Fri Dec 13 16:59:55 UTC 2024 I: starting to build biobambam2/trixie/amd64 on jenkins on '2024-12-13 16:59' Fri Dec 13 16:59:55 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_20/39444/console.log Fri Dec 13 16:59:55 UTC 2024 I: Downloading source for trixie/biobambam2=2.0.185+ds-2 --2024-12-13 16:59:55-- http://deb.debian.org/debian/pool/main/b/biobambam2/biobambam2_2.0.185%2bds-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2254 (2.2K) [text/prs.lines.tag] Saving to: ‘biobambam2_2.0.185+ds-2.dsc’ 0K .. 100% 355M=0s 2024-12-13 16:59:55 (355 MB/s) - ‘biobambam2_2.0.185+ds-2.dsc’ saved [2254/2254] Fri Dec 13 16:59:55 UTC 2024 I: biobambam2_2.0.185+ds-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: biobambam2 Binary: biobambam2 Architecture: any Version: 2.0.185+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://gitlab.com/german.tischler/biobambam2 Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/biobambam2 Vcs-Git: https://salsa.debian.org/med-team/biobambam2.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev Package-List: biobambam2 deb science optional arch=any Checksums-Sha1: 2776b598958c159faa1147765a37a9be788c8725 249000 biobambam2_2.0.185+ds.orig.tar.xz a6d8b9f5865c14806d595f2ac8cd188e3f9edcd2 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Checksums-Sha256: 90cc8328f4e78771cf87cc918d890d12073cbbfbcad7cf94e35b655e3ec2747a 249000 biobambam2_2.0.185+ds.orig.tar.xz 5010ff92699f48db055e33a6ddda005ed339388cc1995503e985325e4d53652c 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Files: d0c485318daa583137b98d18fd0add77 249000 biobambam2_2.0.185+ds.orig.tar.xz bc64f60dd4ccfa2477438dcd2db1131e 1032436 biobambam2_2.0.185+ds-2.debian.tar.xz Dgit: 8e56855700614f8a0ddddf4fd2cb5611e10015e4 debian archive/debian/2.0.185+ds-2 https://git.dgit.debian.org/biobambam2 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmYikWMUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrX1A//dGe1VAwa3juRlsGgmA9kRTYR+J89 x2/kBqtpIS8cO7onEyZ2MDixN7hFFq9QHCh0w7q1vBpdMMmPXJ5doQIQuTVcvWia Ugv0eGCk7v6Mja6dwECg9/JZ9IKn4BDQ0Mxectx/vWqEaa1BDhX4OLA6TfiluenO bYa0mcj4zm4jtlw1MbFYLOmf3d4fkSrDCtAqacc/DfchuesLVBkBaxb6oX/RuPzP T41aTROw4wxydmqd/04LSEXvJ55mZqzjihN+o12VpSsfdjsjQn/1WV9O7MmLbzdz VVDzXzOCrEzT0Um7E91gJ6E1D0RcUDlSCm2HXNcmUA2xc/ZawEQ8cOQMGkUao7NR DjeF38kGLokp/Djwd0LcoJDlIAfssb+T+B/gDndJINQpHzYsggCAlHfqjpJRRwpz CgvdGt2rrIi3ktmRoraoWmqN6XvCyjQFr3XxmLlw4T6p9Mk/5+Oj3IF+suMtm7EZ 1vLUbLoGwrT/zS+3Fdiu5+31uJv3Nm816IkefAEv/FhRqzrXW20IguFdmLFeQFI8 uP3+CcgbQfcs9REtB2MAJ50GQLi84ch3vXjxdizQAiZXgxhMNXXhn6BLNcgsYmVO 9v9u6mbo10JW+0kXVHsrg0f4I+OwdcrT/xuZKrsDM/VPgFdV6g+GQJE0Dkgbb6i2 py7JtzKEuhkACi0= =ZDUq -----END PGP SIGNATURE----- Fri Dec 13 16:59:55 UTC 2024 I: Checking whether the package is not for us Fri Dec 13 16:59:56 UTC 2024 I: Starting 1st build on remote node ionos15-amd64.debian.net. Fri Dec 13 16:59:56 UTC 2024 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Fri Dec 13 17:08:27 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 15 11:22:57 -12 2026 I: pbuilder-time-stamp: 1768519377 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 [biobambam2_2.0.185+ds-2.dsc] I: copying [./biobambam2_2.0.185+ds.orig.tar.xz] I: copying [./biobambam2_2.0.185+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Apr 19 15:44:35 2024 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 ./biobambam2_2.0.185+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting biobambam2 in biobambam2-2.0.185+ds dpkg-source: info: unpacking biobambam2_2.0.185+ds.orig.tar.xz dpkg-source: info: unpacking biobambam2_2.0.185+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3717086/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='9aa4d1f119054f3b8d2a3f497697abb3' 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='3717086' 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.wP6uHb27/pbuilderrc_bvRc --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wP6uHb27/b1 --logfile b1/build.log biobambam2_2.0.185+ds-2.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3717086/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 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 pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libmaus2-dev (>= 2.0.800); however: Package libmaus2-dev is not installed. pbuilder-satisfydepends-dummy depends on libxerces-c-dev; however: Package libxerces-c-dev 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} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libassuan9{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgpgme11t64{a} libgssapi-krb5-2{a} libicu-dev{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmaus2-2{a} libmaus2-dev{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnpth0t64{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libxerces-c-dev{a} libxerces-c3.2t64{a} libxml2{a} m4{a} man-db{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl gnupg-utils gpg-wks-client krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 46.8 MB of archives. After unpacking 254 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-8 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 23 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 gpgconf amd64 2.2.45-2 [120 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libnpth0t64 amd64 1.6-3.1+b1 [18.2 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 dirmngr amd64 2.2.45-2 [368 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 gnupg-l10n all 2.2.45-2 [705 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 gpg amd64 2.2.45-2 [531 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 pinentry-curses amd64 1.2.1-4+b1 [79.7 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 gpg-agent amd64 2.2.45-2 [251 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 gpgsm amd64 2.2.45-2 [255 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 gnupg all 2.2.45-2 [376 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 52 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libgpgme11t64 amd64 1.24.0-2 [344 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libmaus2-2 amd64 2.0.813+ds-3 [1945 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libmaus2-dev amd64 2.0.813+ds-3 [5192 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libxerces-c3.2t64 amd64 3.2.4+debian-1.3+b1 [900 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libxerces-c-dev amd64 3.2.4+debian-1.3+b1 [1708 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Fetched 46.8 MB in 1s (71.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19965 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3+b1_amd64.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.22.5-2_amd64.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-6_amd64.deb ... Unpacking groff-base (1.23.0-6) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40.2-12_amd64.deb ... Unpacking bsdextrautils (2.40.2-12) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package gpgconf. Preparing to unpack .../32-gpgconf_2.2.45-2_amd64.deb ... Unpacking gpgconf (2.2.45-2) ... Selecting previously unselected package libksba8:amd64. Preparing to unpack .../33-libksba8_1.6.7-2+b1_amd64.deb ... Unpacking libksba8:amd64 (1.6.7-2+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. 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Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../53-libnghttp2-14_1.64.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../54-libnghttp3-9_1.6.0-2_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.6.0-2) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../55-libngtcp2-16_1.9.1-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.9.1-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../56-libngtcp2-crypto-gnutls8_1.9.1-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../57-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:amd64. 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Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-4) ... Setting up gnupg-l10n (2.2.45-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up autopoint (0.22.5-2) ... Setting up icu-devtools (72.1-5+b1) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up libnghttp3-9:amd64 (1.6.0-2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libassuan9:amd64 (3.0.1-2) ... Setting up libngtcp2-16:amd64 (1.9.1-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:amd64 (72.1-5+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... 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 pinentry-curses (1.2.1-4+b1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-8) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-6) ... Setting up gpgconf (2.2.45-2) ... Setting up gpg (2.2.45-2) ... Setting up gpg-agent (2.2.45-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up gpgsm (2.2.45-2) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up libxerces-c3.2t64:amd64 (3.2.4+debian-1.3+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.45-2) ... Setting up libxerces-c-dev:amd64 (3.2.4+debian-1.3+b1) ... Setting up gnupg (2.2.45-2) ... Setting up libgpgme11t64:amd64 (1.24.0-2) ... Setting up libmaus2-2:amd64 (2.0.813+ds-3) ... Setting up debhelper (13.20) ... Setting up libmaus2-dev (2.0.813+ds-3) ... Processing triggers for libc-bin (2.40-4) ... 