I: pbuilder: network access will be disabled during build I: Current time: Mon May 13 21:28:26 +14 2024 I: pbuilder-time-stamp: 1715585306 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [biobambam2_2.0.185+ds-2.dsc] I: copying [./biobambam2_2.0.185+ds.orig.tar.xz] I: copying [./biobambam2_2.0.185+ds-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Apr 19 15:44:35 2024 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./biobambam2_2.0.185+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting biobambam2 in biobambam2-2.0.185+ds dpkg-source: info: unpacking biobambam2_2.0.185+ds.orig.tar.xz dpkg-source: info: unpacking biobambam2_2.0.185+ds-2.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/50043/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 13 07:28 /bin/sh -> /bin/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/50043/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/50043/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path 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 parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=ddf74708586e430f82b83eebf4eadbfb 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=50043 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/r-b-build.Qq9hovUO/pbuilderrc_ZgCC --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Qq9hovUO/b2 --logfile b2/build.log biobambam2_2.0.185+ds-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 11 07:44 /bin -> usr/bin I: user script /srv/workspace/pbuilder/50043/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), pkgconf, libmaus2-dev (>= 2.0.800), libxerces-c-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on pkgconf; however: Package pkgconf is not installed. pbuilder-satisfydepends-dummy depends on libmaus2-dev (>= 2.0.800); however: Package libmaus2-dev is not installed. pbuilder-satisfydepends-dummy depends on libxerces-c-dev; however: Package libxerces-c-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libassuan0{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgpgme11t64{a} libgssapi-krb5-2{a} libicu-dev{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libksba8{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libmaus2-2{a} libmaus2-dev{a} libnghttp2-14{a} libnpth0t64{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxerces-c-dev{a} libxerces-c3.2t64{a} libxml2{a} m4{a} man-db{a} pinentry-curses{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 48.8 MB of archives. After unpacking 260 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1+b1 [48.0 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 gpgconf arm64 2.2.40-3 [558 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libksba8 arm64 1.6.6-1 [122 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libnpth0t64 arm64 1.6-3.1 [17.8 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 dirmngr arm64 2.2.40-3 [771 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 gnupg-l10n all 2.2.40-3 [1094 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 gnupg-utils arm64 2.2.40-3 [883 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 gpg arm64 2.2.40-3 [903 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 pinentry-curses arm64 1.2.1-3+b2 [75.9 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 gpg-agent arm64 2.2.40-3 [675 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 gpg-wks-client arm64 2.2.40-3 [533 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 gpg-wks-server arm64 2.2.40-3 [525 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 gpgsm arm64 2.2.40-3 [650 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 gnupg all 2.2.40-3 [847 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 icu-devtools arm64 72.1-4+b1 [194 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 56 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.7.1-5 [405 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libgpgme11t64 arm64 1.18.0-4.1+b1 [287 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libicu-dev arm64 72.1-4+b1 [10.2 MB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libmaus2-2 arm64 2.0.813+ds-1+b2 [1684 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libmaus2-dev arm64 2.0.813+ds-1+b2 [4496 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libxerces-c3.2t64 arm64 3.2.4+debian-1.3 [781 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxerces-c-dev arm64 3.2.4+debian-1.3 [1643 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Fetched 48.8 MB in 0s (116 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19744 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../23-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../25-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../31-libassuan0_2.5.6-1+b1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.6-1+b1) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../32-libreadline8t64_8.2-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package gpgconf. Preparing to unpack .../33-gpgconf_2.2.40-3_arm64.deb ... Unpacking gpgconf (2.2.40-3) ... Selecting previously unselected package libksba8:arm64. Preparing to unpack .../34-libksba8_1.6.6-1_arm64.deb ... Unpacking libksba8:arm64 (1.6.6-1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../35-libsasl2-modules-db_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../36-libsasl2-2_2.1.28+dfsg1-6_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../37-libldap-2.5-0_2.5.17+dfsg-1_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnpth0t64:arm64. Preparing to unpack .../38-libnpth0t64_1.6-3.1_arm64.deb ... Unpacking libnpth0t64:arm64 (1.6-3.1) ... Selecting previously unselected package dirmngr. Preparing to unpack .../39-dirmngr_2.2.40-3_arm64.deb ... Unpacking dirmngr (2.2.40-3) ... Selecting previously unselected package gnupg-l10n. Preparing to unpack .../40-gnupg-l10n_2.2.40-3_all.deb ... Unpacking gnupg-l10n (2.2.40-3) ... Selecting previously unselected package gnupg-utils. 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Unpacking pkgconf-bin (1.8.1-1+b2) ... Selecting previously unselected package pkgconf:arm64. Preparing to unpack .../71-pkgconf_1.8.1-1+b2_arm64.deb ... Unpacking pkgconf:arm64 (1.8.1-1+b2) ... Setting up libksba8:arm64 (1.6.6-1) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libnpth0t64:arm64 (1.6-3.1) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libbrotli1:arm64 (1.1.0-2+b3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up libpsl5t64:arm64 (0.21.2-1.1) ... Setting up libnghttp2-14:arm64 (1.61.0-1+b1) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:arm64 (1.47.1~rc2-1) ... Setting up file (1:5.45-3) ... Setting up libassuan0:arm64 (2.5.6-1+b1) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up libkrb5support0:arm64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-6) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1+b2) ... Setting up gnupg-l10n (2.2.40-3) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up autopoint (0.21-14) ... Setting up icu-devtools (72.1-4+b1) ... Setting up pkgconf-bin (1.8.1-1+b2) ... Setting up libk5crypto3:arm64 (1.20.1-6+b1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-6) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libkrb5-3:arm64 (1.20.1-6+b1) ... Setting up libssh2-1t64:arm64 (1.11.0-4.1+b2) ... Setting up readline-common (8.2-4) ... Setting up libicu-dev:arm64 (72.1-4+b1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up pinentry-curses (1.2.1-3+b2) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up gpgconf (2.2.40-3) ... Setting up gpg (2.2.40-3) ... Setting up gnupg-utils (2.2.40-3) ... Setting up gpg-agent (2.2.40-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up gpgsm (2.2.40-3) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-5) ... Setting up libxerces-c3.2t64:arm64 (3.2.4+debian-1.3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up dirmngr (2.2.40-3) ... Setting up libxerces-c-dev:arm64 (3.2.4+debian-1.3) ... Setting up gpg-wks-server (2.2.40-3) ... Setting up libgpgme11t64:arm64 (1.18.0-4.1+b1) ... Setting up gpg-wks-client (2.2.40-3) ... Setting up libmaus2-2:arm64 (2.0.813+ds-1+b2) ... Setting up debhelper (13.15.3) ... Setting up gnupg (2.2.40-3) ... Setting up libmaus2-dev (2.0.813+ds-1+b2) ... Processing triggers for libc-bin (2.38-11) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/50043/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/50043/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/biobambam2-2.0.185+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_2.0.185+ds-2_source.changes dpkg-buildpackage: info: source package biobambam2 dpkg-buildpackage: info: source version 2.0.185+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_auto_clean rm -f config.log make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:2: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete. configure.ac:2: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:2: the top level configure.ac:3: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:3: You should run autoupdate. m4/libtool.m4:100: