Thu May 4 20:54:37 UTC 2023 I: starting to build bamtools/bookworm/armhf on jenkins on '2023-05-04 20:54' Thu May 4 20:54:37 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_38/6589/console.log Thu May 4 20:54:37 UTC 2023 I: Downloading source for bookworm/bamtools=2.5.2+dfsg-4 --2023-05-04 20:54:37-- http://cdn-fastly.deb.debian.org/debian/pool/main/b/bamtools/bamtools_2.5.2%2bdfsg-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2474 (2.4K) [text/prs.lines.tag] Saving to: ‘bamtools_2.5.2+dfsg-4.dsc’ 0K .. 100% 68.0M=0s 2023-05-04 20:54:37 (68.0 MB/s) - ‘bamtools_2.5.2+dfsg-4.dsc’ saved [2474/2474] Thu May 4 20:54:37 UTC 2023 I: bamtools_2.5.2+dfsg-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: bamtools Binary: bamtools, libbamtools-dev, libbamtools2.5.2, libbamtools-doc Architecture: any all Version: 2.5.2+dfsg-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe , Andreas Tille , Kevin Murray , Homepage: https://github.com/pezmaster31/bamtools/wiki Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bamtools Vcs-Git: https://salsa.debian.org/med-team/bamtools.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkg-config Package-List: bamtools deb science optional arch=any libbamtools-dev deb libdevel optional arch=any libbamtools-doc deb doc optional arch=all libbamtools2.5.2 deb libs optional arch=any Checksums-Sha1: 22affe59a445f08e603c3f9d5378b32d06fbccd7 155732 bamtools_2.5.2+dfsg.orig.tar.xz 555c783a9f64b5c3ed8d8522cd7ceecdb0b49948 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Checksums-Sha256: bba4d268cb9457cd836b59c60eac6a9f25e10cd9aea646f03e5deffb82c1c5c1 155732 bamtools_2.5.2+dfsg.orig.tar.xz 03dbebdc47fa8df6f74cc0180ae92ba5fb82a4c68f47057f0cde400c46d0ea09 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Files: a29fafa8a0f930c3029749245032e886 155732 bamtools_2.5.2+dfsg.orig.tar.xz af47d97bec384ea6a5c62b32113efb9c 10044 bamtools_2.5.2+dfsg-4.debian.tar.xz Dgit: fee001dee532092f05d7db31157b1fc20e33eec4 debian archive/debian/2.5.2+dfsg-4 https://git.dgit.debian.org/bamtools -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmOg3ysUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqKMA//WW/p0BGgck2pI5ZBkl85nfntshBJ TmDTHCoBthP/9FdimOTfmdmyiOYf8jcHubyR+9+2xOYne450K6sesnVn/GhdUdLj t9Vytli7g/u0+47ua+43ybfyyMtlnEJWXvCR4bmSgVAUjoQsEmTlWGLjwkZXDqcy 34IPRhV3rucZp5tfB/i9Y/CBkjov9IECOs1ehRFo8RGMoxq5GDlvvnrtmT+HrHFB MciXGcgPioxJ50eWYFvMhJ/pNfI37PASAmMkeV07BYNl4JMM/RomxrN3pFbeiqYG YN+Tz94qURvwvSBqBizw7DfzGaQSxU3USe8F0s/VgDi2xERn1vHDcPGUAjXaUX0I wQxaKFcIJ7qTZPCeWKrKko0PFwMkNZmmnCO1fHQSvuIgfK/21i2BX42bN3xlQ19k bcRbyuGGmkI39lk3ujqGehyynw2jWycT50Ez9SmJznmpsOXzLNHg3PjMgJ00A6AX 1ueGBDjloSbz/4KzIpzF9YJxULx/bBh+51qgDd5++5QLb4biIE5rNdiw1kmQEo+8 LFve7mG+vZNum+DwPaOGK4+/n0QA3HSdz/f4xXXa4fOBfAhVOdRL/nizGgI0xGj7 WRTHWtgOVcHyKupX+h75/vrsD+dQCzZAt0mUc8FrtupkFMY2PY8k6PD+dHUDJwr5 m5aZ+b2W7i23djo= =MYt6 -----END PGP SIGNATURE----- Thu May 4 20:54:37 UTC 2023 I: Checking whether the package is not for us Thu May 4 20:54:37 UTC 2023 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Thu May 4 20:54:37 UTC 2023 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Thu May 4 21:06:27 UTC 2023 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 4 08:54:45 -12 2023 I: pbuilder-time-stamp: 1683233685 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [bamtools_2.5.2+dfsg-4.dsc] I: copying [./bamtools_2.5.2+dfsg.orig.tar.xz] I: copying [./bamtools_2.5.2+dfsg-4.debian.tar.xz] I: Extracting source gpgv: Signature made Mon Dec 19 10:01:15 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bamtools_2.5.2+dfsg-4.dsc: no acceptable signature found dpkg-source: info: extracting bamtools in bamtools-2.5.2+dfsg dpkg-source: info: unpacking bamtools_2.5.2+dfsg.orig.tar.xz dpkg-source: info: unpacking bamtools_2.5.2+dfsg-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 0001-ignore-thirdparty-and-fix-jsoncpp.patch dpkg-source: info: applying shared_and_static.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25571/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='e1fd0259123249ab8ebe42ccab7c4550' 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='25571' 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.qtsyXzdp/pbuilderrc_BNO9 --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qtsyXzdp/b1 --logfile b1/build.log bamtools_2.5.2+dfsg-4.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux wbq0 5.10.0-22-armmp #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/25571/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: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev, libjsoncpp-dev, help2man, doxygen, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19329 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbsd0{a} libclang-cpp14{a} libclang1-14{a} libcurl4{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{a} libldap-2.5-0{a} libllvm14{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} libz3-4{a} m4{a} man-db{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 72.7 MB of archives. After unpacking 300 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf liblocale-gettext-perl armhf 1.07-5 [14.9 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf d-shlibs all 0.104 [18.6 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 43 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 45 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libbsd0 armhf 0.11.7-2 [113 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libedit2 armhf 3.1-20221030-2 [77.0 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libz3-4 armhf 4.8.12-3.1 [6061 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libllvm14 armhf 1:14.0.6-12 [19.4 MB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libclang-cpp14 armhf 1:14.0.6-12 [9417 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libclang1-14 armhf 1:14.0.6-12 [5175 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf doxygen armhf 1.9.4-4 [4176 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf help2man armhf 1.49.3 [198 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libjsoncpp-dev armhf 1.9.5-4 [26.4 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Fetched 72.7 MB in 5s (15.3 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 ... 19329 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-5_armhf.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libproc2-0:armhf. Preparing to unpack .../01-libproc2-0_2%3a4.0.2-3_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.2-3) ... Selecting previously unselected package procps. 