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/reproducible-path/biobambam2-2.0.185+ds/ && 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 > ../biobambam2_2.0.185+ds-2_source.changes dpkg-buildpackage: info: source package biobambam2 dpkg-buildpackage: info: source version 2.0.185+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_auto_clean rm -f config.log make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:2: warning: The macro 'AC_CANONICAL_SYSTEM' is obsolete. configure.ac:2: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:2: the top level configure.ac:3: warning: The macro 'AC_PROG_LIBTOOL' is obsolete. configure.ac:3: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:3: the top level configure.ac:6: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:6: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:1089: AM_CONFIG_HEADER is expanded from... configure.ac:6: the top level configure.ac:9: warning: The macro 'AC_CANONICAL_SYSTEM' is obsolete. configure.ac:9: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:9: the top level configure.ac:68: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.ac:68: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... configure.ac:68: the top level configure.ac:147: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.ac:147: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.ac:147: the top level configure.ac:464: warning: AC_OUTPUT should be used without arguments. configure.ac:464: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking how to print strings... printf checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking whether we are cross compiling... no checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking dependency style of g++... none checking whether the C++ compiler supports the -fsanitize=address flag... yes configure: Adding optimisation options -O3 to C compiler gcc flags, full list now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 configure: Adding optimisation options -O3 to C++ compiler g++ flags, full list now -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for egrep... (cached) /usr/bin/grep -E checking for libmaus2 >= 2.0.800... yes checking whether we can compile a program using libmaus2... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE_NP... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE... yes checking whether libmaus2 has support for io_lib... no checking for bash... /usr/bin/bash checking for base64... /usr/bin/base64 checking for xerces-c >= 3.1.1... yes configure: Using flags -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 for C compiler gcc configure: Using flags -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 for C++ compiler g++ checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating src/biobambam2/BamBamConfig.hpp config.status: creating config.h config.status: executing libtool commands config.status: executing depfiles commands dh_auto_build make -j42 make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make all-recursive make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making all in src make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamtofastq-bamtofastq.o `test -f 'programs/bamtofastq.cpp' || echo './'`programs/bamtofastq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicates-bammarkduplicates.o `test -f 'programs/bammarkduplicates.cpp' || echo './'`programs/bammarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsort-bamsort.o `test -f 'programs/bamsort.cpp' || echo './'`programs/bamsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammaskflags-bammaskflags.o `test -f 'programs/bammaskflags.cpp' || echo './'`programs/bammaskflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammaskflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrecompress-bamrecompress.o `test -f 'programs/bamrecompress.cpp' || echo './'`programs/bamrecompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrecompress-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamadapterfind-bamadapterfind.o `test -f 'programs/bamadapterfind.cpp' || echo './'`programs/bamadapterfind.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterfind-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterfind-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterfind-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilteraux-bamfilteraux.o `test -f 'programs/bamfilteraux.cpp' || echo './'`programs/bamfilteraux.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilteraux-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamauxsort-bamauxsort.o `test -f 'programs/bamauxsort.cpp' || echo './'`programs/bamauxsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamadapterclip-bamadapterclip.o `test -f 'programs/bamadapterclip.cpp' || echo './'`programs/bamadapterclip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterclip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterclip-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamcollate2-bamcollate2.o `test -f 'programs/bamcollate2.cpp' || echo './'`programs/bamcollate2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcollate2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcollate2-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcollate2-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bam12auxmerge-bam12auxmerge.o `test -f 'programs/bam12auxmerge.cpp' || echo './'`programs/bam12auxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12auxmerge-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bam12split-bam12split.o `test -f 'programs/bam12split.cpp' || echo './'`programs/bam12split.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12split-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12split-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bam12strip-bam12strip.o `test -f 'programs/bam12strip.cpp' || echo './'`programs/bam12strip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12strip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bam12strip-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamreset-bamreset.o `test -f 'programs/bamreset.cpp' || echo './'`programs/bamreset.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreset-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreset-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrank-bamrank.o `test -f 'programs/bamrank.cpp' || echo './'`programs/bamrank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrank-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrank-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamclipreinsert-bamclipreinsert.o `test -f 'programs/bamclipreinsert.cpp' || echo './'`programs/bamclipreinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamclipreinsert-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamclipreinsert-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamclipXT-bamclipXT.o `test -f 'programs/bamclipXT.cpp' || echo './'`programs/bamclipXT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamclipXT-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamzztoname-bamzztoname.o `test -f 'programs/bamzztoname.cpp' || echo './'`programs/bamzztoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamzztoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamzztoname-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamindex-bamindex.o `test -f 'programs/bamindex.cpp' || echo './'`programs/bamindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterflags-bamfilterflags.o `test -f 'programs/bamfilterflags.cpp' || echo './'`programs/bamfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterrg-bamfilterrg.o `test -f 'programs/bamfilterrg.cpp' || echo './'`programs/bamfilterrg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterrg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdownsamplerandom-bamdownsamplerandom.o `test -f 'programs/bamdownsamplerandom.cpp' || echo './'`programs/bamdownsamplerandom.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdownsamplerandom-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicates2-bammarkduplicates2.o `test -f 'programs/bammarkduplicates2.cpp' || echo './'`programs/bammarkduplicates2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicates2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamcat-bamcat.o `test -f 'programs/bamcat.cpp' || echo './'`programs/bamcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammerge-bammerge.o `test -f 'programs/bammerge.cpp' || echo './'`programs/bammerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsplit-bamsplit.o `test -f 'programs/bamsplit.cpp' || echo './'`programs/bamsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastsplit-bamfastsplit.o `test -f 'programs/bamfastsplit.cpp' || echo './'`programs/bamfastsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsplitdiv-bamsplitdiv.o `test -f 'programs/bamsplitdiv.cpp' || echo './'`programs/bamsplitdiv.