I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 17 21:04:59 +14 2022 I: pbuilder-time-stamp: 1660719899 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biobambam2_2.0.179+ds-1.dsc] I: copying [./biobambam2_2.0.179+ds.orig.tar.xz] I: copying [./biobambam2_2.0.179+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.5MFc9l7K/trustedkeys.kbx': General error gpgv: Signature made Mon Jan 4 00:19:42 2021 +14 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./biobambam2_2.0.179+ds-1.dsc dpkg-source: info: extracting biobambam2 in biobambam2-2.0.179+ds dpkg-source: info: unpacking biobambam2_2.0.179+ds.orig.tar.xz dpkg-source: info: unpacking biobambam2_2.0.179+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying manuals.patch dpkg-source: info: applying spelling-error-in-binary.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/15654/tmp/hooks/D01_modify_environment starting debug: Running on codethink13-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/15654/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/15654/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=15654 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.NldVhAtx64/pbuilderrc_uATY --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.NldVhAtx64/b2 --logfile b2/build.log --extrapackages usrmerge biobambam2_2.0.179+ds-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 2021 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Feb 8 2021 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 2021 more -rwsr-xr-x 1 root root 51360 Feb 8 2021 mount -rwxr-xr-x 1 root root 14496 Feb 8 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Aug 17 21:05 sh -> bash lrwxrwxrwx 1 root root 4 Aug 16 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Feb 8 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/15654/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), pkg-config, libmaus2-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 ... 19646 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 pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libmaus2-dev; however: Package libmaus2-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} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libgpgme11{a} libicu67{a} libksba8{a} libldap-2.4-2{a} libmagic-mgc{a} libmagic1{a} libmaus2-2{a} libmaus2-dev{a} libnpth0{a} libpipeline1{a} libreadline8{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} pinentry-curses{a} pkg-config{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 56 newly installed, 0 to remove and 0 not upgraded. Need to get 32.1 MB of archives. After unpacking 128 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 libassuan0 arm64 2.5.3-7.1 [48.0 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 gpgconf arm64 2.2.27-2 [540 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libksba8 arm64 1.5.0-3 [114 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libnpth0 arm64 1.6-3 [18.6 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 dirmngr arm64 2.2.27-2 [744 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 gnupg-l10n all 2.2.27-2 [1084 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 gnupg-utils arm64 2.2.27-2 [863 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 gpg arm64 2.2.27-2 [883 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 pinentry-curses arm64 1.1.0-4 [63.0 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 gpg-agent arm64 2.2.27-2 [651 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 gpg-wks-client arm64 2.2.27-2 [517 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 gpg-wks-server arm64 2.2.27-2 [510 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 gpgsm arm64 2.2.27-2 [627 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 gnupg all 2.2.27-2 [825 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 libgpgme11 arm64 1.14.0-1+b2 [267 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libmaus2-2 arm64 2.0.768+dfsg-2 [1390 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libmaus2-dev arm64 2.0.768+dfsg-2 [2863 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 pkg-config arm64 0.29.2-1 [63.6 kB] Fetched 32.1 MB in 1s (43.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../01-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../03-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../05-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../06-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../07-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../09-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../12-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../18-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../19-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../20-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../21-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... 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Setting up gettext-base (0.21-4) ... Setting up libnpth0:arm64 (1.6-3) ... Setting up file (1:5.39-3) ... Setting up libassuan0:arm64 (2.5.3-7.1) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up gnupg-l10n (2.2.27-2) ... Setting up libsigsegv2:arm64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up pkg-config (0.29.2-1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:arm64 (0.183-1) ... Setting up readline-common (8.1-1) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up pinentry-curses (1.1.0-4) ... Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up gpgconf (2.2.27-2) ... Setting up gpg (2.2.27-2) ... Setting up gnupg-utils (2.2.27-2) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gpg-agent (2.2.27-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up gpgsm (2.2.27-2) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libgpgme11:arm64 (1.14.0-1+b2) ... Setting up dh-autoreconf (20) ... Setting up dirmngr (2.2.27-2) ... Setting up gpg-wks-server (2.2.27-2) ... Setting up gpg-wks-client (2.2.27-2) ... Setting up libmaus2-2 (2.0.768+dfsg-2) ... Setting up debhelper (13.3.4) ... Setting up gnupg (2.2.27-2) ... Setting up libmaus2-dev (2.0.768+dfsg-2) ... Processing triggers for libc-bin (2.31-12) ... 