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Preparing to unpack .../21-libbrotli1_1.0.9-2+b6_armhf.deb ... Unpacking libbrotli1:armhf (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:armhf. Preparing to unpack .../22-libsasl2-modules-db_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:armhf. Preparing to unpack .../23-libsasl2-2_2.1.28+dfsg-10_armhf.deb ... Unpacking libsasl2-2:armhf (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:armhf. Preparing to unpack .../24-libldap-2.5-0_2.5.13+dfsg-5_armhf.deb ... Unpacking libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:armhf. Preparing to unpack .../25-libnghttp2-14_1.52.0-1_armhf.deb ... Unpacking libnghttp2-14:armhf (1.52.0-1) ... Selecting previously unselected package libpsl5:armhf. Preparing to unpack .../26-libpsl5_0.21.2-1_armhf.deb ... Unpacking libpsl5:armhf (0.21.2-1) ... Selecting previously unselected package librtmp1:armhf. Preparing to unpack .../27-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ... Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:armhf. Preparing to unpack .../28-libssh2-1_1.10.0-3+b1_armhf.deb ... Unpacking libssh2-1:armhf (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:armhf. Preparing to unpack .../29-libcurl4_7.88.1-9_armhf.deb ... Unpacking libcurl4:armhf (7.88.1-9) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../30-libexpat1_2.5.0-1_armhf.deb ... Unpacking libexpat1:armhf (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:armhf. Preparing to unpack .../31-libjsoncpp25_1.9.5-4_armhf.deb ... Unpacking libjsoncpp25:armhf (1.9.5-4) ... Selecting previously unselected package librhash0:armhf. Preparing to unpack .../32-librhash0_1.4.3-3_armhf.deb ... Unpacking librhash0:armhf (1.4.3-3) ... 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Setting up libexpat1:armhf (2.5.0-1) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:armhf (4.8.12-3.1) ... Setting up libpkgconf3:armhf (1.8.1-1) ... Setting up libuv1:armhf (1.44.2-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:armhf (2:4.0.2-3) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:armhf (1.9.5-4) ... Setting up d-shlibs (0.104) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up librhash0:armhf (1.4.3-3) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libbsd0:armhf (0.11.7-2) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libjsoncpp-dev:armhf (1.9.5-4) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:armhf (3.6.2-1) ... Setting up libedit2:armhf (3.1-20221030-2) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up pkgconf:armhf (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:armhf (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libllvm14:armhf (1:14.0.6-12) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libcurl4:armhf (7.88.1-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libclang1-14 (1:14.0.6-12) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp14 (1:14.0.6-12) ... Setting up cmake (3.25.1-1) ... Setting up debhelper (13.11.4) ... Setting up doxygen (1.9.4-4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/bamtools-2.5.2+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bamtools_2.5.2+dfsg-4_source.changes dpkg-buildpackage: info: source package bamtools dpkg-buildpackage: info: source version 2.5.2+dfsg-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-arm-linux-gnueabihf && 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/arm-linux-gnueabihf .. -- The CXX compiler identification is GNU 12.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for one of the modules 'jsoncpp>=1' Found system JsonCpp, not using bundled version -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13") -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY -- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success -- Performing Test COMPILER_HAS_DEPRECATED_ATTR -- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf debian/rules override_dh_auto_build-indep make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' doxygen -u docs/Doxyfile warning: Tag 'SYMBOL_CACHE_SIZE' at line 300 of file 'docs/Doxyfile' has become obsolete. 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Searching for files to exclude Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/index Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/bam Searching INPUT for files to process... Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/algorithms Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/index Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/utils Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/io Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/sam Searching for files in directory /build/bamtools-2.5.2+dfsg/src/api/internal/bam Reading and parsing tag files Parsing files Preprocessing /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/api_global.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/api_global.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamAux.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamAux.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamConstants.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamIndex.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamReader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamReader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/BamWriter.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/IBamIODevice.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamConstants.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamHeader.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgram.h... Preprocessing /build/bamtools-2.5.2+d/build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:25: warning: Documentation for undefined enum 'MergeOrder' found. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:187: warning: documented symbol 'bool BamTools::AddTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:307: warning: documented symbol 'template< typename T > bool BamTools::AddTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:377: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:407: warning: documented symbol 'template< typename T > bool BamTools::EditTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:434: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.h:559: warning: documented symbol 'template< typename T > bool BamTools::GetTag' was not declared or defined. fsg/src/api/SamProgramChain.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequence.h... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp... Preprocessing /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Parsing file /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file Sort.h... Generating code for file api_global.h... Generating code for file BamAlgorithms.h... Generating code for file BamAlignment.h... Generating code for file BamAux.h... Generating code for file BamConstants.h... Generating code for file BamIndex.h... Generating code for file BamMultiReader.h... Generating code for file BamReader.h... Generating code for file BamWriter.h... Generating code for file IBamIODevice.h... Generating code for file SamConstants.h... Generating code for file SamHeader.h... Generating code for file SamProgram.h... Generating code for file SamProgramChain.h... Generating code for file SamReadGroup.h... Generating code for file SamReadGroupDictionary.h... Generating code for file SamSequence.h... Generating code for file SamSequenceDictionary.h... Generating file documentation... Generating docs for file Sort.h... Generating docs for file api_global.h... Generating docs for file BamAlgorithms.h... Generating docs for file BamAlignment.cpp... Generating docs for file BamAlignment.h... Generating docs for file BamAux.h... Generating docs for file BamConstants.h... Generating docs for file BamIndex.h... Generating docs for file BamMultiReader.cpp... Generating docs for file BamMultiReader.h... Generating docs for file BamReader.cpp... Generating docs for file BamReader.h... Generating docs for file BamWriter.cpp... Generating docs for file BamWriter.h... Generating docs for file IBamIODevice.h... Generating docs for file SamConstants.h... Generating docs for file SamHeader.cpp... Generating docs for file SamHeader.h... Generating docs for file SamProgram.cpp... Generating docs for file SamProgram.h... Generating docs for file SamProgramChain.cpp... Generating docs for file SamProgramChain.h... Generating docs for file SamReadGroup.cpp... Generating docs for file SamReadGroup.h... Generating docs for file SamReadGroupDictionary.cpp... Generating docs for file SamReadGroupDictionary.h... Generating docs for file SamSequence.cpp... Generating docs for file SamSequence.h... Generating docs for file SamSequenceDictionary.cpp... Generating docs for file SamSequenceDictionary.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating concept documentation... Generating namespace index... Generating docs for namespace BamTools Generating docs for compound BamTools::BamAlignment... Generating docs for compound BamTools::BamIndex... Generating docs for compound BamTools::BamMultiReader... Generating docs for compound BamTools::BamReader... Generating docs for compound BamTools::BamRegion... Generating docs for compound BamTools::BamWriter... Generating docs for compound BamTools::CigarOp... Generating docs for compound BamTools::CustomHeaderTag... Generating docs for compound BamTools::IBamIODevice... Generating docs for compound BamTools::RefData... Generating docs for compound BamTools::SamHeader... Generating docs for compound BamTools::SamProgram... Generating docs for compound BamTools::SamProgramChain... Generating docs for compound BamTools::SamReadGroup... Generating docs for compound BamTools::SamReadGroupDictionary... Generating docs for compound BamTools::SamSequence... Generating docs for compound BamTools::SamSequenceDictionary... Generating docs for namespace BamTools::Algorithms Generating docs for compound BamTools::Algorithms::Sort... Generating docs for nested compound BamTools::Algorithms::Sort::ByName... Generating docs for nested compound BamTools::Algorithms::Sort::ByPosition... Generating docs for nested compound BamTools::Algorithms::Sort::ByTag... Generating docs for nested compound BamTools::Algorithms::Sort::Unsorted... Generating docs for namespace BamTools::Constants Generating graph info page... Generating directory documentation... Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... lookup cache used 1133/65536 hits=3617 misses=1174 finished... make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' dh_auto_build -Nlibbamtools-doc cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/bamtools-2.5.2+dfsg -B/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/BamTools.dir/build.make src/CMakeFiles/BamTools.dir/depend make -f src/CMakeFiles/BamTools_static.dir/build.make src/CMakeFiles/BamTools_static.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/BamTools.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/BamTools_static.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' 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/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' [ 2%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o [ 2%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 3%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamAlignment.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamAlignment.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 4%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 5%] Building CXX object src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o [ 6%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools.dir/api/BamWriter.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamMultiReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp [ 7%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamHeader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:16: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.h:13, from /build/bamtools-2.5.2+dfsg/src/api/BamMultiReader.cpp:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 8%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgram.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp [ 9%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamReader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamReader.cpp [ 10%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 11%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -MF CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/BamWriter.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/BamWriter.cpp [ 12%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp [ 13%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamHeader.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamHeader.cpp [ 14%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp [ 15%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequence.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 16%] Building CXX object src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 17%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgram.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgram.cpp [ 18%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamProgramChain.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamProgramChain.cpp [ 19%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 20%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp [ 21%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroup.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamReadGroup.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/stdexcept:39, from /build/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamReadGroupDictionary.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamReadGroupDictionary.cpp [ 23%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 24%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 25%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequence.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequence.cpp [ 26%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -MF CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/SamSequenceDictionary.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/SamSequenceDictionary.cpp [ 27%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 28%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 29%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 30%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamHeader_p.cpp [ 31%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:18: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:880:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:880:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.h:27, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:589:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.h:28, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:634:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:655:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:384:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'virtual bool BamTools::Internal::BamToolsIndex::Create()' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:206:46: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'virtual bool BamTools::Internal::BamToolsIndex::Create()' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:248:42: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'virtual bool BamTools::Internal::BamToolsIndex::Create()' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:266:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:813:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:806:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:837:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 32%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:179:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamMultiReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:489:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:489:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp [ 35%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:32, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:29, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.cpp:10: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/stdexcept:39, from /build/bamtools-2.5.2+dfsg/src/shared/bamtools_global.h:72, from /build/bamtools-2.5.2+dfsg/src/api/api_global.h:14, from /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiReader_p.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamMultiMerger_p.h:52:52: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 52 | struct API_NO_EXPORT MergeItemSorter : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 36%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 37%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamPipe_p.cpp [ 38%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BgzfStream_p.cpp [ 39%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/ByteArray_p.cpp [ 40%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostAddress_p.cpp [ 41%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HostInfo_p.cpp [ 42%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamRandomAccessController_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamRandomAccessController_p.cpp [ 43%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/HttpHeader_p.cpp [ 44%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 45%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 46%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamReader_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamReader_p.cpp [ 47%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_p.cpp [ 48%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocket_p.cpp [ 50%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatParser_p.cpp [ 51%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/bam/BamWriter_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/bam/BamWriter_p.cpp [ 52%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatPrinter_p.cpp [ 53%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamIndexFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamIndexFactory_p.cpp [ 54%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamHeaderValidator_p.cpp [ 55%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/utils/BamException_p.cpp [ 56%] Building CXX object src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DBamTools_EXPORTS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -MF CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o.d -o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp [ 57%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamStandardIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp [ 58%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/index/BamToolsIndex_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp [ 59%] Linking CXX shared library libbamtools.so cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/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/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbamtools.so.2.5.2 -o libbamtools.so.2.5.2 CMakeFiles/BamTools.dir/api/BamAlignment.cpp.o CMakeFiles/BamTools.dir/api/BamMultiReader.cpp.o CMakeFiles/BamTools.dir/api/BamReader.cpp.o CMakeFiles/BamTools.dir/api/BamWriter.cpp.o CMakeFiles/BamTools.dir/api/SamHeader.cpp.o CMakeFiles/BamTools.dir/api/SamProgram.cpp.o CMakeFiles/BamTools.dir/api/SamProgramChain.cpp.o CMakeFiles/BamTools.dir/api/SamReadGroup.cpp.o CMakeFiles/BamTools.dir/api/SamReadGroupDictionary.cpp.o CMakeFiles/BamTools.dir/api/SamSequence.cpp.o CMakeFiles/BamTools.dir/api/SamSequenceDictionary.