AC_PROG_LIBTOOL is expanded from... configure.ac:3: the top level configure.ac:6: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.ac:6: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:1089: AM_CONFIG_HEADER is expanded from... configure.ac:6: the top level configure.ac:9: warning: The macro `AC_CANONICAL_SYSTEM' is obsolete. configure.ac:9: You should run autoupdate. ./lib/autoconf/general.m4:2081: AC_CANONICAL_SYSTEM is expanded from... configure.ac:9: the top level configure.ac:68: warning: The macro `AC_TRY_COMPILE' is obsolete. configure.ac:68: You should run autoupdate. ./lib/autoconf/general.m4:2847: AC_TRY_COMPILE is expanded from... configure.ac:68: the top level configure.ac:147: warning: The macro `AC_HEADER_STDC' is obsolete. configure.ac:147: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.ac:147: the top level configure.ac:464: warning: AC_OUTPUT should be used without arguments. configure.ac:464: You should run autoupdate. configure.ac:3: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:5: installing './install-sh' configure.ac:5: installing './missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=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 the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert 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 file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking for gawk... no checking for mawk... mawk checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of gcc... none checking whether we are cross compiling... no checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for g++... g++ checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld 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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 configure: Adding optimisation options -O3 to C++ compiler g++ flags, full list now -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for egrep... (cached) /usr/bin/grep -E checking for libmaus2 >= 2.0.800... yes checking whether we can compile a program using libmaus2... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE_NP... yes checking whether pthread_mutexattr_settype supports PTHREAD_MUTEX_RECURSIVE... yes checking whether libmaus2 has support for io_lib... no checking for bash... /usr/bin/bash checking for base64... /usr/bin/base64 checking for xerces-c >= 3.1.1... yes configure: Using flags -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 for C compiler gcc configure: Using flags -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -j12 make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make all-recursive make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making all in src make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammarkduplicates-bammarkduplicates.o `test -f 'programs/bammarkduplicates.cpp' || echo './'`programs/bammarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamsort-bamsort.o `test -f 'programs/bamsort.cpp' || echo './'`programs/bamsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammaskflags-bammaskflags.o `test -f 'programs/bammaskflags.cpp' || echo './'`programs/bammaskflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammaskflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamrecompress-bamrecompress.o `test -f 'programs/bamrecompress.cpp' || echo './'`programs/bamrecompress.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrecompress-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamadapterfind-bamadapterfind.o `test -f 'programs/bamadapterfind.cpp' || echo './'`programs/bamadapterfind.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamadapterfind-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamadapterfind-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamadapterfind-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilteraux-bamfilteraux.o `test -f 'programs/bamfilteraux.cpp' || echo './'`programs/bamfilteraux.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilteraux-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamauxsort-bamauxsort.o `test -f 'programs/bamauxsort.cpp' || echo './'`programs/bamauxsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamauxsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamadapterclip-bamadapterclip.o `test -f 'programs/bamadapterclip.cpp' || echo './'`programs/bamadapterclip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamadapterclip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamadapterclip-ClipAdapters.o `test -f 'biobambam2/ClipAdapters.cpp' || echo './'`biobambam2/ClipAdapters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamcollate2-bamcollate2.o `test -f 'programs/bamcollate2.cpp' || echo './'`programs/bamcollate2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamcollate2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamcollate2-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamcollate2-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bam12auxmerge-bam12auxmerge.o `test -f 'programs/bam12auxmerge.cpp' || echo './'`programs/bam12auxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12auxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12auxmerge-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12auxmerge-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12auxmerge-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12auxmerge-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bam12split-bam12split.o `test -f 'programs/bam12split.cpp' || echo './'`programs/bam12split.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12split-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12split-Split12.o `test -f 'biobambam2/Split12.cpp' || echo './'`biobambam2/Split12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bam12strip-bam12strip.o `test -f 'programs/bam12strip.cpp' || echo './'`programs/bam12strip.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12strip-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bam12strip-Strip12.o `test -f 'biobambam2/Strip12.cpp' || echo './'`biobambam2/Strip12.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamreset-bamreset.o `test -f 'programs/bamreset.cpp' || echo './'`programs/bamreset.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreset-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreset-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamrank-bamrank.o `test -f 'programs/bamrank.cpp' || echo './'`programs/bamrank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrank-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrank-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamclipreinsert-bamclipreinsert.o `test -f 'programs/bamclipreinsert.cpp' || echo './'`programs/bamclipreinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamclipreinsert-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamclipreinsert-ClipReinsert.o `test -f 'biobambam2/ClipReinsert.cpp' || echo './'`biobambam2/ClipReinsert.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamclipXT-bamclipXT.o `test -f 'programs/bamclipXT.cpp' || echo './'`programs/bamclipXT.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamclipXT-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamzztoname-bamzztoname.o `test -f 'programs/bamzztoname.cpp' || echo './'`programs/bamzztoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamzztoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamzztoname-zzToName.o `test -f 'biobambam2/zzToName.cpp' || echo './'`biobambam2/zzToName.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamindex-bamindex.o `test -f 'programs/bamindex.cpp' || echo './'`programs/bamindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterflags-bamfilterflags.o `test -f 'programs/bamfilterflags.cpp' || echo './'`programs/bamfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterrg-bamfilterrg.o `test -f 'programs/bamfilterrg.cpp' || echo './'`programs/bamfilterrg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterrg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamdownsamplerandom-bamdownsamplerandom.o `test -f 'programs/bamdownsamplerandom.cpp' || echo './'`programs/bamdownsamplerandom.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdownsamplerandom-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammarkduplicates2-bammarkduplicates2.o `test -f 'programs/bammarkduplicates2.cpp' || echo './'`programs/bammarkduplicates2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammarkduplicates2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamcat-bamcat.o `test -f 'programs/bamcat.cpp' || echo './'`programs/bamcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammerge-bammerge.o `test -f 'programs/bammerge.cpp' || echo './'`programs/bammerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamsplit-bamsplit.o `test -f 'programs/bamsplit.cpp' || echo './'`programs/bamsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfastsplit-bamfastsplit.o `test -f 'programs/bamfastsplit.cpp' || echo './'`programs/bamfastsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfastsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamsplitdiv-bamsplitdiv.o `test -f 'programs/bamsplitdiv.cpp' || echo './'`programs/bamsplitdiv.