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 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (874 kB/s) Selecting previously unselected package libnumber-compare-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 23602 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... Unpacking libfile-find-rule-perl (0.34-1) ... Selecting previously unselected package usrmerge. Preparing to unpack .../archives/usrmerge_25_all.deb ... Unpacking usrmerge (25) ... Setting up libtext-glob-perl (0.11-1) ... Setting up libnumber-compare-perl (0.03-1.1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up usrmerge (25) ... The system has been successfully converted. Processing triggers for man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. I: Building the package hostname: Temporary failure in name resolution I: Running cd /build/biobambam2-2.0.179+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../biobambam2_2.0.179+ds-1_source.changes dpkg-buildpackage: info: source package biobambam2 dpkg-buildpackage: info: source version 2.0.179+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/biobambam2-2.0.179+ds' dh_auto_clean rm -f config.log make[1]: Leaving directory '/build/biobambam2-2.0.179+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: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=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking target system type... aarch64-unknown-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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... 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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r 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 how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.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) 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 thread-safe 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 we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) 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) 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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 configure: Adding optimisation options -O3 to C++ compiler g++ flags, full list now -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for ANSI C header files... (cached) yes checking for libmaus2 >= 2.0.767... 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 whether libmaus2 has support for iRODS... no checking for bash... /usr/bin/bash checking for base64... /usr/bin/base64 checking for xerces-c >= 3.1.1... no configure: Using flags -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 for C compiler gcc configure: Using flags -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -j8 make[1]: Entering directory '/build/biobambam2-2.0.179+ds' make all-recursive make[2]: Entering directory '/build/biobambam2-2.0.179+ds' Making all in src make[3]: Entering directory '/build/biobambam2-2.0.179+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamreplacechecksums-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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamfiltereofblocks-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp programs/bamrefextract.cpp: In function 'void handle(libmaus2::sorting::SerialisingSortingBufferedOutputFile::unique_ptr_type&, int64_t, const libmaus2::bambam::BamHeader&)': programs/bamrefextract.cpp:106:28: warning: 'GP.libmaus2::aio::GenericPeeker > >::slot.Element::p' may be used uninitialized in this function [-Wmaybe-uninitialized] 106 | while ( GP.peekNext(EL) && EL.p == p ) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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:210:25: 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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamheadercat-bamheadercat.o `test -f 'programs/bamheadercat.cpp' || echo './'`programs/bamheadercat.cpp In file included from /usr/include/c++/10/cassert:44, from /usr/include/libmaus2/avl/AVLSet.hpp:24, from programs/bamexondepth.cpp:43: programs/bamexondepth.cpp: In function 'void handleFile(const string&, uint64_t, const libmaus2::bambam::BamHeader&, std::ostream&, std::ostream&, const string&)': programs/bamexondepth.cpp:121:16: 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:371:11: 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 ) | ~~^~~~~~~~~~~~~ In file included from /usr/include/c++/10/cassert:44, from /usr/include/libmaus2/avl/AVLSet.hpp:24, from programs/bamexondepth.cpp:43: programs/bamexondepth.cpp:375:17: 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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/bamdepthmerge-bamdepthmerge.o `test -f 'programs/bamdepthmerge.cpp' || echo './'`programs/bamdepthmerge.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:210:25: 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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bamcountflags-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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o `test -f 'programs/vcfreplacecontigsmap.cpp' || echo './'`programs/vcfreplacecontigsmap.