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamHeader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamMultiReader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamRandomAccessController_p.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamReader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/bam/BamWriter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamIndexFactory_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamStandardIndex_p.cpp.o CMakeFiles/BamTools.dir/api/internal/index/BamToolsIndex_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamDeviceFactory_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamFile_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamFtp_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamHttp_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BamPipe_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/BgzfStream_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ByteArray_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HostAddress_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HostInfo_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/HttpHeader_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/ILocalIODevice_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/RollingBuffer_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocket_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatParser_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamFormatPrinter_p.cpp.o CMakeFiles/BamTools.dir/api/internal/sam/SamHeaderValidator_p.cpp.o CMakeFiles/BamTools.dir/api/internal/utils/BamException_p.cpp.o CMakeFiles/BamTools.dir/api/internal/io/TcpSocketEngine_unix_p.cpp.o -lz In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:18: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_symlink_library libbamtools.so.2.5.2 libbamtools.so.2.5.2 libbamtools.so /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = long long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 [ 59%] Built target BamTools make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/BamTools-utils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/BamTools-utils.dir/build.make src/CMakeFiles/BamTools-utils.dir/build make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' [ 60%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o -c /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/12/vector:70, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.h:27, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BtiBlock&}; _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamToolsIndex::ReadBlocks(const BamTools::Internal::BtiReferenceSummary&, BamTools::Internal::BtiBlockVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:589:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp: In member function 'bool BamTools::Fasta::FastaPrivate::CreateIndex(const std::string&)': /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp:161:15: warning: comparison is always true due to limited range of data type [-Wtype-limits] 161 | while ((c >= 0) && (c != '\n')) { | ~~^~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {BamTools::Internal::BtiReferenceSummary}; _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = BamTools::Internal::BtiReferenceSummary; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void BamTools::Internal::BamToolsIndex::InitializeFileSummary(const int&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:384:37: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:880:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::SortLinearOffsets(BamTools::Internal::BaiLinearOffsetVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:880:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'virtual bool BamTools::Internal::BamToolsIndex::Create()' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:206:46: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'virtual bool BamTools::Internal::BamToolsIndex::Create()' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:248:42: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BtiBlock; _Alloc = std::allocator]', inlined from 'virtual bool BamTools::Internal::BamToolsIndex::Create()' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamToolsIndex_p.cpp:266:38: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.h:28, from /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BamTools::Internal::BaiAlignmentChunk&}; _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:634:27: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::MergeAlignmentChunks(BamTools::Internal::BaiAlignmentChunkVector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:655:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 61%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamDeviceFactory_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamDeviceFactory_p.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:813:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Internal::BaiAlignmentChunk; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::SaveAlignmentChunkToBin(BamTools::Internal::BaiBinMap&, const uint32_t&, const uint64_t&, const uint64_t&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:806:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'void BamTools::Internal::BamStandardIndex::SaveLinearOffsetEntry(BamTools::Internal::BaiLinearOffsetVector&, const int&, const int&, const uint64_t&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:837:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp:21: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const BamTools::Fasta::FastaPrivate::FastaIndexData&}; _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator]', inlined from 'bool BamTools::Fasta::FastaPrivate::CreateIndex(const std::string&)' at /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp:208:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 62%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamFile_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFile_p.