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsplitdiv-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamchecksort-bamchecksort.o `test -f 'programs/bamchecksort.cpp' || echo './'`programs/bamchecksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamchecksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/fastqtobam-fastqtobam.o `test -f 'programs/fastqtobam.cpp' || echo './'`programs/fastqtobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastqtobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfixmateinformation-bamfixmateinformation.o `test -f 'programs/bamfixmateinformation.cpp' || echo './'`programs/bamfixmateinformation.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfixmateinformation-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamseqchksum-bamseqchksum.o `test -f 'programs/bamseqchksum.cpp' || echo './'`programs/bamseqchksum.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamseqchksum-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/normalisefasta-normalisefasta.o `test -f 'programs/normalisefasta.cpp' || echo './'`programs/normalisefasta.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/normalisefasta-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterheader-bamfilterheader.o `test -f 'programs/bamfilterheader.cpp' || echo './'`programs/bamfilterheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterheader2-bamfilterheader2.o `test -f 'programs/bamfilterheader2.cpp' || echo './'`programs/bamfilterheader2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterheader2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammdnm-bammdnm.o `test -f 'programs/bammdnm.cpp' || echo './'`programs/bammdnm.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammdnm-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammapdist-bammapdist.o `test -f 'programs/bammapdist.cpp' || echo './'`programs/bammapdist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammapdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamvalidate-bamvalidate.o `test -f 'programs/bamvalidate.cpp' || echo './'`programs/bamvalidate.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamvalidate-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamflagsplit-bamflagsplit.o `test -f 'programs/bamflagsplit.cpp' || echo './'`programs/bamflagsplit.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamflagsplit-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamintervalcomment-bamintervalcomment.o `test -f 'programs/bamintervalcomment.cpp' || echo './'`programs/bamintervalcomment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamintervalcomment-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamintervalcommenthist-bamintervalcommenthist.o `test -f 'programs/bamintervalcommenthist.cpp' || echo './'`programs/bamintervalcommenthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamintervalcommenthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o `test -f 'programs/bamstreamingmarkduplicates.cpp' || echo './'`programs/bamstreamingmarkduplicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamstreamingmarkduplicates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamalignfrac-bamalignfrac.o `test -f 'programs/bamalignfrac.cpp' || echo './'`programs/bamalignfrac.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamalignfrac-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilternames-bamfilternames.o `test -f 'programs/bamfilternames.cpp' || echo './'`programs/bamfilternames.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilternames-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamsormadup-bamsormadup.o `test -f 'programs/bamsormadup.cpp' || echo './'`programs/bamsormadup.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsormadup-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamexplode-bamexplode.o `test -f 'programs/bamexplode.cpp' || echo './'`programs/bamexplode.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamexplode-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamexploderef-bamexploderef.o `test -f 'programs/bamexploderef.cpp' || echo './'`programs/bamexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfastexploderef-bamfastexploderef.o `test -f 'programs/bamfastexploderef.cpp' || echo './'`programs/bamfastexploderef.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfastexploderef-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfastnumextract-bamfastnumextract.o `test -f 'programs/bamfastnumextract.cpp' || echo './'`programs/bamfastnumextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfastnumextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamranksort-bamranksort.o `test -f 'programs/bamranksort.cpp' || echo './'`programs/bamranksort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamranksort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/fastaexplod-fastaexplod.o `test -f 'programs/fastaexplod.cpp' || echo './'`programs/fastaexplod.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastaexplod-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamrecalculatecigar-bamrecalculatecigar.o `test -f 'programs/bamrecalculatecigar.cpp' || echo './'`programs/bamrecalculatecigar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrecalculatecigar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfiltermc-bamfiltermc.o `test -f 'programs/bamfiltermc.cpp' || echo './'`programs/bamfiltermc.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfiltermc-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamnumericalindex-bamnumericalindex.o `test -f 'programs/bamnumericalindex.cpp' || echo './'`programs/bamnumericalindex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamnumericalindex-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamnumericalindexstats-bamnumericalindexstats.o `test -f 'programs/bamnumericalindexstats.cpp' || echo './'`programs/bamnumericalindexstats.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamnumericalindexstats-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammarkduplicatesopt-bammarkduplicatesopt.o `test -f 'programs/bammarkduplicatesopt.cpp' || echo './'`programs/bammarkduplicatesopt.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammarkduplicatesopt-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterlength-bamfilterlength.o `test -f 'programs/bamfilterlength.cpp' || echo './'`programs/bamfilterlength.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterlength-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamauxmerge-bamauxmerge.o `test -f 'programs/bamauxmerge.cpp' || echo './'`programs/bamauxmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamauxmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamrefinterval-bamrefinterval.o `test -f 'programs/bamrefinterval.cpp' || echo './'`programs/bamrefinterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrefinterval-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamscrapcount-bamscrapcount.o `test -f 'programs/bamscrapcount.cpp' || echo './'`programs/bamscrapcount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamscrapcount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterrefid-bamfilterrefid.o `test -f 'programs/bamfilterrefid.cpp' || echo './'`programs/bamfilterrefid.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterrefid-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfillquery-bamfillquery.o `test -f 'programs/bamfillquery.cpp' || echo './'`programs/bamfillquery.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfillquery-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfillquery-AttachRank.o `test -f 'biobambam2/AttachRank.cpp' || echo './'`biobambam2/AttachRank.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamrefextract-bamrefextract.o `test -f 'programs/bamrefextract.cpp' || echo './'`programs/bamrefextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrefextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/fastqtobam2-fastqtobam2.o `test -f 'programs/fastqtobam2.cpp' || echo './'`programs/fastqtobam2.cpp programs/fastqtobam2.cpp: In member function 'virtual void BlockReadControl::checkBgzfWriteQueue()': programs/fastqtobam2.cpp:3861:29: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 3861 | while ( ptr = bgzfGetNext() ) | ~~~~^~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastqtobam2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastqtobam2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastqtobam2-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamauxmerge2-bamauxmerge2.o `test -f 'programs/bamauxmerge2.cpp' || echo './'`programs/bamauxmerge2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamauxmerge2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamauxmerge2-KmerPoisson.o `test -f 'biobambam2/KmerPoisson.cpp' || echo './'`biobambam2/KmerPoisson.