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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/fastaselectreg-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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o biobambam2/bammarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 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programs/bamexplode-bamexplode.o biobambam2/bamexplode-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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsormadup programs/bamsormadup-bamsormadup.o biobambam2/bamsormadup-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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfastnumextract programs/bamfastnumextract-bamfastnumextract.o biobambam2/bamfastnumextract-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamranksort programs/bamranksort-bamranksort.o biobambam2/bamranksort-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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastexploderef programs/bamfastexploderef-bamfastexploderef.o biobambam2/bamfastexploderef-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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecalculatecigar programs/bamrecalculatecigar-bamrecalculatecigar.o biobambam2/bamrecalculatecigar-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamnumericalindexstats programs/bamnumericalindexstats-bamnumericalindexstats.o biobambam2/bamnumericalindexstats-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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamnumericalindexstats programs/bamnumericalindexstats-bamnumericalindexstats.o biobambam2/bamnumericalindexstats-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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicatesopt programs/bammarkduplicatesopt-bammarkduplicatesopt.o biobambam2/bammarkduplicatesopt-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterlength programs/bamfilterlength-bamfilterlength.o biobambam2/bamfilterlength-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrefinterval programs/bamrefinterval-bamrefinterval.o biobambam2/bamrefinterval-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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicatesopt programs/bammarkduplicatesopt-bammarkduplicatesopt.o 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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterk programs/bamfilterk-bamfilterk.o biobambam2/bamfilterk-Licensing.o biobambam2/bamfilterk-DepthInterval.o biobambam2/bamfilterk-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixpairinfo programs/bamfixpairinfo-bamfixpairinfo.o biobambam2/bamfixpairinfo-Licensing.o biobambam2/bamfixpairinfo-DepthInterval.o biobambam2/bamfixpairinfo-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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterk programs/bamfilterk-bamfilterk.o biobambam2/bamfilterk-Licensing.o biobambam2/bamfilterk-DepthInterval.o biobambam2/bamfilterk-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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixpairinfo programs/bamfixpairinfo-bamfixpairinfo.o biobambam2/bamfixpairinfo-Licensing.o biobambam2/bamfixpairinfo-DepthInterval.o biobambam2/bamfixpairinfo-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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdifference programs/bamdifference-bamdifference.o biobambam2/bamdifference-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdifference programs/bamdifference-bamdifference.o biobambam2/bamdifference-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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilter programs/bamfilter-bamfilter.o biobambam2/bamfilter-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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterbyname programs/bamfilterbyname-bamfilterbyname.o biobambam2/bamfilterbyname-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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfeaturecount programs/bamfeaturecount-bamfeaturecount.o biobambam2/bamfeaturecount-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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 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-lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamaddne programs/bamaddne-bamaddne.o biobambam2/bamaddne-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 -ldl -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtofastq programs/bamtofastq-bamtofastq.o biobambam2/bamtofastq-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 -ldl -lz -fopenmp make[3]: Leaving directory '/build/biobambam2-2.0.179+ds/src' Making all in test make[3]: Entering directory '/build/biobambam2-2.0.179+ds/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/biobambam2-2.0.179+ds/test' make[3]: Entering directory '/build/biobambam2-2.0.179+ds' make[3]: Leaving directory '/build/biobambam2-2.0.179+ds' make[2]: Leaving directory '/build/biobambam2-2.0.179+ds' make[1]: Leaving directory '/build/biobambam2-2.0.179+ds' dh_auto_test make -j8 check VERBOSE=1 make[1]: Entering directory '/build/biobambam2-2.0.179+ds' Making check in src make[2]: Entering directory '/build/biobambam2-2.0.179+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/biobambam2-2.0.179+ds/src' Making check in test make[2]: Entering directory '/build/biobambam2-2.0.179+ds/test' make bamcmp bamtosam make[3]: Entering directory '/build/biobambam2-2.0.179+ds/test' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -c -o bamtosam-bamtosam.o `test -f 'bamtosam.cpp' || echo './'`bamtosam.cpp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -fopenmp -lz libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp libtool: link: g++ -g -O2 -fdebug-prefix-map=/build/biobambam2-2.0.179+ds=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ldl -lz -fopenmp make[3]: Leaving directory '/build/biobambam2-2.0.179+ds/test' make check-TESTS make[3]: Entering directory '/build/biobambam2-2.0.179+ds/test' make[4]: Entering directory '/build/biobambam2-2.0.179+ds/test' PASS: testshortsortqueryname.sh PASS: testshortsort.sh PASS: testshortsortcoordinate.sh PASS: testdupsinglemarkedsortedqreset.sh PASS: testdupsingle.sh PASS: testfastqbamloop.sh ============================================================================ Testsuite summary for biobambam2 2.0.179 ============================================================================ # TOTAL: 6 # PASS: 6 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/biobambam2-2.0.179+ds/test' make[3]: Leaving directory '/build/biobambam2-2.0.179+ds/test' make[2]: Leaving directory '/build/biobambam2-2.0.179+ds/test' make[2]: Entering directory '/build/biobambam2-2.0.179+ds' make[2]: Leaving directory '/build/biobambam2-2.0.179+ds' make[1]: Leaving directory '/build/biobambam2-2.0.179+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/biobambam2-2.0.179\+ds/debian/biobambam2 AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/biobambam2-2.0.179+ds' Making install in src make[2]: Entering directory '/build/biobambam2-2.0.179+ds/src' make[3]: Entering directory '/build/biobambam2-2.0.179+ds/src' /usr/bin/mkdir -p '/build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin' /bin/sh ../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/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin' libtool: install: /usr/bin/install -c bamtofastq /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamtofastq libtool: install: /usr/bin/install -c bammarkduplicates /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammarkduplicates libtool: install: /usr/bin/install -c bamsort /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamsort libtool: install: /usr/bin/install -c bammaskflags /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammaskflags libtool: install: /usr/bin/install -c bamrecompress /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamrecompress libtool: install: /usr/bin/install -c bamadapterfind /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamadapterfind libtool: install: /usr/bin/install -c bamfilteraux /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilteraux libtool: install: /usr/bin/install -c bamauxsort /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamauxsort libtool: install: /usr/bin/install -c bamadapterclip /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamadapterclip libtool: install: /usr/bin/install -c bamcollate2 /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamcollate2 libtool: install: /usr/bin/install -c bam12auxmerge /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bam12auxmerge libtool: install: /usr/bin/install -c bam12split /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bam12split libtool: install: /usr/bin/install -c bam12strip /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bam12strip libtool: install: /usr/bin/install -c bamreset /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamreset libtool: install: /usr/bin/install -c bamrank /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamrank libtool: install: /usr/bin/install -c bamclipreinsert /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamclipreinsert libtool: install: /usr/bin/install -c bamclipXT /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamclipXT libtool: install: /usr/bin/install -c bamzztoname /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamzztoname libtool: install: /usr/bin/install -c bamindex /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamindex libtool: install: /usr/bin/install -c bamfilterflags /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterflags libtool: install: /usr/bin/install -c bamfilterrg /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterrg libtool: install: /usr/bin/install -c bamdownsamplerandom /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamdownsamplerandom libtool: install: /usr/bin/install -c bammarkduplicates2 /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammarkduplicates2 libtool: install: /usr/bin/install -c bamcat /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamcat libtool: install: /usr/bin/install -c bammerge /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammerge libtool: install: /usr/bin/install -c bamsplit /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamsplit libtool: install: /usr/bin/install -c bamfastsplit /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfastsplit libtool: install: /usr/bin/install -c bamsplitdiv /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamsplitdiv libtool: install: /usr/bin/install -c bamchecksort /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamchecksort libtool: install: /usr/bin/install -c fastqtobam /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/fastqtobam libtool: install: /usr/bin/install -c bamfixmateinformation /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfixmateinformation libtool: install: /usr/bin/install -c bamseqchksum /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamseqchksum libtool: install: /usr/bin/install -c normalisefasta /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/normalisefasta libtool: install: /usr/bin/install -c bamfilterheader /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterheader libtool: install: /usr/bin/install -c bamfilterheader2 /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterheader2 libtool: install: /usr/bin/install -c bammdnm /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammdnm libtool: install: /usr/bin/install -c bammapdist /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammapdist libtool: install: /usr/bin/install -c bamvalidate /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamvalidate libtool: install: /usr/bin/install -c bamflagsplit /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamflagsplit libtool: install: /usr/bin/install -c bamintervalcomment /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamintervalcomment libtool: install: /usr/bin/install -c