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = BamTools::Fasta::FastaPrivate::FastaIndexData; _Alloc = std::allocator]', inlined from 'bool BamTools::Fasta::FastaPrivate::LoadIndexData()' at /build/bamtools-2.5.2+dfsg/src/utils/bamtools_fasta.cpp:556:24: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long int}; _Tp = long long int; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void BamTools::Internal::BamStandardIndex::CalculateCandidateOffsets(const BamTools::Internal::BaiReferenceSummary&, const uint64_t&, std::set&, std::vector&)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:179:38: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:489:9: /usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1937 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1938 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1939 | __comp); | ~~~~~~~ In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]', inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' at /usr/include/c++/12/bits/stl_algo.h:4820:18, inlined from 'void BamTools::Internal::BamStandardIndex::GetOffset(const BamTools::BamRegion&, int64_t&, bool*)' at /build/bamtools-2.5.2+dfsg/src/api/internal/index/BamStandardIndex_p.cpp:489:9: /usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ [ 63%] Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o -c /build/bamtools-2.5.2+dfsg/src/utils/bamtools_options.cpp [ 64%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamFtp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamFtp_p.cpp [ 65%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/BamHttp_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/BamHttp_p.cpp [ 66%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/BamPipe_p.cpp.o.d -o 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src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -MF CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o.d -o CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o -c /build/bamtools-2.5.2+dfsg/src/utils/bamtools_pileup_engine.cpp [ 69%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/ByteArray_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/ByteArray_p.cpp [ 70%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/HostAddress_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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Building CXX object src/CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools-utils.dir/utils/bamtools_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/bamtools-2.5.2+dfsg/src/utils/bamtools_utilities.cpp [ 74%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/ILocalIODevice_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/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/bamtools-2.5.2+dfsg/src/api/internal/io/ILocalIODevice_p.cpp [ 75%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/RollingBuffer_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/io/RollingBuffer_p.cpp [ 76%] Linking CXX static library libBamTools-utils.a cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -P CMakeFiles/BamTools-utils.dir/cmake_clean_target.cmake cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/BamTools-utils.dir/link.txt --verbose=1 /usr/bin/ar qc libBamTools-utils.a "CMakeFiles/BamTools-utils.dir/utils/bamtools_fasta.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_options.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_pileup_engine.cpp.o" "CMakeFiles/BamTools-utils.dir/utils/bamtools_utilities.cpp.o" /usr/bin/ranlib libBamTools-utils.a make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' [ 76%] Built target BamTools-utils [ 77%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/io/TcpSocketEngine_p.cpp.o -c 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-I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -MF CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o.d -o CMakeFiles/BamTools_static.dir/api/internal/sam/SamFormatPrinter_p.cpp.o -c /build/bamtools-2.5.2+dfsg/src/api/internal/sam/SamFormatPrinter_p.cpp [ 81%] Building CXX object src/CMakeFiles/BamTools_static.dir/api/internal/sam/SamHeaderValidator_p.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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/build/bamtools-2.5.2+dfsg/src/api/internal/io/TcpSocketEngine_unix_p.cpp make -f src/CMakeFiles/bamtools_cmd.dir/build.make src/CMakeFiles/bamtools_cmd.dir/depend make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/bamtools-2.5.2+dfsg /build/bamtools-2.5.2+dfsg/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src/CMakeFiles/bamtools_cmd.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make -f src/CMakeFiles/bamtools_cmd.dir/build.make src/CMakeFiles/bamtools_cmd.dir/build make[3]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' [ 84%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o cd 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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 [ 87%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp /usr/bin/ranlib libbamtools.a make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' [ 87%] Built target BamTools_static [ 88%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_coverage.cpp In file included from /build/bamtools-2.5.2+dfsg/src/api/BamAlgorithms.h:15, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:12: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.h:13, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_count.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 89%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_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/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/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_header.cpp [ 91%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_index.cpp [ 92%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_merge.cpp [ 93%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_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/bamtools-2.5.2+dfsg/src/toolkit/bamtools_random.cpp [ 94%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_resolve.cpp [ 95%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_revert.cpp [ 96%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp In file included from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:15: /build/bamtools-2.5.2+dfsg/src/api/algorithms/Sort.h:64:18: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 64 | typedef std::binary_function AlignmentSortBase; | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_tool.h:14, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.h:13, from /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_sort.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_split.cpp [ 98%] Building CXX object src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -I/usr/include/jsoncpp -I/build/bamtools-2.5.2+dfsg/src -I/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT src/CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -MF CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o.d -o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -c /build/bamtools-2.5.2+dfsg/src/toolkit/bamtools_stats.cpp [100%] Linking CXX executable bamtools cd /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bamtools_cmd.