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamreheader-bamreheader.o `test -f 'programs/bamreheader.cpp' || echo './'`programs/bamreheader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreheader-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreheader-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreheader-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreheader-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamreplacechecksums-bamreplacechecksums.o `test -f 'programs/bamreplacechecksums.cpp' || echo './'`programs/bamreplacechecksums.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreplacechecksums-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp In file included from /usr/include/libmaus2/parallel/SimpleThreadPoolThreadIdNode.hpp:22, from /usr/include/libmaus2/parallel/SimpleThreadPoolThreadIdTree.hpp:21, from /usr/include/libmaus2/parallel/SimpleThreadPool.hpp:22, from programs/fastqtobam2.cpp:18: In static member function 'static void libmaus2::autoarray::ArrayErase::erase(N*, uint64_t) [with N = FastQPtr]', inlined from 'libmaus2::autoarray::AutoArray::AutoArray(uint64_t, bool) [with N = FastQPtr; libmaus2::autoarray::alloc_type atype = libmaus2::autoarray::alloc_type_cxx; erase_type = libmaus2::autoarray::ArrayErase]' at /usr/include/libmaus2/autoarray/AutoArray.hpp:921:23, inlined from 'FastQPtrList::FastQPtrList()' at programs/fastqtobam2.cpp:240:19, inlined from 'FastQPtrListTypeInfo::pointer_type FastQPtrListAllocator::operator()() const' at programs/fastqtobam2.cpp:272:68, inlined from 'typename libmaus2::util::GrowingFreeList<_element_type, _allocator_type, _type_info_type>::type_info_type::pointer_type libmaus2::util::GrowingFreeList<_element_type, _allocator_type, _type_info_type>::get() [with _element_type = FastQPtrList; _allocator_type = FastQPtrListAllocator; _type_info_type = FastQPtrListTypeInfo]' at /usr/include/libmaus2/util/GrowingFreeList.hpp:123:10: /usr/include/libmaus2/autoarray/AutoArray.hpp:1152:33: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1152 | array[i] = N(); | ^~~~~ /usr/include/libmaus2/autoarray/AutoArray.hpp: In member function 'typename libmaus2::util::GrowingFreeList<_element_type, _allocator_type, _type_info_type>::type_info_type::pointer_type libmaus2::util::GrowingFreeList<_element_type, _allocator_type, _type_info_type>::get() [with _element_type = FastQPtrList; _allocator_type = FastQPtrListAllocator; _type_info_type = FastQPtrListTypeInfo]': /usr/include/libmaus2/autoarray/AutoArray.hpp:1152:44: note: '' declared here 1152 | array[i] = N(); | ^~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreplacechecksums-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o `test -f 'biobambam2/UpdateNumericalIndex.cpp' || echo './'`biobambam2/UpdateNumericalIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfastcat-bamfastcat.o `test -f 'programs/bamfastcat.cpp' || echo './'`programs/bamfastcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfastcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfastcat-ReadHeader.o `test -f 'biobambam2/ReadHeader.cpp' || echo './'`biobambam2/ReadHeader.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfastcat-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/populaterefcache-populaterefcache.o `test -f 'programs/populaterefcache.cpp' || echo './'`programs/populaterefcache.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/populaterefcache-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfiltereofblocks-bamfiltereofblocks.o `test -f 'programs/bamfiltereofblocks.cpp' || echo './'`programs/bamfiltereofblocks.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfiltereofblocks-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfiltereofblocks-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamdepth-bamdepth.o `test -f 'programs/bamdepth.cpp' || echo './'`programs/bamdepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamdepthintersect-bamdepthintersect.o `test -f 'programs/bamdepthintersect.cpp' || echo './'`programs/bamdepthintersect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdepthintersect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdepthintersect-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterk-bamfilterk.o `test -f 'programs/bamfilterk.cpp' || echo './'`programs/bamfilterk.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterk-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterk-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterk-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfixpairinfo-bamfixpairinfo.o `test -f 'programs/bamfixpairinfo.cpp' || echo './'`programs/bamfixpairinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfixpairinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfixpairinfo-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfixpairinfo-RunEOFFilter.o `test -f 'biobambam2/RunEOFFilter.cpp' || echo './'`biobambam2/RunEOFFilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamdifference-bamdifference.o `test -f 'programs/bamdifference.cpp' || echo './'`programs/bamdifference.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdifference-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfeaturecount-bamfeaturecount.o `test -f 'programs/bamfeaturecount.cpp' || echo './'`programs/bamfeaturecount.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfeaturecount-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/blastnxmltobam-blastnxmltobam.o `test -f 'programs/blastnxmltobam.cpp' || echo './'`programs/blastnxmltobam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/blastnxmltobam-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilter-bamfilter.o `test -f 'programs/bamfilter.cpp' || echo './'`programs/bamfilter.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilter-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfilterbyname-bamfilterbyname.o `test -f 'programs/bamfilterbyname.cpp' || echo './'`programs/bamfilterbyname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfilterbyname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfixmatecoordinates-bamfixmatecoordinates.o `test -f 'programs/bamfixmatecoordinates.cpp' || echo './'`programs/bamfixmatecoordinates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfixmatecoordinates-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o `test -f 'programs/bamfixmatecoordinatesnamesorted.cpp' || echo './'`programs/bamfixmatecoordinatesnamesorted.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamtoname-bamtoname.o `test -f 'programs/bamtoname.cpp' || echo './'`programs/bamtoname.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamtoname-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamdisthist-bamdisthist.o `test -f 'programs/bamdisthist.cpp' || echo './'`programs/bamdisthist.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdisthist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/fastabgzfextract-fastabgzfextract.o `test -f 'programs/fastabgzfextract.cpp' || echo './'`programs/fastabgzfextract.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastabgzfextract-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamheap-bamheap.o `test -f 'programs/bamheap.cpp' || echo './'`programs/bamheap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamheap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamfrontback-bamfrontback.o `test -f 'programs/bamfrontback.cpp' || echo './'`programs/bamfrontback.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfrontback-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamfrontback-ResetAlignment.o `test -f 'biobambam2/ResetAlignment.cpp' || echo './'`biobambam2/ResetAlignment.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamrandomtag-bamrandomtag.o `test -f 'programs/bamrandomtag.cpp' || echo './'`programs/bamrandomtag.cpp In file included from /usr/include/libmaus2/aio/BufferedOutput.hpp:23, from /usr/include/libmaus2/sorting/MergingReadBack.hpp:23, from /usr/include/libmaus2/sorting/SortingBufferedOutputFile.hpp:22, from /usr/include/libmaus2/aio/OutputStreamInstanceArray.hpp:21, from programs/bamfeaturecount.cpp:22: In static member function 'static void libmaus2::autoarray::ArrayErase::erase(N*, uint64_t) [with N = libmaus2::gtf::Gene]', inlined from 'libmaus2::autoarray::AutoArray::AutoArray(uint64_t, bool) [with N = libmaus2::gtf::Gene; libmaus2::autoarray::alloc_type atype = libmaus2::autoarray::alloc_type_cxx; erase_type = libmaus2::autoarray::ArrayErase]' at /usr/include/libmaus2/autoarray/AutoArray.hpp:921:23, inlined from 'libmaus2::gtf::GTFData::GTFData(const std::string&, int)' at /usr/include/libmaus2/gtf/GTFData.hpp:1308:79: /usr/include/libmaus2/autoarray/AutoArray.hpp:1152:33: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1152 | array[i] = N(); | ^~~~~ /usr/include/libmaus2/autoarray/AutoArray.hpp: In constructor 'libmaus2::gtf::GTFData::GTFData(const std::string&, int)': /usr/include/libmaus2/autoarray/AutoArray.hpp:1152:44: note: '' declared here 1152 | array[i] = N(); | ^~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamrandomtag-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamheap2-bamheap2.o `test -f 'programs/bamheap2.cpp' || echo './'`programs/bamheap2.