignment.h... Generating code for file BamAux.h... Generating code for file BamConstants.h... Generating code for file BamIndex.h... Generating code for file BamMultiReader.h... Generating code for file BamReader.h... Generating code for file BamWriter.h... Generating code for file IBamIODevice.h... Generating code for file SamConstants.h... Generating code for file SamHeader.h... Generating code for file SamProgram.h... Generating code for file SamProgramChain.h... Generating code for file SamReadGroup.h... Generating code for file SamReadGroupDictionary.h... Generating code for file SamSequence.h... Generating code for file SamSequenceDictionary.h... Generating file documentation... Generating docs for file Sort.h... Generating docs for file api_global.h... Generating docs for file BamAlgorithms.h... Generating docs for file BamAlignment.cpp... Generating docs for file BamAlignment.h... Generating docs for file BamAux.h... Generating docs for file BamConstants.h... Generating docs for file BamIndex.h... Generating docs for file BamMultiReader.cpp... Generating docs for file BamMultiReader.h... Generating docs for file BamReader.cpp... Generating docs for file BamReader.h... Generating docs for file BamWriter.cpp... Generating docs for file BamWriter.h... Generating docs for file IBamIODevice.h... Generating docs for file SamConstants.h... Generating docs for file SamHeader.cpp... Generating docs for file SamHeader.h... Generating docs for file SamProgram.cpp... Generating docs for file SamProgram.h... Generating docs for file SamProgramChain.cpp... Generating docs for file SamProgramChain.h... Generating docs for file SamReadGroup.cpp... Generating docs for file SamReadGroup.h... Generating docs for file SamReadGroupDictionary.cpp... Generating docs for file SamReadGroupDictionary.h... Generating docs for file SamSequence.cpp... Generating docs for file SamSequence.h... Generating docs for file SamSequenceDictionary.cpp... Generating docs for file SamSequenceDictionary.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating docs for namespace BamTools Generating docs for compound BamTools::BamAlignment... Generating docs for compound BamTools::BamIndex... Generating docs for compound BamTools::BamMultiReader... Generating docs for compound BamTools::BamReader... Generating docs for compound BamTools::BamRegion... Generating docs for compound BamTools::BamWriter... Generating docs for compound BamTools::CigarOp... Generating docs for compound BamTools::CustomHeaderTag... Generating docs for compound BamTools::IBamIODevice... Generating docs for compound BamTools::RefData... Generating docs for compound BamTools::SamHeader... Generating docs for compound BamTools::SamProgram... Generating docs for compound BamTools::SamProgramChain... Generating docs for compound BamTools::SamReadGroup... Generating docs for compound BamTools::SamReadGroupDictionary... Generating docs for compound BamTools::SamSequence... Generating docs for compound BamTools::SamSequenceDictionary... Generating docs for namespace BamTools::Algorithms Generating docs for compound BamTools::Algorithms::Sort... Generating docs for nested compound BamTools::Algorithms::Sort::ByName... Generating docs for nested compound BamTools::Algorithms::Sort::ByPosition... Generating docs for nested compound BamTools::Algorithms::Sort::ByTag... Generating docs for nested compound BamTools::Algorithms::Sort::Unsorted... Generating docs for namespace BamTools::Constants Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... type lookup cache used 1077/65536 hits=2076 misses=1118 symbol lookup cache used 1050/65536 hits=5949 misses=1050 finished... make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_auto_build -Nlibbamtools-doc cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/bamtools-2.5.2+dfsg -B/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/BamTools.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/depend make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/BamTools_static.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/build make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/build make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp [ 2%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o [ 3%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o [ 4%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o [ 5%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp [ 6%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o [ 7%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 8%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 9%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp [ 11%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o [ 12%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o [ 10%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgram.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 13%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/bits/stl_tree.h:65, from /usr/include/c++/14/map:62, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp [ 15%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp [ 16%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 17%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 18%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp [ 19%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 20%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp [ 21%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 22%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 24%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 24%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 25%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 26%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 27%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 28%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 29%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 30%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -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/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 31%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /usr/include/c++/14/stdexcept:39, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 32%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 33%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 34%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 35%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 36%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 37%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 38%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 39%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE 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-I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 41%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 42%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamPipe_p.cpp [ 