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsplitdiv-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamchecksort-bamchecksort.o `test -f 'programs/bamchecksort.cpp' || echo './'`programs/bamchecksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamchecksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastqtobam-fastqtobam.o `test -f 'programs/fastqtobam.cpp' || echo './'`programs/fastqtobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixmateinformation-bamfixmateinformation.o `test -f 'programs/bamfixmateinformation.cpp' || echo './'`programs/bamfixmateinformation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixmateinformation-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamseqchksum-bamseqchksum.o `test -f 'programs/bamseqchksum.cpp' || echo './'`programs/bamseqchksum.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamseqchksum-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/normalisefasta-normalisefasta.o `test -f 'programs/normalisefasta.cpp' || echo './'`programs/normalisefasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/normalisefasta-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterheader-bamfilterheader.o `test -f 'programs/bamfilterheader.cpp' || echo './'`programs/bamfilterheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterheader2-bamfilterheader2.o `test -f 'programs/bamfilterheader2.cpp' || echo './'`programs/bamfilterheader2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterheader2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammdnm-bammdnm.o `test -f 'programs/bammdnm.cpp' || echo './'`programs/bammdnm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammdnm-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammapdist-bammapdist.o `test -f 'programs/bammapdist.cpp' || echo './'`programs/bammapdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammapdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamvalidate-bamvalidate.o `test -f 'programs/bamvalidate.cpp' || echo './'`programs/bamvalidate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamvalidate-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamflagsplit-bamflagsplit.o `test -f 'programs/bamflagsplit.cpp' || echo './'`programs/bamflagsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamflagsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamintervalcomment-bamintervalcomment.o `test -f 'programs/bamintervalcomment.cpp' || echo './'`programs/bamintervalcomment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamintervalcomment-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamintervalcommenthist-bamintervalcommenthist.o `test -f 'programs/bamintervalcommenthist.cpp' || echo './'`programs/bamintervalcommenthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamintervalcommenthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o `test -f 'programs/bamstreamingmarkduplicates.cpp' || echo './'`programs/bamstreamingmarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamstreamingmarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamalignfrac-bamalignfrac.o `test -f 'programs/bamalignfrac.cpp' || echo './'`programs/bamalignfrac.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamalignfrac-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilternames-bamfilternames.o `test -f 'programs/bamfilternames.cpp' || echo './'`programs/bamfilternames.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilternames-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsormadup-bamsormadup.o `test -f 'programs/bamsormadup.cpp' || echo './'`programs/bamsormadup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsormadup-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexplode-bamexplode.o `test -f 'programs/bamexplode.cpp' || echo './'`programs/bamexplode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexplode-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexploderef-bamexploderef.o `test -f 'programs/bamexploderef.cpp' || echo './'`programs/bamexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastexploderef-bamfastexploderef.o `test -f 'programs/bamfastexploderef.cpp' || echo './'`programs/bamfastexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastnumextract-bamfastnumextract.o `test -f 'programs/bamfastnumextract.cpp' || echo './'`programs/bamfastnumextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastnumextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamranksort-bamranksort.o `test -f 'programs/bamranksort.cpp' || echo './'`programs/bamranksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamranksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastaexplod-fastaexplod.o `test -f 'programs/fastaexplod.cpp' || echo './'`programs/fastaexplod.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastaexplod-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrecalculatecigar-bamrecalculatecigar.o `test -f 'programs/bamrecalculatecigar.cpp' || echo './'`programs/bamrecalculatecigar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrecalculatecigar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfiltermc-bamfiltermc.o `test -f 'programs/bamfiltermc.cpp' || echo './'`programs/bamfiltermc.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfiltermc-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamnumericalindex-bamnumericalindex.o `test -f 'programs/bamnumericalindex.cpp' || echo './'`programs/bamnumericalindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamnumericalindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamnumericalindexstats-bamnumericalindexstats.o `test -f 'programs/bamnumericalindexstats.cpp' || echo './'`programs/bamnumericalindexstats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamnumericalindexstats-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicatesopt-bammarkduplicatesopt.o `test -f 'programs/bammarkduplicatesopt.cpp' || echo './'`programs/bammarkduplicatesopt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicatesopt-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterlength-bamfilterlength.o `test -f 'programs/bamfilterlength.cpp' || echo './'`programs/bamfilterlength.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterlength-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamauxmerge-bamauxmerge.o `test -f 'programs/bamauxmerge.cpp' || echo './'`programs/bamauxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrefinterval-bamrefinterval.o `test -f 'programs/bamrefinterval.cpp' || echo './'`programs/bamrefinterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrefinterval-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamscrapcount-bamscrapcount.o `test -f 'programs/bamscrapcount.cpp' || echo './'`programs/bamscrapcount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamscrapcount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterrefid-bamfilterrefid.o `test -f 'programs/bamfilterrefid.cpp' || echo './'`programs/bamfilterrefid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterrefid-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfillquery-bamfillquery.o `test -f 'programs/bamfillquery.cpp' || echo './'`programs/bamfillquery.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfillquery-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfillquery-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrefextract-bamrefextract.o `test -f 'programs/bamrefextract.cpp' || echo './'`programs/bamrefextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrefextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastqtobam2-fastqtobam2.o `test -f 'programs/fastqtobam2.cpp' || echo './'`programs/fastqtobam2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobam2-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamauxmerge2-bamauxmerge2.o `test -f 'programs/bamauxmerge2.cpp' || echo './'`programs/bamauxmerge2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxmerge2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamauxmerge2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamreheader-bamreheader.o `test -f 'programs/bamreheader.cpp' || echo './'`programs/bamreheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreheader-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamreplacechecksums-bamreplacechecksums.o `test -f 'programs/bamreplacechecksums.cpp' || echo './'`programs/bamreplacechecksums.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp programs/fastqtobam2.cpp: In member function 'virtual void BlockReadControl::checkBgzfWriteQueue()': programs/fastqtobam2.cpp:3861:43: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3861 | while ( ptr = bgzfGetNext() ) | ^ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfastcat-bamfastcat.o `test -f 'programs/bamfastcat.cpp' || echo './'`programs/bamfastcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastcat-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfastcat-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/populaterefcache-populaterefcache.o `test -f 'programs/populaterefcache.cpp' || echo './'`programs/populaterefcache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/populaterefcache-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfiltereofblocks-bamfiltereofblocks.o `test -f 'programs/bamfiltereofblocks.cpp' || echo './'`programs/bamfiltereofblocks.