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/bamtools-2.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bamtools_cmd.dir/toolkit/bamtools.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_convert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_count.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_coverage.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_filter.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_header.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_index.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_merge.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_random.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_resolve.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_revert.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_sort.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_split.cpp.o CMakeFiles/bamtools_cmd.dir/toolkit/bamtools_stats.cpp.o -o bamtools -Wl,-rpath,/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src: libBamTools-utils.a -L/usr/lib/arm-linux-gnueabihf -ljsoncpp libbamtools.so.2.5.2 make[3]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' [100%] Built target bamtools_cmd make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' cd obj-* && ln -s src/toolkit/ bin dh_auto_test --arch cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j3 UpdateCTestConfiguration from :/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl UpdateCTestConfiguration from :/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/DartConfiguration.tcl Test project /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end test 1 Start 1: bamtools_help 1: Test command: /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src/bamtools "--help" 1: Working Directory: /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/tests 1: Test timeout computed to be: 1500 test 2 Start 2: bamtools_stats 2: Test command: /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/src/bamtools "stats" "-in" "/build/bamtools-2.5.2+dfsg/tests/data/sam_spec_example.bam" 2: Working Directory: /build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf/tests 2: Test timeout computed to be: 1500 1: 1: usage: bamtools [--help] COMMAND [ARGS] 1: 1: Available bamtools commands: 1: convert Converts between BAM and a number of other formats 1: count Prints number of alignments in BAM file(s) 1: coverage Prints coverage statistics from the input BAM file 1: filter Filters BAM file(s) by user-specified criteria 1: header Prints BAM header information 1: index Generates index for BAM file 1: merge Merge multiple BAM files into single file 1: random Select random alignments from existing BAM file(s), intended more as a testing tool. 1: resolve Resolves paired-end reads (marking the IsProperPair flag as needed) 1: revert Removes duplicate marks and restores original base qualities 1: sort Sorts the BAM file according to some criteria 1: split Splits a BAM file on user-specified property, creating a new BAM output file for each value found 1: stats Prints some basic statistics from input BAM file(s) 1: 1: See 'bamtools help COMMAND' for more information on a specific command. 1: 1/2 Test #1: bamtools_help .................... Passed 0.02 sec 2: 2: ********************************************** 2: Stats for BAM file(s): 2: ********************************************** 2: 2: Total reads: 6 2: Mapped reads: 6 (100%) 2: Forward strand: 4 (66.6667%) 2: Reverse strand: 2 (33.3333%) 2: Failed QC: 0 (0%) 2: Duplicates: 0 (0%) 2: Paired-end reads: 2 (33.3333%) 2: 'Proper-pairs': 2 (100%) 2: Both pairs mapped: 2 (100%) 2: Read 1: 1 2: Read 2: 1 2: Singletons: 0 (0%) 2: 2/2 Test #2: bamtools_stats ................... Passed 0.02 sec 100% tests passed, 0 tests failed out of 2 Total Test time (real) = 0.04 sec make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install -Nlibbamtools-doc cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/bamtools-2.5.2\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/bamtools-2.5.2+dfsg -B/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libbamtools.so.2.5.2 -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libbamtools.so -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libbamtools.a -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools -- Set runtime path of "/build/bamtools-2.5.2+dfsg/debian/tmp/usr/bin/bamtools" to "" -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlgorithms.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAlignment.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamAux.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamConstants.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamIndex.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamMultiReader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamReader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/BamWriter.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/IBamIODevice.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamConstants.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamHeader.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgram.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamProgramChain.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroup.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamReadGroupDictionary.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequence.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/SamSequenceDictionary.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/api_global.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/bamtools_api_export.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/api/algorithms/Sort.