43%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 44%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 45%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp [ 46%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong 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src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 51%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 52%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o.d 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CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 54%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o 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Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 58%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 59%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -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/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/BamPipe_p.cpp [ 60%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd 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/usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 68%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 69%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 70%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 71%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 72%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 73%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 74%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -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/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatPrinter_p.cpp [ 75%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/sam/SamHeaderValidator_p.cpp [ 76%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/utils/BamException_p.cpp [ 77%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -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/reproducible-path/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 78%] Linking CXX shared library libbamtools.so cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong 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CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -lz cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-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/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 78%] Built target BamTools make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/BamTools-utils.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 79%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp [ 80%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_options.cpp [ 81%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o [ 82%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_pileup_engine.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_utilities.cpp /build/reproducible-path/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp: In member function 'bool BamTools::Fasta::FastaPrivate::CreateIndex(const std::string&)': /build/reproducible-path/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')) { | ~~^~~~ [ 83%] Linking CXX static library libbamtools.a cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P 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CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/utils/BamException_p.cpp.o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o /usr/bin/ranlib libbamtools.a make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 83%] Built target BamTools_static [ 84%] Linking CXX static library libBamTools-utils.a cd 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/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bamtools-2.5.2+dfsg /build/reproducible-path/bamtools-2.5.2+dfsg/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bamtools_cmd.dir/build.make src/CMakeFiles/bamtools_cmd.dir/build make[3]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [ 85%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o [ 87%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o [ 86%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools.cpp [ 88%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_convert.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp [ 89%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_coverage.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_filter.cpp [ 90%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_header.cpp [ 91%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o [ 92%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o [ 93%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -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/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_index.cpp cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_merge.cpp [ 94%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_random.cpp cd /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_resolve.cpp [ 95%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_revert.cpp [ 96%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h:15, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:12: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:10: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:15: /build/reproducible-path/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:49, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.h:13, from /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:10: /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_split.cpp [ 98%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/src -I/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Wextra -pedantic -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -c /build/reproducible-path/bamtools-2.5.2+dfsg/src/toolkit/bamtools_stats.cpp [100%] Linking CXX executable bamtools cd /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -o bamtools -Wl,-rpath,/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src: libBamTools-utils.a -L/usr/lib/aarch64-linux-gnu -ljsoncpp libbamtools.so.2.5.2 make[3]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' [100%] Built target bamtools_cmd make[2]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' cd obj-* && ln -s src/toolkit/ bin dh_auto_test --arch cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[2]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/bamtools "--help" 1: Working Directory: /build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu/src/bamtools "stats" "-in" "/build/reproducible-path/bamtools-2.5.2+dfsg/tests/data/sam_spec_example.bam" 2: Working Directory: /build/reproducible-path/bamtools-2.5.2+dfsg/obj-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: 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: 1/2 Test #1: bamtools_help .................... Passed 0.04 sec 2/2 Test #2: bamtools_stats ................... Passed 0.02 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.04 sec make[2]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -Nlibbamtools-doc cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/bamtools-2.5.