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfiltereofblocks-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfiltereofblocks-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdepth-bamdepth.o `test -f 'programs/bamdepth.cpp' || echo './'`programs/bamdepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdepthintersect-bamdepthintersect.o `test -f 'programs/bamdepthintersect.cpp' || echo './'`programs/bamdepthintersect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepthintersect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepthintersect-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterk-bamfilterk.o `test -f 'programs/bamfilterk.cpp' || echo './'`programs/bamfilterk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterk-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterk-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterk-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixpairinfo-bamfixpairinfo.o `test -f 'programs/bamfixpairinfo.cpp' || echo './'`programs/bamfixpairinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixpairinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixpairinfo-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixpairinfo-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdifference-bamdifference.o `test -f 'programs/bamdifference.cpp' || echo './'`programs/bamdifference.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdifference-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfeaturecount-bamfeaturecount.o `test -f 'programs/bamfeaturecount.cpp' || echo './'`programs/bamfeaturecount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfeaturecount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/blastnxmltobam-blastnxmltobam.o `test -f 'programs/blastnxmltobam.cpp' || echo './'`programs/blastnxmltobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/blastnxmltobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilter-bamfilter.o `test -f 'programs/bamfilter.cpp' || echo './'`programs/bamfilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilter-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfilterbyname-bamfilterbyname.o `test -f 'programs/bamfilterbyname.cpp' || echo './'`programs/bamfilterbyname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfilterbyname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixmatecoordinates-bamfixmatecoordinates.o `test -f 'programs/bamfixmatecoordinates.cpp' || echo './'`programs/bamfixmatecoordinates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixmatecoordinates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o `test -f 'programs/bamfixmatecoordinatesnamesorted.cpp' || echo './'`programs/bamfixmatecoordinatesnamesorted.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamtoname-bamtoname.o `test -f 'programs/bamtoname.cpp' || echo './'`programs/bamtoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamtoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdisthist-bamdisthist.o `test -f 'programs/bamdisthist.cpp' || echo './'`programs/bamdisthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdisthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastabgzfextract-fastabgzfextract.o `test -f 'programs/fastabgzfextract.cpp' || echo './'`programs/fastabgzfextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastabgzfextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheap-bamheap.o `test -f 'programs/bamheap.cpp' || echo './'`programs/bamheap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamfrontback-bamfrontback.o `test -f 'programs/bamfrontback.cpp' || echo './'`programs/bamfrontback.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfrontback-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamfrontback-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamrandomtag-bamrandomtag.o `test -f 'programs/bamrandomtag.cpp' || echo './'`programs/bamrandomtag.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamrandomtag-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheap2-bamheap2.o `test -f 'programs/bamheap2.cpp' || echo './'`programs/bamheap2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheap2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheap3-bamheap3.o `test -f 'programs/bamheap3.cpp' || echo './'`programs/bamheap3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheap3-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamtagconversion-bamtagconversion.o `test -f 'programs/bamtagconversion.cpp' || echo './'`programs/bamtagconversion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamtagconversion-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastqtobampar-fastqtobampar.o `test -f 'programs/fastqtobampar.cpp' || echo './'`programs/fastqtobampar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastqtobampar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bambisect-bambisect.o `test -f 'programs/bambisect.cpp' || echo './'`programs/bambisect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bambisect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcffilterinfo-vcffilterinfo.o `test -f 'programs/vcffilterinfo.cpp' || echo './'`programs/vcffilterinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcffilterinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o `test -f 'programs/vcfpatchcontigprepend.cpp' || echo './'`programs/vcfpatchcontigprepend.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfpatchcontigprepend-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfconcat-vcfconcat.o `test -f 'programs/vcfconcat.cpp' || echo './'`programs/vcfconcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfconcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfsort-vcfsort.o `test -f 'programs/vcfsort.cpp' || echo './'`programs/vcfsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/filtergtf-filtergtf.o `test -f 'programs/filtergtf.cpp' || echo './'`programs/filtergtf.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/filtergtf-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamconsensus-bamconsensus.o `test -f 'programs/bamconsensus.cpp' || echo './'`programs/bamconsensus.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamconsensus-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfreplacecontigs-vcfreplacecontigs.o `test -f 'programs/vcfreplacecontigs.cpp' || echo './'`programs/vcfreplacecontigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfreplacecontigs-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcffiltersamples-vcffiltersamples.o `test -f 'programs/vcffiltersamples.cpp' || echo './'`programs/vcffiltersamples.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcffiltersamples-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexploderg-bamexploderg.o `test -f 'programs/bamexploderg.cpp' || echo './'`programs/bamexploderg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexploderg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamexondepth-bamexondepth.o `test -f 'programs/bamexondepth.cpp' || echo './'`programs/bamexondepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexondepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamexondepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp In file included from programs/bamexondepth.cpp:22: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ In file included from /usr/include/c++/14/cassert:44, from /usr/include/libmaus2/avl/AVLSet.hpp:24, from programs/bamexondepth.cpp:43: programs/bamexondepth.cpp: In function 'void handleFile(const std::string&, uint64_t, const libmaus2::bambam::BamHeader&, std::ostream&, std::ostream&, const std::string&)': programs/bamexondepth.cpp:121:44: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] 121 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ programs/bamexondepth.cpp:371:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long unsigned int'} and 'int64_t' {aka 'long int'} [-Wsign-compare] 371 | if ( d <= thresdepth ) | ~~^~~~~~~~~~~~~ programs/bamexondepth.cpp:375:52: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] 375 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamheadercat-bamheadercat.o `test -f 'programs/bamheadercat.cpp' || echo './'`programs/bamheadercat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamheadercat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o `test -f 'programs/bammarkduplicatesoptdist.cpp' || echo './'`programs/bammarkduplicatesoptdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicatesoptdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfdiff-vcfdiff.o `test -f 'programs/vcfdiff.cpp' || echo './'`programs/vcfdiff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfdiff-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsimpledepth-bamsimpledepth.o `test -f 'programs/bamsimpledepth.cpp' || echo './'`programs/bamsimpledepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsimpledepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsimpledepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamdepthmerge-bamdepthmerge.o `test -f 'programs/bamdepthmerge.cpp' || echo './'`programs/bamdepthmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamdepthmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamcountflags-bamcountflags.o `test -f 'programs/bamcountflags.cpp' || echo './'`programs/bamcountflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamcountflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp In file included from programs/bamdepthmerge.cpp:23: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcffilterfilterflags-vcffilterfilterflags.o `test -f 'programs/vcffilterfilterflags.cpp' || echo './'`programs/vcffilterfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcffilterfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o `test -f 'programs/vcfreplacecontigsmap.cpp' || echo './'`programs/vcfreplacecontigsmap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/vcfreplacecontigsmap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/fastaselectreg-fastaselectreg.o `test -f 'programs/fastaselectreg.cpp' || echo './'`programs/fastaselectreg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/fastaselectreg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp programs/vcfreplacecontigsmap.cpp:29:12: warning: 'int getDefaultGZ()' defined but not used [-Wunused-function] 29 | static int getDefaultGZ() { return 0; } | ^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamaddne-bamaddne.o `test -f 'programs/bamaddne.cpp' || echo './'`programs/bamaddne.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamaddne-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamadapterhistogram-bamadapterhistogram.o `test -f 'programs/bamadapterhistogram.cpp' || echo './'`programs/bamadapterhistogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamadapterhistogram-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o programs/bamsalvage-bamsalvage.o `test -f 'programs/bamsalvage.cpp' || echo './'`programs/bamsalvage.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamsalvage-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bamtofastq-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o biobambam2/bammarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcollate2 programs/bamcollate2-bamcollate2.o biobambam2/bamcollate2-Licensing.o biobambam2/bamcollate2-AttachRank.o biobambam2/bamcollate2-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bam12auxmerge programs/bam12auxmerge-bam12auxmerge.o biobambam2/bam12auxmerge-Licensing.o biobambam2/bam12auxmerge-Split12.o biobambam2/bam12auxmerge-Strip12.o biobambam2/bam12auxmerge-ClipReinsert.o biobambam2/bam12auxmerge-zzToName.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bam12split programs/bam12split-bam12split.o biobambam2/bam12split-Licensing.o biobambam2/bam12split-Split12.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bam12strip programs/bam12strip-bam12strip.o biobambam2/bam12strip-Licensing.o biobambam2/bam12strip-Strip12.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcollate2 programs/bamcollate2-bamcollate2.o biobambam2/bamcollate2-Licensing.o biobambam2/bamcollate2-AttachRank.o biobambam2/bamcollate2-ResetAlignment.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreset programs/bamreset-bamreset.o biobambam2/bamreset-Licensing.o biobambam2/bamreset-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bam12auxmerge programs/bam12auxmerge-bam12auxmerge.o biobambam2/bam12auxmerge-Licensing.o biobambam2/bam12auxmerge-Split12.o biobambam2/bam12auxmerge-Strip12.o biobambam2/bam12auxmerge-ClipReinsert.o biobambam2/bam12auxmerge-zzToName.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrank programs/bamrank-bamrank.o biobambam2/bamrank-Licensing.o biobambam2/bamrank-AttachRank.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bam12split programs/bam12split-bam12split.o biobambam2/bam12split-Licensing.o biobambam2/bam12split-Split12.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bam12strip programs/bam12strip-bam12strip.o biobambam2/bam12strip-Licensing.o biobambam2/bam12strip-Strip12.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamreset programs/bamreset-bamreset.o biobambam2/bamreset-Licensing.o biobambam2/bamreset-ResetAlignment.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrank programs/bamrank-bamrank.o biobambam2/bamrank-Licensing.o biobambam2/bamrank-AttachRank.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamclipreinsert programs/bamclipreinsert-bamclipreinsert.o biobambam2/bamclipreinsert-Licensing.o biobambam2/bamclipreinsert-ClipReinsert.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamclipXT programs/bamclipXT-bamclipXT.o biobambam2/bamclipXT-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamzztoname programs/bamzztoname-bamzztoname.o biobambam2/bamzztoname-Licensing.o biobambam2/bamzztoname-zzToName.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamclipreinsert programs/bamclipreinsert-bamclipreinsert.o biobambam2/bamclipreinsert-Licensing.o biobambam2/bamclipreinsert-ClipReinsert.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamindex programs/bamindex-bamindex.o biobambam2/bamindex-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace 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-fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterrg programs/bamfilterrg-bamfilterrg.o biobambam2/bamfilterrg-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterflags programs/bamfilterflags-bamfilterflags.o biobambam2/bamfilterflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamindex programs/bamindex-bamindex.o biobambam2/bamindex-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterrg programs/bamfilterrg-bamfilterrg.o biobambam2/bamfilterrg-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicates2 programs/bammarkduplicates2-bammarkduplicates2.o biobambam2/bammarkduplicates2-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix 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biobambam2/bammarkduplicates2-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcat programs/bamcat-bamcat.o biobambam2/bamcat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammerge programs/bammerge-bammerge.o biobambam2/bammerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsplit programs/bamsplit-bamsplit.o biobambam2/bamsplit-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastsplit programs/bamfastsplit-bamfastsplit.o biobambam2/bamfastsplit-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsplitdiv programs/bamsplitdiv-bamsplitdiv.o biobambam2/bamsplitdiv-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcat programs/bamcat-bamcat.o biobambam2/bamcat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamchecksort programs/bamchecksort-bamchecksort.o biobambam2/bamchecksort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 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-lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastsplit programs/bamfastsplit-bamfastsplit.o biobambam2/bamfastsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobam programs/fastqtobam-fastqtobam.o biobambam2/fastqtobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixmateinformation programs/bamfixmateinformation-bamfixmateinformation.o biobambam2/bamfixmateinformation-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsplitdiv programs/bamsplitdiv-bamsplitdiv.o biobambam2/bamsplitdiv-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamchecksort programs/bamchecksort-bamchecksort.o biobambam2/bamchecksort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmateinformation programs/bamfixmateinformation-bamfixmateinformation.o biobambam2/bamfixmateinformation-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobam programs/fastqtobam-fastqtobam.o biobambam2/fastqtobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamseqchksum programs/bamseqchksum-bamseqchksum.o biobambam2/bamseqchksum-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o normalisefasta programs/normalisefasta-normalisefasta.o biobambam2/normalisefasta-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamflagsplit programs/bamflagsplit-bamflagsplit.o biobambam2/bamflagsplit-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamseqchksum programs/bamseqchksum-bamseqchksum.o biobambam2/bamseqchksum-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamintervalcomment programs/bamintervalcomment-bamintervalcomment.o biobambam2/bamintervalcomment-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o normalisefasta programs/normalisefasta-normalisefasta.o biobambam2/normalisefasta-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch 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-rdynamic -o bamfilterheader programs/bamfilterheader-bamfilterheader.o biobambam2/bamfilterheader-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammapdist programs/bammapdist-bammapdist.o biobambam2/bammapdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamvalidate programs/bamvalidate-bamvalidate.o biobambam2/bamvalidate-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamflagsplit programs/bamflagsplit-bamflagsplit.o biobambam2/bamflagsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamintervalcomment programs/bamintervalcomment-bamintervalcomment.o biobambam2/bamintervalcomment-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamstreamingmarkduplicates programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o biobambam2/bamstreamingmarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexplode programs/bamexplode-bamexplode.o biobambam2/bamexplode-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexploderef programs/bamexploderef-bamexploderef.o biobambam2/bamexploderef-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastexploderef programs/bamfastexploderef-bamfastexploderef.o biobambam2/bamfastexploderef-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamstreamingmarkduplicates programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o biobambam2/bamstreamingmarkduplicates-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception 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-ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastaexplod programs/fastaexplod-fastaexplod.o biobambam2/fastaexplod-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamexploderef programs/bamexploderef-bamexploderef.o biobambam2/bamexploderef-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 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-fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfiltermc programs/bamfiltermc-bamfiltermc.o biobambam2/bamfiltermc-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastnumextract programs/bamfastnumextract-bamfastnumextract.o biobambam2/bamfastnumextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamranksort programs/bamranksort-bamranksort.o biobambam2/bamranksort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastaexplod programs/fastaexplod-fastaexplod.o biobambam2/fastaexplod-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecalculatecigar programs/bamrecalculatecigar-bamrecalculatecigar.o biobambam2/bamrecalculatecigar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltermc programs/bamfiltermc-bamfiltermc.o biobambam2/bamfiltermc-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamnumericalindex programs/bamnumericalindex-bamnumericalindex.o biobambam2/bamnumericalindex-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix 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-ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamnumericalindex programs/bamnumericalindex-bamnumericalindex.o biobambam2/bamnumericalindex-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrefinterval programs/bamrefinterval-bamrefinterval.o biobambam2/bamrefinterval-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterlength programs/bamfilterlength-bamfilterlength.o biobambam2/bamfilterlength-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamscrapcount programs/bamscrapcount-bamscrapcount.o biobambam2/bamscrapcount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfillquery programs/bamfillquery-bamfillquery.o biobambam2/bamfillquery-Licensing.o biobambam2/bamfillquery-AttachRank.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrefextract programs/bamrefextract-bamrefextract.o biobambam2/bamrefextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobam2 programs/fastqtobam2-fastqtobam2.o biobambam2/fastqtobam2-Licensing.o biobambam2/fastqtobam2-KmerPoisson.o biobambam2/fastqtobam2-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxmerge2 programs/bamauxmerge2-bamauxmerge2.o biobambam2/bamauxmerge2-Licensing.o biobambam2/bamauxmerge2-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamscrapcount programs/bamscrapcount-bamscrapcount.o biobambam2/bamscrapcount-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreheader programs/bamreheader-bamreheader.o biobambam2/bamreheader-Licensing.o biobambam2/bamreheader-ReadHeader.o biobambam2/bamreheader-RunEOFFilter.o biobambam2/bamreheader-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreplacechecksums programs/bamreplacechecksums-bamreplacechecksums.o biobambam2/bamreplacechecksums-Licensing.o biobambam2/bamreplacechecksums-ReadHeader.o biobambam2/bamreplacechecksums-RunEOFFilter.o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfillquery programs/bamfillquery-bamfillquery.o biobambam2/bamfillquery-Licensing.o biobambam2/bamfillquery-AttachRank.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrefextract programs/bamrefextract-bamrefextract.o biobambam2/bamrefextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastcat programs/bamfastcat-bamfastcat.o biobambam2/bamfastcat-Licensing.o biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobam2 programs/fastqtobam2-fastqtobam2.o biobambam2/fastqtobam2-Licensing.o biobambam2/fastqtobam2-KmerPoisson.o biobambam2/fastqtobam2-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge2 programs/bamauxmerge2-bamauxmerge2.o biobambam2/bamauxmerge2-Licensing.o biobambam2/bamauxmerge2-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamreheader programs/bamreheader-bamreheader.o biobambam2/bamreheader-Licensing.o biobambam2/bamreheader-ReadHeader.o biobambam2/bamreheader-RunEOFFilter.o biobambam2/bamreheader-UpdateNumericalIndex.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamreplacechecksums programs/bamreplacechecksums-bamreplacechecksums.o biobambam2/bamreplacechecksums-Licensing.o biobambam2/bamreplacechecksums-ReadHeader.o biobambam2/bamreplacechecksums-RunEOFFilter.o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastcat programs/bamfastcat-bamfastcat.o biobambam2/bamfastcat-Licensing.o biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepth programs/bamdepth-bamdepth.o biobambam2/bamdepth-Licensing.o biobambam2/bamdepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz -lxerces-c /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepth programs/bamdepth-bamdepth.o biobambam2/bamdepth-Licensing.o biobambam2/bamdepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -lxerces-c -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicates programs/bammarkduplicates-bammarkduplicates.o biobambam2/bammarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtofastq programs/bamtofastq-bamtofastq.o biobambam2/bamtofastq-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicates 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biobambam2/bammarkduplicatesopt-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfeaturecount programs/bamfeaturecount-bamfeaturecount.o biobambam2/bamfeaturecount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 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biobambam2/bamsimpledepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsimpledepth programs/bamsimpledepth-bamsimpledepth.o biobambam2/bamsimpledepth-Licensing.o biobambam2/bamsimpledepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicatesoptdist programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o biobambam2/bammarkduplicatesoptdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making all in test make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_auto_test make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making check in src make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making check in test make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make bamcmp bamtosam make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o bamcmp-bamcmp.o `test -f 'bamcmp.cpp' || echo './'`bamcmp.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -c -o bamtosam-bamtosam.o `test -f 'bamtosam.cpp' || echo './'`bamtosam.cpp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtosam bamtosam-bamtosam.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtosam bamtosam-bamtosam.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/bash ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcmp bamcmp-bamcmp.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcmp bamcmp-bamcmp.