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamheap2-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamheap3-bamheap3.o `test -f 'programs/bamheap3.cpp' || echo './'`programs/bamheap3.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamheap3-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamtagconversion-bamtagconversion.o `test -f 'programs/bamtagconversion.cpp' || echo './'`programs/bamtagconversion.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamtagconversion-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/fastqtobampar-fastqtobampar.o `test -f 'programs/fastqtobampar.cpp' || echo './'`programs/fastqtobampar.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/fastqtobampar-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bambisect-bambisect.o `test -f 'programs/bambisect.cpp' || echo './'`programs/bambisect.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bambisect-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcffilterinfo-vcffilterinfo.o `test -f 'programs/vcffilterinfo.cpp' || echo './'`programs/vcffilterinfo.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcffilterinfo-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o `test -f 'programs/vcfpatchcontigprepend.cpp' || echo './'`programs/vcfpatchcontigprepend.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcfpatchcontigprepend-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcfconcat-vcfconcat.o `test -f 'programs/vcfconcat.cpp' || echo './'`programs/vcfconcat.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcfconcat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcfsort-vcfsort.o `test -f 'programs/vcfsort.cpp' || echo './'`programs/vcfsort.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcfsort-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/filtergtf-filtergtf.o `test -f 'programs/filtergtf.cpp' || echo './'`programs/filtergtf.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/filtergtf-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamconsensus-bamconsensus.o `test -f 'programs/bamconsensus.cpp' || echo './'`programs/bamconsensus.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamconsensus-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcfreplacecontigs-vcfreplacecontigs.o `test -f 'programs/vcfreplacecontigs.cpp' || echo './'`programs/vcfreplacecontigs.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcfreplacecontigs-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcffiltersamples-vcffiltersamples.o `test -f 'programs/vcffiltersamples.cpp' || echo './'`programs/vcffiltersamples.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcffiltersamples-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamexploderg-bamexploderg.o `test -f 'programs/bamexploderg.cpp' || echo './'`programs/bamexploderg.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamexploderg-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamexondepth-bamexondepth.o `test -f 'programs/bamexondepth.cpp' || echo './'`programs/bamexondepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamexondepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamexondepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamheadercat-bamheadercat.o `test -f 'programs/bamheadercat.cpp' || echo './'`programs/bamheadercat.cpp In file included from programs/bamexondepth.cpp:22: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamheadercat-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bammarkduplicatesoptdist-bammarkduplicatesoptdist.o `test -f 'programs/bammarkduplicatesoptdist.cpp' || echo './'`programs/bammarkduplicatesoptdist.cpp In file included from /usr/include/c++/13/cassert:44, from /usr/include/libmaus2/avl/AVLSet.hpp:24, from programs/bamexondepth.cpp:43: programs/bamexondepth.cpp: In function 'void handleFile(const std::string&, uint64_t, const libmaus2::bambam::BamHeader&, std::ostream&, std::ostream&, const std::string&)': programs/bamexondepth.cpp:121:44: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] 121 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bammarkduplicatesoptdist-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp programs/bamexondepth.cpp:371:32: warning: comparison of integer expressions of different signedness: 'const uint64_t' {aka 'const long unsigned int'} and 'int64_t' {aka 'long int'} [-Wsign-compare] 371 | if ( d <= thresdepth ) | ~~^~~~~~~~~~~~~ programs/bamexondepth.cpp:375:52: warning: comparison of integer expressions of different signedness: 'uint64_t' {aka 'long unsigned int'} and 'long int' [-Wsign-compare] 375 | assert ( p < GC.e-GC.a ); | ~~^~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcfdiff-vcfdiff.o `test -f 'programs/vcfdiff.cpp' || echo './'`programs/vcfdiff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcfdiff-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamsimpledepth-bamsimpledepth.o `test -f 'programs/bamsimpledepth.cpp' || echo './'`programs/bamsimpledepth.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsimpledepth-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsimpledepth-DepthInterval.o `test -f 'biobambam2/DepthInterval.cpp' || echo './'`biobambam2/DepthInterval.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamdepthmerge-bamdepthmerge.o `test -f 'programs/bamdepthmerge.cpp' || echo './'`programs/bamdepthmerge.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamdepthmerge-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamcountflags-bamcountflags.o `test -f 'programs/bamcountflags.cpp' || echo './'`programs/bamcountflags.cpp In file included from programs/bamdepthmerge.cpp:23: ./biobambam2/DepthIntervalGetter.hpp: In member function 'uint64_t biobambam2::DepthIntervalGetterMerge::getNext(uint64_t&, uint64_t&, libmaus2::autoarray::AutoArray >&)': ./biobambam2/DepthIntervalGetter.hpp:210:53: warning: unused variable 'HE' [-Wunused-variable] 210 | HeapElement const & HE = H.top(); | ^~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcffilterfilterflags-vcffilterfilterflags.o `test -f 'programs/vcffilterfilterflags.cpp' || echo './'`programs/vcffilterfilterflags.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcffilterfilterflags-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o `test -f 'programs/vcfreplacecontigsmap.cpp' || echo './'`programs/vcfreplacecontigsmap.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/vcfreplacecontigsmap-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/fastaselectreg-fastaselectreg.o `test -f 'programs/fastaselectreg.cpp' || echo './'`programs/fastaselectreg.cpp programs/vcfreplacecontigsmap.cpp:29:12: warning: 'int getDefaultGZ()' defined but not used [-Wunused-function] 29 | static int getDefaultGZ() { return 0; } | ^~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamaddne-bamaddne.o `test -f 'programs/bamaddne.cpp' || echo './'`programs/bamaddne.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamaddne-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamadapterhistogram-bamadapterhistogram.o `test -f 'programs/bamadapterhistogram.cpp' || echo './'`programs/bamadapterhistogram.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamadapterhistogram-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamsalvage-bamsalvage.o `test -f 'programs/bamsalvage.cpp' || echo './'`programs/bamsalvage.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamsalvage-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o programs/bamtofastq-bamtofastq.o `test -f 'programs/bamtofastq.cpp' || echo './'`programs/bamtofastq.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o biobambam2/bamtofastq-Licensing.o `test -f 'biobambam2/Licensing.cpp' || echo './'`biobambam2/Licensing.cpp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammarkduplicates programs/bammarkduplicates-bammarkduplicates.o biobambam2/bammarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammarkduplicates programs/bammarkduplicates-bammarkduplicates.o biobambam2/bammarkduplicates-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsort programs/bamsort-bamsort.o biobambam2/bamsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammaskflags programs/bammaskflags-bammaskflags.o biobambam2/bammaskflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrecompress programs/bamrecompress-bamrecompress.o biobambam2/bamrecompress-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterfind programs/bamadapterfind-bamadapterfind.o biobambam2/bamadapterfind-Licensing.o biobambam2/bamadapterfind-ClipAdapters.o biobambam2/bamadapterfind-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilteraux programs/bamfilteraux-bamfilteraux.o biobambam2/bamfilteraux-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxsort programs/bamauxsort-bamauxsort.o biobambam2/bamauxsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcollate2 programs/bamcollate2-bamcollate2.o biobambam2/bamcollate2-Licensing.o biobambam2/bamcollate2-AttachRank.o biobambam2/bamcollate2-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamadapterclip programs/bamadapterclip-bamadapterclip.o biobambam2/bamadapterclip-Licensing.o biobambam2/bamadapterclip-ClipAdapters.