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/include/bamtools/shared/bamtools_global.h -- Installing: /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/pkgconfig/bamtools-1.pc make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg/obj-arm-linux-gnueabihf' debian/rules override_dh_install-arch make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' dh_install --arch d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev "debian/tmp/usr/lib/*/pkgconfig/*.pc" usr/lib/arm-linux-gnueabihf/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/arm-linux-gnueabihf install -d -m 755 debian/libbamtools2.5.2/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbamtools.a debian/libbamtools-dev/usr/lib/arm-linux-gnueabihf mv debian/tmp/usr/lib/arm-linux-gnueabihf/libbamtools.so debian/libbamtools-dev/usr/lib/arm-linux-gnueabihf mv /build/bamtools-2.5.2+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libbamtools.so.2.5.2 debian/libbamtools2.5.2/usr/lib/arm-linux-gnueabihf 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/arm-linux-gnueabihf/pkgconfig mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libbamtools-dev/usr/lib/arm-linux-gnueabihf/pkgconfig make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' debian/rules override_dh_install-indep make[1]: Entering directory '/build/bamtools-2.5.2+dfsg' dh_install --indep rm -f debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js ln -s /usr/share/javascript/jquery/jquery.js debian/libbamtools-doc/usr/share/doc/libbamtools-dev/html/jquery.js make[1]: Leaving directory '/build/bamtools-2.5.2+dfsg' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libbamtools2.5.2/usr/lib/arm-linux-gnueabihf/libbamtools.so.2.5.2 found in none of the libraries dpkg-shlibdeps: warning: debian/bamtools/usr/bin/bamtools contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'bamtools' in '../bamtools_2.5.2+dfsg-4_armhf.deb'. dpkg-deb: building package 'libbamtools-dev' in '../libbamtools-dev_2.5.2+dfsg-4_armhf.deb'. dpkg-deb: building package 'libbamtools2.5.2-dbgsym' in '../libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_armhf.deb'. dpkg-deb: building package 'bamtools-dbgsym' in '../bamtools-dbgsym_2.5.2+dfsg-4_armhf.deb'. dpkg-deb: building package 'libbamtools2.5.2' in '../libbamtools2.5.2_2.5.2+dfsg-4_armhf.deb'. dpkg-deb: building package 'libbamtools-doc' in '../libbamtools-doc_2.5.2+dfsg-4_all.deb'. dpkg-genbuildinfo --build=binary -O../bamtools_2.5.2+dfsg-4_armhf.buildinfo dpkg-genchanges --build=binary -O../bamtools_2.5.2+dfsg-4_armhf.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/25571 and its subdirectories I: Current time: Thu May 4 09:06:13 -12 2023 I: pbuilder-time-stamp: 1683234373 Thu May 4 21:06:30 UTC 2023 I: 1st build successful. Starting 2nd build on remote node virt64b-armhf-rb.debian.net. Thu May 4 21:06:30 UTC 2023 I: Preparing to do remote build '2' on virt64b-armhf-rb.debian.net. Thu May 4 21:17:01 UTC 2023 I: Deleting $TMPDIR on virt64b-armhf-rb.debian.net. Thu May 4 21:17:03 UTC 2023 I: bamtools_2.5.2+dfsg-4_armhf.changes: Format: 1.8 Date: Mon, 19 Dec 2022 22:45:16 +0100 Source: bamtools Binary: bamtools bamtools-dbgsym libbamtools-dev libbamtools-doc libbamtools2.5.2 libbamtools2.5.2-dbgsym Architecture: armhf all Version: 2.5.2+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: bamtools - toolkit for manipulating BAM (genome alignment) files libbamtools-dev - C++ API for manipulating BAM (genome alignment) files libbamtools-doc - docs for dynamic library for manipulating BAM (genome alignment) libbamtools2.5.2 - dynamic library for manipulating BAM (genome alignment) files Closes: 988848 Changes: bamtools (2.5.2+dfsg-4) unstable; urgency=medium . * Team upload. * d/control: libbamtools-doc depends on libjs-jquery. Thanks to Andreas Beckmann (Closes: #988848) * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 11ec588207fadc45867f0b9b3aef4fc0da4c312f 3704240 bamtools-dbgsym_2.5.2+dfsg-4_armhf.deb 530c1dd92152c5d70e3d9ec87bf3d18a872151ad 7660 bamtools_2.5.2+dfsg-4_armhf.buildinfo 79cac60bd38eafc862c44b8bbc10e84d1854c8c4 172512 bamtools_2.5.2+dfsg-4_armhf.deb dd1cdf180c6b19fe7d9bd54358b146518c60b260 198224 libbamtools-dev_2.5.2+dfsg-4_armhf.deb e56466023933d7854010c5bf0f5fb74417156b96 160752 libbamtools-doc_2.5.2+dfsg-4_all.deb 40d900b55b04d239bab18cc8926df34ae819e13f 2788504 libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_armhf.deb 0c788f49c8227cf7d3dc6077612be3c567b6ed29 129772 libbamtools2.5.2_2.5.2+dfsg-4_armhf.deb Checksums-Sha256: 90222a6f85391cb5cd95e7ab76f2017f9cb53b9b403be4169f9cac1b02004ed3 3704240 bamtools-dbgsym_2.5.2+dfsg-4_armhf.deb 767d64487c46fdbcae003f6b2155c80e01b6861e8274bdfd1e0ac3567e97126c 7660 bamtools_2.5.2+dfsg-4_armhf.buildinfo 76daaaeb8a14e5c355b46a6da471f6c11635aa898e4dd7c310a657e12226d197 172512 bamtools_2.5.2+dfsg-4_armhf.deb 8a73063f093fa2f85cb2c12ffbd422c3e3e8c0533f0bf1cac7186282e69de691 198224 libbamtools-dev_2.5.2+dfsg-4_armhf.deb ba25a3543338262fe9722acb5ed17fb6fe3f5635c0ebf8cf29138e0c864b54af 160752 libbamtools-doc_2.5.2+dfsg-4_all.deb 7a690f629672ff9e442cb4454a29af818fe6709ecdd614d5a0289d09f1c88128 2788504 libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_armhf.deb bb7b1ddcec4a0f662fba8c42644cd25f903c7b16f516096927403a531ad8ee5c 129772 libbamtools2.5.2_2.5.2+dfsg-4_armhf.deb Files: be903b81d0952ed1a839c220768806ee 3704240 debug optional bamtools-dbgsym_2.5.2+dfsg-4_armhf.deb 35a44a321f2deacd2ca25787af269be7 7660 science optional bamtools_2.5.2+dfsg-4_armhf.buildinfo 144157a14a6f1a13939522c4f542a017 172512 science optional bamtools_2.5.2+dfsg-4_armhf.deb 55e739ebe8524dff300f4369766f85f1 198224 libdevel optional libbamtools-dev_2.5.2+dfsg-4_armhf.deb 5b204fe0fceccbf208e3830fd8b00f37 160752 doc optional libbamtools-doc_2.5.2+dfsg-4_all.deb d552eaf6280c91571203d00cfb851ba2 2788504 debug optional libbamtools2.5.2-dbgsym_2.5.2+dfsg-4_armhf.deb 4cb83b0aa60939acfdc18501b0ff378f 129772 libs optional libbamtools2.5.2_2.5.2+dfsg-4_armhf.deb Thu May 4 21:17:07 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.qtsyXzdp/bamtools_2.5.2+dfsg-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.qtsyXzdp/bamtools_2.5.2+dfsg-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.qtsyXzdp/bamtools_2.5.2+dfsg-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.qtsyXzdp/b1/bamtools_2.5.2+dfsg-4_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.qtsyXzdp/b2/bamtools_2.5.2+dfsg-4_armhf.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: 1.324s) 1.324s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.749s) 0.749s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Thu May 4 21:17:13 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Thu May 4 21:17:14 UTC 2023 I: bamtools from bookworm built successfully and reproducibly on armhf. Thu May 4 21:17:22 UTC 2023 I: Submitting .buildinfo files to external archives: Thu May 4 21:17:22 UTC 2023 I: Submitting 12K b1/bamtools_2.5.2+dfsg-4_armhf.buildinfo.asc Thu May 4 21:17:24 UTC 2023 I: Submitting 12K b2/bamtools_2.5.2+dfsg-4_armhf.buildinfo.asc Thu May 4 21:17:30 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 4 21:17:30 UTC 2023 I: Done submitting .buildinfo files. Thu May 4 21:17:30 UTC 2023 I: Removing signed bamtools_2.5.2+dfsg-4_armhf.buildinfo.asc files: removed './b1/bamtools_2.5.2+dfsg-4_armhf.buildinfo.asc' removed './b2/bamtools_2.5.2+dfsg-4_armhf.buildinfo.asc'