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/bamtools-2.5.2+dfsg -B/build/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.so.2.5.2 -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.so -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/libbamtools.a -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools -- Set non-toolchain portion of runtime path of "/build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools" to "" -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/bamtools_api_export.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /build/reproducible-path/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/aarch64-linux-gnu/pkgconfig/bamtools-1.pc make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg/obj-aarch64-linux-gnu' debian/rules override_dh_install-arch make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_install --arch d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/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/reproducible-path/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/reproducible-path/bamtools-2.5.2+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_install --indep rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js make[1]: Leaving directory '/build/reproducible-path/bamtools-2.5.2+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbamtools2.5.2' in '../libbamtools2.5.2_2.5.2+dfsg-6_arm64.deb'. dpkg-deb: building package 'libbamtools-dev' in '../libbamtools-dev_2.5.2+dfsg-6_arm64.deb'. dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.5.2+dfsg-6_arm64.deb'. dpkg-deb: building package 'libbamtools2.5.2-dbgsym' in '../libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_arm64.deb'. dpkg-deb: building package 'libbamtools-doc' in '../libbamtools-doc_2.5.2+dfsg-6_all.deb'. dpkg-deb: building package 'bamtools' in '../bamtools_2.5.2+dfsg-6_arm64.deb'. dpkg-genbuildinfo --build=binary -O../bamtools_2.5.2+dfsg-6_arm64.buildinfo dpkg-genchanges --build=binary -O../bamtools_2.5.2+dfsg-6_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/2103394 and its subdirectories I: Current time: Thu Sep 5 23:46:34 -12 2024 I: pbuilder-time-stamp: 1725623194 Fri Sep 6 11:46:36 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri Sep 6 11:46:36 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri Sep 6 11:48:53 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri Sep 6 11:48:54 UTC 2024 I: bamtools_2.5.2+dfsg-6_arm64.changes: Format: 1.8 Date: Fri, 12 Jul 2024 13:46:23 +0200 Source: bamtools Binary: bamtools bamtools-dbgsym libbamtools-dev libbamtools-doc libbamtools2.5.2 libbamtools2.5.2-dbgsym Architecture: arm64 all Version: 2.5.2+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dynamic library for manipulating BAM (genome alignment) libbamtools2.5.2 - dynamic library for manipulating BAM (genome alignment) files Closes: 1075990 Changes: bamtools (2.5.2+dfsg-6) unstable; urgency=medium . * Fix output data on bigendian architectures (Thanks a lot for the patch from Vladimir Petko !) Closes: #1075990 * Standards-Version: 4.7.0 (routine-update) * Build-Depends: s/pkg-config/pkgconf/ Checksums-Sha1: 18425562dbe1ad9e746fd7add14b58576a70c30a 3449588 bamtools-dbgsym_2.5.2+dfsg-6_arm64.deb 2a135ab9cbbda71a1bd793ad13e3da53b946da33 7901 bamtools_2.5.2+dfsg-6_arm64.buildinfo 6ae5059b7bcbc0d374b301985a41c21de3d6643a 172740 bamtools_2.5.2+dfsg-6_arm64.deb 55d070264adbb89d3141d97e794923a502de40e8 209528 libbamtools-dev_2.5.2+dfsg-6_arm64.deb f9306a30d994e5f269e8a175e05ecb9ca55ba63f 161144 libbamtools-doc_2.5.2+dfsg-6_all.deb 6d97338404d42810353a32ad659894f6c389810e 2694908 libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_arm64.deb 9360910adbb0ca06c512a5a0b762ef6cdc1f67a0 140348 libbamtools2.5.2_2.5.2+dfsg-6_arm64.deb Checksums-Sha256: c1d7f6f8e59ac05589965e67a8ddcf6adc74ec397673f03dec5fab20c5c22243 3449588 bamtools-dbgsym_2.5.2+dfsg-6_arm64.deb ccab97bee41b7894faa6e4a20ad5b12f1e1bf98a198116466113306e505211d3 7901 bamtools_2.5.2+dfsg-6_arm64.buildinfo 49d15197010831d351256dee00c04b4cd8f3428c4177e947b667e385d8f6a6cf 172740 bamtools_2.5.2+dfsg-6_arm64.deb f2db45ca8b5a2b10c437c5bba8867ae227b27ed9771df5a2c3d541203fbb99a7 209528 libbamtools-dev_2.5.2+dfsg-6_arm64.deb 192d96bc78fff3165af2b7c4377f2178ba57a1704bbee04443305bdd8eb966c7 161144 libbamtools-doc_2.5.2+dfsg-6_all.deb e4cb0bf2ce6512088fb4ba3e6b1673d5f618f3d3b6ac9637c75a9926050d9497 2694908 libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_arm64.deb 7a9309e5f5dfec7ca0c6009021f68da9af1d37615b69f6336d6fa5d0f69a2882 140348 libbamtools2.5.2_2.5.2+dfsg-6_arm64.deb Files: 80a482a5179bfb7fe8727bd76804c3d3 3449588 debug optional bamtools-dbgsym_2.5.2+dfsg-6_arm64.deb 1f0b91b1ffe8093f8a15c6d9b6ce16b2 7901 science optional bamtools_2.5.2+dfsg-6_arm64.buildinfo 9ec92a052435ccec1154553b83c8cb2a 172740 science optional bamtools_2.5.2+dfsg-6_arm64.deb 0ddf4ea187a1c90001068008528bd019 209528 libdevel optional libbamtools-dev_2.5.2+dfsg-6_arm64.deb b1dcbc565d1eb5900a7057ba1431feb5 161144 doc optional libbamtools-doc_2.5.2+dfsg-6_all.deb c3d9bda0faa9de58920a8ab30861b93d 2694908 debug optional libbamtools2.5.2-dbgsym_2.5.2+dfsg-6_arm64.deb 4d1ecd1da28d82c55e9398e2089fd8f5 140348 libs optional libbamtools2.5.2_2.5.2+dfsg-6_arm64.deb Fri Sep 6 11:48:55 UTC 2024 I: diffoscope 277 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_20-35855.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.iPpFhUcy/bamtools_2.5.2+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.iPpFhUcy/bamtools_2.5.2+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.iPpFhUcy/bamtools_2.5.2+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.iPpFhUcy/b1/bamtools_2.5.2+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.iPpFhUcy/b2/bamtools_2.5.2+dfsg-6_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: 0.486s) 0.486s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.095s) 0.095s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 842ms CPU time consumed: 839ms Fri Sep 6 11:48:56 UTC 2024 I: diffoscope 277 found no differences in the changes files, and a .buildinfo file also exists. Fri Sep 6 11:48:56 UTC 2024 I: bamtools from unstable built successfully and reproducibly on arm64. Fri Sep 6 11:48:58 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Sep 6 11:48:58 UTC 2024 I: Submitting 12K b1/bamtools_2.5.2+dfsg-6_arm64.buildinfo.asc Fri Sep 6 11:48:59 UTC 2024 I: Submitting 12K b2/bamtools_2.5.2+dfsg-6_arm64.buildinfo.asc Fri Sep 6 11:49:00 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Sep 6 11:49:00 UTC 2024 I: Done submitting .buildinfo files. Fri Sep 6 11:49:00 UTC 2024 I: Removing signed bamtools_2.5.2+dfsg-6_arm64.buildinfo.asc files: removed './b1/bamtools_2.5.2+dfsg-6_arm64.buildinfo.asc' removed './b2/bamtools_2.5.2+dfsg-6_arm64.buildinfo.asc'