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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programs/bamsplit-bamsplit.o biobambam2/bamsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsplitdiv programs/bamsplitdiv-bamsplitdiv.o biobambam2/bamsplitdiv-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastsplit programs/bamfastsplit-bamfastsplit.o biobambam2/bamfastsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamchecksort programs/bamchecksort-bamchecksort.o biobambam2/bamchecksort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsplitdiv programs/bamsplitdiv-bamsplitdiv.o biobambam2/bamsplitdiv-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobam programs/fastqtobam-fastqtobam.o biobambam2/fastqtobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamchecksort programs/bamchecksort-bamchecksort.o biobambam2/bamchecksort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobam programs/fastqtobam-fastqtobam.o biobambam2/fastqtobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixmateinformation programs/bamfixmateinformation-bamfixmateinformation.o biobambam2/bamfixmateinformation-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamseqchksum programs/bamseqchksum-bamseqchksum.o biobambam2/bamseqchksum-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmateinformation programs/bamfixmateinformation-bamfixmateinformation.o biobambam2/bamfixmateinformation-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamseqchksum programs/bamseqchksum-bamseqchksum.o biobambam2/bamseqchksum-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o normalisefasta programs/normalisefasta-normalisefasta.o biobambam2/normalisefasta-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterheader programs/bamfilterheader-bamfilterheader.o biobambam2/bamfilterheader-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o normalisefasta programs/normalisefasta-normalisefasta.o biobambam2/normalisefasta-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterheader2 programs/bamfilterheader2-bamfilterheader2.o biobambam2/bamfilterheader2-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterheader programs/bamfilterheader-bamfilterheader.o biobambam2/bamfilterheader-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterheader2 programs/bamfilterheader2-bamfilterheader2.o biobambam2/bamfilterheader2-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammdnm programs/bammdnm-bammdnm.o biobambam2/bammdnm-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bammapdist programs/bammapdist-bammapdist.o biobambam2/bammapdist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz In file included from /usr/include/libmaus2/bambam/BamHeaderParserState.hpp:22, from /usr/include/libmaus2/bambam/BamHeader.hpp:23, from ./biobambam2/DepthInterval.hpp:23, from programs/bamexondepth.cpp:21: In static member function 'static void libmaus2::autoarray::ArrayErase::erase(N*, uint64_t) [with N = libmaus2::gtf::Gene]', inlined from 'libmaus2::autoarray::AutoArray::AutoArray(uint64_t, bool) [with N = libmaus2::gtf::Gene; libmaus2::autoarray::alloc_type atype = libmaus2::autoarray::alloc_type_cxx; erase_type = libmaus2::autoarray::ArrayErase]' at /usr/include/libmaus2/autoarray/AutoArray.hpp:921:23, inlined from 'libmaus2::gtf::GTFData::GTFData(const std::string&, int)' at /usr/include/libmaus2/gtf/GTFData.hpp:1308:79: /usr/include/libmaus2/autoarray/AutoArray.hpp:1152:33: warning: '' may be used uninitialized [-Wmaybe-uninitialized] 1152 | array[i] = N(); | ^~~~~ /usr/include/libmaus2/autoarray/AutoArray.hpp: In constructor 'libmaus2::gtf::GTFData::GTFData(const std::string&, int)': /usr/include/libmaus2/autoarray/AutoArray.hpp:1152:44: note: '' declared here 1152 | array[i] = N(); | ^~~ libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammdnm programs/bammdnm-bammdnm.o biobambam2/bammdnm-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bammapdist programs/bammapdist-bammapdist.o biobambam2/bammapdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamvalidate programs/bamvalidate-bamvalidate.o biobambam2/bamvalidate-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamflagsplit programs/bamflagsplit-bamflagsplit.o biobambam2/bamflagsplit-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamintervalcomment programs/bamintervalcomment-bamintervalcomment.o biobambam2/bamintervalcomment-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamvalidate programs/bamvalidate-bamvalidate.o biobambam2/bamvalidate-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamflagsplit programs/bamflagsplit-bamflagsplit.o biobambam2/bamflagsplit-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamintervalcomment programs/bamintervalcomment-bamintervalcomment.o biobambam2/bamintervalcomment-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamintervalcommenthist programs/bamintervalcommenthist-bamintervalcommenthist.o biobambam2/bamintervalcommenthist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamstreamingmarkduplicates programs/bamstreamingmarkduplicates-bamstreamingmarkduplicates.o biobambam2/bamstreamingmarkduplicates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 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-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 -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterlength programs/bamfilterlength-bamfilterlength.o biobambam2/bamfilterlength-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge programs/bamauxmerge-bamauxmerge.o biobambam2/bamauxmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamscrapcount programs/bamscrapcount-bamscrapcount.o biobambam2/bamscrapcount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrefinterval programs/bamrefinterval-bamrefinterval.o biobambam2/bamrefinterval-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfilterrefid programs/bamfilterrefid-bamfilterrefid.o biobambam2/bamfilterrefid-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfillquery programs/bamfillquery-bamfillquery.o biobambam2/bamfillquery-Licensing.o biobambam2/bamfillquery-AttachRank.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrefextract programs/bamrefextract-bamrefextract.o biobambam2/bamrefextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 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programs/fastqtobam2-fastqtobam2.o biobambam2/fastqtobam2-Licensing.o biobambam2/fastqtobam2-KmerPoisson.o biobambam2/fastqtobam2-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrefextract programs/bamrefextract-bamrefextract.o biobambam2/bamrefextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 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biobambam2/bamreheader-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamreplacechecksums programs/bamreplacechecksums-bamreplacechecksums.o biobambam2/bamreplacechecksums-Licensing.o biobambam2/bamreplacechecksums-ReadHeader.o biobambam2/bamreplacechecksums-RunEOFFilter.o biobambam2/bamreplacechecksums-UpdateNumericalIndex.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 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biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamauxmerge2 programs/bamauxmerge2-bamauxmerge2.o biobambam2/bamauxmerge2-Licensing.o biobambam2/bamauxmerge2-KmerPoisson.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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-Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfastcat programs/bamfastcat-bamfastcat.o biobambam2/bamfastcat-Licensing.o biobambam2/bamfastcat-ReadHeader.o biobambam2/bamfastcat-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o populaterefcache programs/populaterefcache-populaterefcache.o biobambam2/populaterefcache-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfiltereofblocks programs/bamfiltereofblocks-bamfiltereofblocks.o biobambam2/bamfiltereofblocks-Licensing.o biobambam2/bamfiltereofblocks-RunEOFFilter.