bamintervalcommenthist /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamintervalcommenthist libtool: install: /usr/bin/install -c bamstreamingmarkduplicates /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamstreamingmarkduplicates libtool: install: /usr/bin/install -c bamalignfrac /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamalignfrac libtool: install: /usr/bin/install -c bamfilternames /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilternames libtool: install: /usr/bin/install -c bamsormadup /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamsormadup libtool: install: /usr/bin/install -c bamexplode /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamexplode libtool: install: /usr/bin/install -c bamexploderef /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamexploderef libtool: install: /usr/bin/install -c bamfastexploderef /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfastexploderef libtool: install: /usr/bin/install -c bamfastnumextract /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfastnumextract libtool: install: /usr/bin/install -c bamranksort /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamranksort libtool: install: /usr/bin/install -c fastaexplod /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/fastaexplod libtool: install: /usr/bin/install -c bamrecalculatecigar /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamrecalculatecigar libtool: install: /usr/bin/install -c bamfiltermc /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfiltermc libtool: install: /usr/bin/install -c bamnumericalindex /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamnumericalindex libtool: install: /usr/bin/install -c bamnumericalindexstats /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamnumericalindexstats libtool: install: /usr/bin/install -c bammarkduplicatesopt /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bammarkduplicatesopt libtool: install: /usr/bin/install -c bamfilterlength /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterlength libtool: install: /usr/bin/install -c bamauxmerge /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamauxmerge libtool: install: /usr/bin/install -c bamrefinterval /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamrefinterval libtool: install: /usr/bin/install -c bamscrapcount /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamscrapcount libtool: install: /usr/bin/install -c bamfilterrefid /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterrefid libtool: install: /usr/bin/install -c bamfillquery /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfillquery libtool: install: /usr/bin/install -c bamrefextract /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamrefextract libtool: install: /usr/bin/install -c fastqtobam2 /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/fastqtobam2 libtool: install: /usr/bin/install -c bamauxmerge2 /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamauxmerge2 libtool: install: /usr/bin/install -c bamreheader /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamreheader libtool: install: /usr/bin/install -c bamreplacechecksums /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamreplacechecksums libtool: install: /usr/bin/install -c bamfastcat /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfastcat libtool: install: /usr/bin/install -c populaterefcache /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/populaterefcache libtool: install: /usr/bin/install -c bamfiltereofblocks /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfiltereofblocks libtool: install: /usr/bin/install -c bamdepth /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamdepth libtool: install: /usr/bin/install -c bamdepthintersect /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamdepthintersect libtool: install: /usr/bin/install -c bamfilterk /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfilterk libtool: install: /usr/bin/install -c bamfixpairinfo /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfixpairinfo libtool: install: /usr/bin/install -c bamdifference /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamdifference libtool: install: /usr/bin/install -c bamfeaturecount /build/biobambam2-2.0.179+ds/debian/biobambam2/usr/bin/bamfeaturecount /usr/bin/mkdir -p '/build/biobambam2-2.0.179+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/biobambam2-2.0.179+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/biobambam2-2.0.179+ds/debian/biobambam2/usr/share/man/man1' make[3]: Leaving directory '/build/biobambam2-2.0.179+ds/src' make[2]: Leaving directory '/build/biobambam2-2.0.179+ds/src' Making install in test make[2]: Entering directory '/build/biobambam2-2.0.179+ds/test' make[3]: Entering directory '/build/biobambam2-2.0.179+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/biobambam2-2.0.179+ds/test' make[2]: Leaving directory '/build/biobambam2-2.0.179+ds/test' make[2]: Entering directory '/build/biobambam2-2.0.179+ds' make[3]: Entering directory '/build/biobambam2-2.0.179+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/biobambam2-2.0.179+ds' make[2]: Leaving directory '/build/biobambam2-2.0.179+ds' make[1]: Leaving directory '/build/biobambam2-2.0.179+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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.179+ds-1_arm64.deb'. dpkg-deb: building package 'biobambam2-dbgsym' in '../biobambam2-dbgsym_2.0.179+ds-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../biobambam2_2.0.179+ds-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/15654/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/15654/tmp/hooks/B01_cleanup finished 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/15654 and its subdirectories I: Current time: Wed Aug 17 22:55:25 +14 2022 I: pbuilder-time-stamp: 1660726525