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make check-TESTS make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[4]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' PASS: testshortsortcoordinate.sh PASS: testshortsort.sh PASS: testshortsortqueryname.sh PASS: testdupsinglemarkedsortedqreset.sh PASS: testdupsingle.sh PASS: testfastqbamloop.sh ============================================================================ Testsuite summary for biobambam2 2.0.185 ============================================================================ # TOTAL: 6 # PASS: 6 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/biobambam2/ make -j1 install DESTDIR=/build/reproducible-path/biobambam2-2.0.185\+ds/debian/biobambam2 AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making install in src make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' /usr/bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c bamtofastq bammarkduplicates bamsort bammaskflags bamrecompress bamadapterfind bamfilteraux bamauxsort bamadapterclip bamcollate2 bam12auxmerge bam12split bam12strip bamreset bamrank bamclipreinsert bamclipXT bamzztoname bamindex bamfilterflags bamfilterrg bamdownsamplerandom bammarkduplicates2 bamcat bammerge bamsplit bamfastsplit bamsplitdiv bamchecksort fastqtobam bamfixmateinformation bamseqchksum normalisefasta bamfilterheader bamfilterheader2 bammdnm bammapdist bamvalidate bamflagsplit bamintervalcomment bamintervalcommenthist bamstreamingmarkduplicates bamalignfrac bamfilternames bamsormadup bamexplode bamexploderef bamfastexploderef bamfastnumextract bamranksort fastaexplod bamrecalculatecigar bamfiltermc bamnumericalindex bamnumericalindexstats bammarkduplicatesopt bamfilterlength bamauxmerge bamrefinterval bamscrapcount bamfilterrefid bamfillquery bamrefextract fastqtobam2 bamauxmerge2 bamreheader bamreplacechecksums bamfastcat populaterefcache bamfiltereofblocks bamdepth bamdepthintersect bamfilterk bamfixpairinfo bamdifference bamfeaturecount '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin' libtool: install: /usr/bin/install -c bamtofastq /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamtofastq libtool: install: /usr/bin/install -c bammarkduplicates /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicates libtool: install: /usr/bin/install -c bamsort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsort libtool: install: /usr/bin/install -c bammaskflags /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammaskflags libtool: install: /usr/bin/install -c bamrecompress /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrecompress libtool: install: /usr/bin/install -c bamadapterfind /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamadapterfind libtool: install: /usr/bin/install -c bamfilteraux /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilteraux libtool: install: /usr/bin/install -c bamauxsort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxsort libtool: install: /usr/bin/install -c bamadapterclip /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamadapterclip libtool: install: /usr/bin/install -c bamcollate2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamcollate2 libtool: install: /usr/bin/install -c bam12auxmerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12auxmerge libtool: install: /usr/bin/install -c bam12split /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12split libtool: install: /usr/bin/install -c bam12strip /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12strip libtool: install: /usr/bin/install -c bamreset /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreset libtool: install: /usr/bin/install -c bamrank /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrank libtool: install: /usr/bin/install -c bamclipreinsert /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamclipreinsert libtool: install: /usr/bin/install -c bamclipXT /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamclipXT libtool: install: /usr/bin/install -c bamzztoname /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamzztoname libtool: install: /usr/bin/install -c bamindex /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamindex libtool: install: /usr/bin/install -c bamfilterflags /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterflags libtool: install: /usr/bin/install -c bamfilterrg /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterrg libtool: install: /usr/bin/install -c bamdownsamplerandom /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdownsamplerandom libtool: install: /usr/bin/install -c bammarkduplicates2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicates2 libtool: install: /usr/bin/install -c bamcat /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamcat libtool: install: /usr/bin/install -c bammerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammerge libtool: install: /usr/bin/install -c bamsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsplit libtool: install: /usr/bin/install -c bamfastsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastsplit libtool: install: /usr/bin/install -c bamsplitdiv /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsplitdiv libtool: install: /usr/bin/install -c bamchecksort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamchecksort libtool: install: /usr/bin/install -c fastqtobam /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastqtobam libtool: install: /usr/bin/install -c bamfixmateinformation /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfixmateinformation libtool: install: /usr/bin/install -c bamseqchksum /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamseqchksum libtool: install: /usr/bin/install -c normalisefasta /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/normalisefasta libtool: install: /usr/bin/install -c bamfilterheader /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterheader libtool: install: /usr/bin/install -c bamfilterheader2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterheader2 libtool: install: /usr/bin/install -c bammdnm /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammdnm libtool: install: /usr/bin/install -c bammapdist /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammapdist libtool: install: /usr/bin/install -c bamvalidate /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamvalidate libtool: install: /usr/bin/install -c bamflagsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamflagsplit libtool: install: /usr/bin/install -c bamintervalcomment /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamintervalcomment libtool: install: /usr/bin/install -c bamintervalcommenthist /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamintervalcommenthist libtool: install: /usr/bin/install -c bamstreamingmarkduplicates /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamstreamingmarkduplicates libtool: install: /usr/bin/install -c bamalignfrac /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamalignfrac libtool: install: /usr/bin/install -c bamfilternames /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilternames libtool: install: /usr/bin/install -c bamsormadup /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsormadup libtool: install: /usr/bin/install -c bamexplode /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamexplode libtool: install: /usr/bin/install -c bamexploderef /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamexploderef libtool: install: /usr/bin/install -c bamfastexploderef /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastexploderef libtool: install: /usr/bin/install -c bamfastnumextract /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastnumextract libtool: install: /usr/bin/install -c bamranksort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamranksort libtool: install: /usr/bin/install -c fastaexplod /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastaexplod libtool: install: /usr/bin/install -c bamrecalculatecigar /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrecalculatecigar libtool: install: /usr/bin/install -c bamfiltermc /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfiltermc libtool: install: /usr/bin/install -c bamnumericalindex /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamnumericalindex libtool: install: /usr/bin/install -c bamnumericalindexstats /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamnumericalindexstats libtool: install: /usr/bin/install -c bammarkduplicatesopt /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicatesopt libtool: install: /usr/bin/install -c bamfilterlength /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterlength libtool: install: /usr/bin/install -c bamauxmerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxmerge libtool: install: /usr/bin/install -c bamrefinterval /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrefinterval libtool: install: /usr/bin/install -c bamscrapcount /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamscrapcount libtool: install: /usr/bin/install -c bamfilterrefid /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterrefid libtool: install: /usr/bin/install -c bamfillquery /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfillquery libtool: install: /usr/bin/install -c bamrefextract /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrefextract libtool: install: /usr/bin/install -c fastqtobam2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastqtobam2 libtool: install: /usr/bin/install -c bamauxmerge2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxmerge2 libtool: install: /usr/bin/install -c bamreheader /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreheader libtool: install: /usr/bin/install -c bamreplacechecksums /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreplacechecksums libtool: install: /usr/bin/install -c bamfastcat /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastcat libtool: install: /usr/bin/install -c populaterefcache /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/populaterefcache libtool: install: /usr/bin/install -c bamfiltereofblocks /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfiltereofblocks libtool: install: /usr/bin/install -c bamdepth /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdepth libtool: install: /usr/bin/install -c bamdepthintersect /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdepthintersect libtool: install: /usr/bin/install -c bamfilterk /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterk libtool: install: /usr/bin/install -c bamfixpairinfo /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfixpairinfo libtool: install: /usr/bin/install -c bamdifference /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdifference libtool: install: /usr/bin/install -c bamfeaturecount /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfeaturecount /usr/bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/bamtofastq.1 programs/bamsort.1 programs/bammarkduplicates.1 programs/bammarkduplicatesopt.1 programs/bammaskflags.1 programs/bamrecompress.1 programs/bamadapterfind.1 programs/bamfilteraux.1 programs/bamauxsort.1 programs/bamadapterclip.1 programs/bamcollate2.1 programs/bam12auxmerge.1 programs/bam12split.1 programs/bam12strip.1 programs/bamreset.1 programs/bamrank.1 programs/bamclipreinsert.1 programs/bamzztoname.1 programs/bamindex.1 programs/bamfilterflags.1 programs/bamfilterrg.1 programs/bamdownsamplerandom.1 programs/bammarkduplicates2.1 programs/bamcat.1 programs/bammerge.1 programs/bamsplit.1 programs/bamsplitdiv.1 programs/bamchecksort.1 programs/fastqtobam.1 programs/bamfixmateinformation.1 programs/normalisefasta.1 programs/bamfilterheader.1 programs/bamfilterheader2.1 programs/bammdnm.1 programs/bamseqchksum.1 programs/bamvalidate.1 programs/bamflagsplit.1 programs/bamintervalcomment.1 programs/bamstreamingmarkduplicates.1 programs/bamsormadup.1 '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/fastaexplod.1 programs/bamrecalculatecigar.1 programs/bamfiltermc.1 programs/bamfillquery.1 programs/bamalignfrac.1 programs/bamauxmerge.1 programs/bamauxmerge2.1 programs/bambisect.1 programs/bamclipXT.1 programs/bamconsensus.1 programs/filtergtf.1 programs/bamfeaturecount.1 '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making install in test make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_installdocs dh_installchangelogs dh_installexamples 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: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamrefextract were not linked against libmaus2_simd_align_256.so.2 (they use none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/biobambam2/usr/bin/bamauxmerge debian/biobambam2/usr/bin/bamfeaturecount debian/biobambam2/usr/bin/bamflagsplit debian/biobambam2/usr/bin/bamfilteraux debian/biobambam2/usr/bin/bamreplacechecksums debian/biobambam2/usr/bin/bamexplode debian/biobambam2/usr/bin/bamfastnumextract debian/biobambam2/usr/bin/bamrecompress debian/biobambam2/usr/bin/normalisefasta debian/biobambam2/usr/bin/bamfiltermc debian/biobambam2/usr/bin/bam12split debian/biobambam2/usr/bin/bamindex debian/biobambam2/usr/bin/bamfastcat debian/biobambam2/usr/bin/bamdownsamplerandom debian/biobambam2/usr/bin/bamchecksort debian/biobambam2/usr/bin/bamrecalculatecigar debian/biobambam2/usr/bin/bamnumericalindex debian/biobambam2/usr/bin/bamfiltereofblocks debian/biobambam2/usr/bin/bamfilterheader debian/biobambam2/usr/bin/bamfilterlength debian/biobambam2/usr/bin/bamauxsort debian/biobambam2/usr/bin/bamdepthintersect debian/biobambam2/usr/bin/bamfastsplit debian/biobambam2/usr/bin/bamdifference debian/biobambam2/usr/bin/bamfilternames debian/biobambam2/usr/bin/bammarkduplicates debian/biobambam2/usr/bin/bammapdist debian/biobambam2/usr/bin/bamfastexploderef debian/biobambam2/usr/bin/bamsort debian/biobambam2/usr/bin/bamalignfrac debian/biobambam2/usr/bin/bamranksort debian/biobambam2/usr/bin/fastqtobam debian/biobambam2/usr/bin/bamfilterflags debian/biobambam2/usr/bin/bammerge debian/biobambam2/usr/bin/bamadapterfind debian/biobambam2/usr/bin/bammarkduplicates2 debian/biobambam2/usr/bin/bamcollate2 debian/biobambam2/usr/bin/bamfillquery debian/biobambam2/usr/bin/bamadapterclip debian/biobambam2/usr/bin/bamrefinterval debian/biobambam2/usr/bin/bamsplitdiv debian/biobambam2/usr/bin/bamclipXT debian/biobambam2/usr/bin/bamcat debian/biobambam2/usr/bin/bamzztoname debian/biobambam2/usr/bin/bamintervalcommenthist debian/biobambam2/usr/bin/fastaexplod debian/biobambam2/usr/bin/bamauxmerge2 debian/biobambam2/usr/bin/bamfilterheader2 debian/biobambam2/usr/bin/populaterefcache debian/biobambam2/usr/bin/bamfixmateinformation debian/biobambam2/usr/bin/bam12strip debian/biobambam2/usr/bin/bamfilterk debian/biobambam2/usr/bin/bamfilterrg debian/biobambam2/usr/bin/bamsplit debian/biobambam2/usr/bin/bamnumericalindexstats debian/biobambam2/usr/bin/bamvalidate debian/biobambam2/usr/bin/bamreset debian/biobambam2/usr/bin/fastqtobam2 debian/biobambam2/usr/bin/bamclipreinsert debian/biobambam2/usr/bin/bamrank debian/biobambam2/usr/bin/bamsormadup debian/biobambam2/usr/bin/bamscrapcount debian/biobambam2/usr/bin/bamreheader debian/biobambam2/usr/bin/bamexploderef debian/biobambam2/usr/bin/bamseqchksum debian/biobambam2/usr/bin/bamfilterrefid debian/biobambam2/usr/bin/bammaskflags debian/biobambam2/usr/bin/bam12auxmerge debian/biobambam2/usr/bin/bammarkduplicatesopt debian/biobambam2/usr/bin/bamstreamingmarkduplicates debian/biobambam2/usr/bin/bamfixpairinfo debian/biobambam2/usr/bin/bammdnm debian/biobambam2/usr/bin/bamdepth debian/biobambam2/usr/bin/bamtofastq debian/biobambam2/usr/bin/bamintervalcomment debian/biobambam2/usr/bin/bamrefextract were not linked against libmaus2_simd_align_128.so.2 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'biobambam2-dbgsym' in '../biobambam2-dbgsym_2.0.185+ds-2_amd64.deb'. dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.185+ds-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../biobambam2_2.0.185+ds-2_amd64.buildinfo dpkg-genchanges --build=binary -O../biobambam2_2.0.185+ds-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3717086 and its subdirectories I: Current time: Thu Jan 15 11:31:25 -12 2026 I: pbuilder-time-stamp: 1768519885 Fri Dec 13 17:08:31 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Fri Dec 13 17:08:31 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Fri Dec 13 17:29:53 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Fri Dec 13 17:29:53 UTC 2024 I: biobambam2_2.0.185+ds-2_amd64.changes: Format: 1.8 Date: Fri, 19 Apr 2024 17:24:26 +0200 Source: biobambam2 Binary: biobambam2 biobambam2-dbgsym Architecture: amd64 Version: 2.0.185+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: biobambam2 - tools for early stage alignment file processing Changes: biobambam2 (2.0.185+ds-2) unstable; urgency=medium . * d/watch: repair gitlab watch file. This instructs uscan to use git ls-remote mode. * d/control: declare compliance to standards version 4.7.0. * d/control: move from pkg-config to pkgconf. Checksums-Sha1: 2bcad60727faf80fbfd48484e74b425c003979dc 221883828 biobambam2-dbgsym_2.0.185+ds-2_amd64.deb f505531106897bdaa5c1bfb53e17b014b3a00535 6835 biobambam2_2.0.185+ds-2_amd64.buildinfo 401d71b742c6f925703de4a75542b2fa2c0d1dba 9573604 biobambam2_2.0.185+ds-2_amd64.deb Checksums-Sha256: a879a57f1c688a53f70fbbd0ae4375f17d2e6891e41b808bce7bac8b66355757 221883828 biobambam2-dbgsym_2.0.185+ds-2_amd64.deb a780b0c433b62b9f78ccfa31f1bcff9b0519f144a495f23416e4b7f58fd6014a 6835 biobambam2_2.0.185+ds-2_amd64.buildinfo 5191b8a07768c30d7691f1516d05ec5880c4fdf45150fc08d027cf28a79fd853 9573604 biobambam2_2.0.185+ds-2_amd64.deb Files: 8fc217be250d9d364bf7cc00b0d50e51 221883828 debug optional biobambam2-dbgsym_2.0.185+ds-2_amd64.deb fe00db490eeb84e474f1cba3d7cd62d3 6835 science optional biobambam2_2.0.185+ds-2_amd64.buildinfo 97ecc13027bc3f6ed5447c968153175e 9573604 science optional biobambam2_2.0.185+ds-2_amd64.deb Fri Dec 13 17:29:54 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_20-39444.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.wP6uHb27/biobambam2_2.0.185+ds-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.wP6uHb27/biobambam2_2.0.185+ds-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.wP6uHb27/biobambam2_2.0.185+ds-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.wP6uHb27/b1/biobambam2_2.0.185+ds-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.wP6uHb27/b2/biobambam2_2.0.185+ds-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 2.348s) 2.348s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 2.035s) 2.035s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2.635s CPU time consumed: 2.633s Fri Dec 13 17:29:58 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Fri Dec 13 17:29:58 UTC 2024 I: biobambam2 from trixie built successfully and reproducibly on amd64. Fri Dec 13 17:29:59 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Dec 13 17:29:59 UTC 2024 I: Submitting 8.0K b1/biobambam2_2.0.185+ds-2_amd64.buildinfo.asc Fri Dec 13 17:30:00 UTC 2024 I: Submitting 8.0K b2/biobambam2_2.0.185+ds-2_amd64.buildinfo.asc Fri Dec 13 17:30:01 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Dec 13 17:30:01 UTC 2024 I: Done submitting .buildinfo files. Fri Dec 13 17:30:01 UTC 2024 I: Removing signed biobambam2_2.0.185+ds-2_amd64.buildinfo.asc files: removed './b1/biobambam2_2.0.185+ds-2_amd64.buildinfo.asc' removed './b2/biobambam2_2.0.185+ds-2_amd64.buildinfo.asc'