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepth programs/bamdepth-bamdepth.o biobambam2/bamdepth-Licensing.o biobambam2/bamdepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthintersect programs/bamdepthintersect-bamdepthintersect.o biobambam2/bamdepthintersect-Licensing.o biobambam2/bamdepthintersect-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfeaturecount programs/bamfeaturecount-bamfeaturecount.o biobambam2/bamfeaturecount-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz -lxerces-c /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o blastnxmltobam programs/blastnxmltobam-blastnxmltobam.o biobambam2/blastnxmltobam-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -lxerces-c -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixmatecoordinates programs/bamfixmatecoordinates-bamfixmatecoordinates.o biobambam2/bamfixmatecoordinates-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilterbyname programs/bamfilterbyname-bamfilterbyname.o biobambam2/bamfilterbyname-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfilter programs/bamfilter-bamfilter.o biobambam2/bamfilter-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfixmatecoordinatesnamesorted programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtoname programs/bamtoname-bamtoname.o biobambam2/bamtoname-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdisthist programs/bamdisthist-bamdisthist.o biobambam2/bamdisthist-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmatecoordinates programs/bamfixmatecoordinates-bamfixmatecoordinates.o biobambam2/bamfixmatecoordinates-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfixmatecoordinatesnamesorted programs/bamfixmatecoordinatesnamesorted-bamfixmatecoordinatesnamesorted.o biobambam2/bamfixmatecoordinatesnamesorted-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtoname programs/bamtoname-bamtoname.o biobambam2/bamtoname-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheap programs/bamheap-bamheap.o biobambam2/bamheap-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdisthist programs/bamdisthist-bamdisthist.o biobambam2/bamdisthist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamfrontback programs/bamfrontback-bamfrontback.o biobambam2/bamfrontback-Licensing.o biobambam2/bamfrontback-ResetAlignment.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamrandomtag programs/bamrandomtag-bamrandomtag.o biobambam2/bamrandomtag-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastabgzfextract programs/fastabgzfextract-fastabgzfextract.o biobambam2/fastabgzfextract-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheap2 programs/bamheap2-bamheap2.o biobambam2/bamheap2-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap programs/bamheap-bamheap.o biobambam2/bamheap-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheap3 programs/bamheap3-bamheap3.o biobambam2/bamheap3-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamrandomtag programs/bamrandomtag-bamrandomtag.o biobambam2/bamrandomtag-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamfrontback programs/bamfrontback-bamfrontback.o biobambam2/bamfrontback-Licensing.o biobambam2/bamfrontback-ResetAlignment.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtagconversion programs/bamtagconversion-bamtagconversion.o biobambam2/bamtagconversion-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap2 programs/bamheap2-bamheap2.o biobambam2/bamheap2-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheap3 programs/bamheap3-bamheap3.o biobambam2/bamheap3-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtagconversion programs/bamtagconversion-bamtagconversion.o biobambam2/bamtagconversion-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastqtobampar programs/fastqtobampar-fastqtobampar.o biobambam2/fastqtobampar-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bambisect programs/bambisect-bambisect.o biobambam2/bambisect-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterinfo programs/vcffilterinfo-vcffilterinfo.o biobambam2/vcffilterinfo-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfpatchcontigprepend programs/vcfpatchcontigprepend-vcfpatchcontigprepend.o biobambam2/vcfpatchcontigprepend-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfconcat programs/vcfconcat-vcfconcat.o biobambam2/vcfconcat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexploderg programs/bamexploderg-bamexploderg.o biobambam2/bamexploderg-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfsort programs/vcfsort-vcfsort.o biobambam2/vcfsort-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o filtergtf programs/filtergtf-filtergtf.o biobambam2/filtergtf-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigs programs/vcfreplacecontigs-vcfreplacecontigs.o biobambam2/vcfreplacecontigs-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamconsensus programs/bamconsensus-bamconsensus.o biobambam2/bamconsensus-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamheadercat programs/bamheadercat-bamheadercat.o biobambam2/bamheadercat-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffiltersamples programs/vcffiltersamples-vcffiltersamples.o biobambam2/vcffiltersamples-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfdiff programs/vcfdiff-vcfdiff.o biobambam2/vcfdiff-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsimpledepth programs/bamsimpledepth-bamsimpledepth.o biobambam2/bamsimpledepth-Licensing.o biobambam2/bamsimpledepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamexploderg programs/bamexploderg-bamexploderg.o biobambam2/bamexploderg-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamheadercat programs/bamheadercat-bamheadercat.o biobambam2/bamheadercat-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfdiff programs/vcfdiff-vcfdiff.o biobambam2/vcfdiff-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsimpledepth programs/bamsimpledepth-bamsimpledepth.o biobambam2/bamsimpledepth-Licensing.o biobambam2/bamsimpledepth-DepthInterval.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcffilterfilterflags programs/vcffilterfilterflags-vcffilterfilterflags.o biobambam2/vcffilterfilterflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamdepthmerge programs/bamdepthmerge-bamdepthmerge.o biobambam2/bamdepthmerge-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o fastaselectreg programs/fastaselectreg-fastaselectreg.o biobambam2/fastaselectreg-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamsalvage programs/bamsalvage-bamsalvage.o biobambam2/bamsalvage-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o vcfreplacecontigsmap programs/vcfreplacecontigsmap-vcfreplacecontigsmap.o biobambam2/vcfreplacecontigsmap-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o fastaselectreg programs/fastaselectreg-fastaselectreg.o biobambam2/fastaselectreg-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamsalvage programs/bamsalvage-bamsalvage.o biobambam2/bamsalvage-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcountflags programs/bamcountflags-bamcountflags.o biobambam2/bamcountflags-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamexondepth programs/bamexondepth-bamexondepth.o biobambam2/bamexondepth-Licensing.o biobambam2/bamexondepth-DepthInterval.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray 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biobambam2/bammarkduplicatesoptdist-Licensing.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtofastq programs/bamtofastq-bamtofastq.o biobambam2/bamtofastq-Licensing.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making all in test make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making check in src make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making check in test make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make bamcmp bamtosam make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o bamcmp-bamcmp.o `test -f 'bamcmp.cpp' || echo './'`bamcmp.cpp g++ -DHAVE_CONFIG_H -I. -I.. -fopenmp -std=c++17 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -c -o bamtosam-bamtosam.o `test -f 'bamtosam.cpp' || echo './'`bamtosam.cpp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamtosam bamtosam-bamtosam.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamtosam bamtosam-bamtosam.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp /bin/sh ../libtool --tag=CXX --mode=link g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z,relro -Wl,-z,now -rdynamic -o bamcmp bamcmp-bamcmp.o -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -fopenmp -lz libtool: link: g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/biobambam2-2.0.185+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -fopenmp -std=c++17 -Wl,-z -Wl,relro -Wl,-z -Wl,now -rdynamic -o bamcmp bamcmp-bamcmp.o -fopenmp -lmaus2 -lmaus2_parallel -lmaus2_autoarray -lmaus2_exception -lmaus2_stacktrace -lmaus2_posix -lmaus2_arch -lmaus2_simd_align_128 -lmaus2_simd_align_256 -lmaus2_demangle -lz -fopenmp make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make check-TESTS make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[4]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' PASS: testshortsort.sh PASS: testshortsortqueryname.sh PASS: testshortsortcoordinate.sh PASS: testdupsinglemarkedsortedqreset.sh PASS: testdupsingle.sh PASS: testfastqbamloop.sh ============================================================================ Testsuite summary for biobambam2 2.0.185 ============================================================================ # TOTAL: 6 # PASS: 6 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/biobambam2/ make -j1 install DESTDIR=/build/reproducible-path/biobambam2-2.0.185\+ds/debian/biobambam2 AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' Making install in src make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' /usr/bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin' /bin/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/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin' libtool: install: /usr/bin/install -c bamtofastq /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamtofastq libtool: install: /usr/bin/install -c bammarkduplicates /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicates libtool: install: /usr/bin/install -c bamsort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsort libtool: install: /usr/bin/install -c bammaskflags /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammaskflags libtool: install: /usr/bin/install -c bamrecompress /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrecompress libtool: install: /usr/bin/install -c bamadapterfind /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamadapterfind libtool: install: /usr/bin/install -c bamfilteraux /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilteraux libtool: install: /usr/bin/install -c bamauxsort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxsort libtool: install: /usr/bin/install -c bamadapterclip /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamadapterclip libtool: install: /usr/bin/install -c bamcollate2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamcollate2 libtool: install: /usr/bin/install -c bam12auxmerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12auxmerge libtool: install: /usr/bin/install -c bam12split /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12split libtool: install: /usr/bin/install -c bam12strip /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bam12strip libtool: install: /usr/bin/install -c bamreset /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreset libtool: install: /usr/bin/install -c bamrank /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrank libtool: install: /usr/bin/install -c bamclipreinsert /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamclipreinsert libtool: install: /usr/bin/install -c bamclipXT /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamclipXT libtool: install: /usr/bin/install -c bamzztoname /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamzztoname libtool: install: /usr/bin/install -c bamindex /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamindex libtool: install: /usr/bin/install -c bamfilterflags /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterflags libtool: install: /usr/bin/install -c bamfilterrg /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterrg libtool: install: /usr/bin/install -c bamdownsamplerandom /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdownsamplerandom libtool: install: /usr/bin/install -c bammarkduplicates2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicates2 libtool: install: /usr/bin/install -c bamcat /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamcat libtool: install: /usr/bin/install -c bammerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammerge libtool: install: /usr/bin/install -c bamsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsplit libtool: install: /usr/bin/install -c bamfastsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastsplit libtool: install: /usr/bin/install -c bamsplitdiv /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsplitdiv libtool: install: /usr/bin/install -c bamchecksort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamchecksort libtool: install: /usr/bin/install -c fastqtobam /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastqtobam libtool: install: /usr/bin/install -c bamfixmateinformation /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfixmateinformation libtool: install: /usr/bin/install -c bamseqchksum /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamseqchksum libtool: install: /usr/bin/install -c normalisefasta /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/normalisefasta libtool: install: /usr/bin/install -c bamfilterheader /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterheader libtool: install: /usr/bin/install -c bamfilterheader2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterheader2 libtool: install: /usr/bin/install -c bammdnm /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammdnm libtool: install: /usr/bin/install -c bammapdist /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammapdist libtool: install: /usr/bin/install -c bamvalidate /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamvalidate libtool: install: /usr/bin/install -c bamflagsplit /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamflagsplit libtool: install: /usr/bin/install -c bamintervalcomment /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamintervalcomment libtool: install: /usr/bin/install -c bamintervalcommenthist /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamintervalcommenthist libtool: install: /usr/bin/install -c bamstreamingmarkduplicates /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamstreamingmarkduplicates libtool: install: /usr/bin/install -c bamalignfrac /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamalignfrac libtool: install: /usr/bin/install -c bamfilternames /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilternames libtool: install: /usr/bin/install -c bamsormadup /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamsormadup libtool: install: /usr/bin/install -c bamexplode /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamexplode libtool: install: /usr/bin/install -c bamexploderef /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamexploderef libtool: install: /usr/bin/install -c bamfastexploderef /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastexploderef libtool: install: /usr/bin/install -c bamfastnumextract /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastnumextract libtool: install: /usr/bin/install -c bamranksort /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamranksort libtool: install: /usr/bin/install -c fastaexplod /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastaexplod libtool: install: /usr/bin/install -c bamrecalculatecigar /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrecalculatecigar libtool: install: /usr/bin/install -c bamfiltermc /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfiltermc libtool: install: /usr/bin/install -c bamnumericalindex /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamnumericalindex libtool: install: /usr/bin/install -c bamnumericalindexstats /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamnumericalindexstats libtool: install: /usr/bin/install -c bammarkduplicatesopt /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bammarkduplicatesopt libtool: install: /usr/bin/install -c bamfilterlength /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterlength libtool: install: /usr/bin/install -c bamauxmerge /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxmerge libtool: install: /usr/bin/install -c bamrefinterval /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrefinterval libtool: install: /usr/bin/install -c bamscrapcount /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamscrapcount libtool: install: /usr/bin/install -c bamfilterrefid /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterrefid libtool: install: /usr/bin/install -c bamfillquery /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfillquery libtool: install: /usr/bin/install -c bamrefextract /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamrefextract libtool: install: /usr/bin/install -c fastqtobam2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/fastqtobam2 libtool: install: /usr/bin/install -c bamauxmerge2 /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamauxmerge2 libtool: install: /usr/bin/install -c bamreheader /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreheader libtool: install: /usr/bin/install -c bamreplacechecksums /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamreplacechecksums libtool: install: /usr/bin/install -c bamfastcat /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfastcat libtool: install: /usr/bin/install -c populaterefcache /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/populaterefcache libtool: install: /usr/bin/install -c bamfiltereofblocks /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfiltereofblocks libtool: install: /usr/bin/install -c bamdepth /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdepth libtool: install: /usr/bin/install -c bamdepthintersect /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdepthintersect libtool: install: /usr/bin/install -c bamfilterk /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfilterk libtool: install: /usr/bin/install -c bamfixpairinfo /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfixpairinfo libtool: install: /usr/bin/install -c bamdifference /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamdifference libtool: install: /usr/bin/install -c bamfeaturecount /build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/bin/bamfeaturecount /usr/bin/mkdir -p '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/bamtofastq.1 programs/bamsort.1 programs/bammarkduplicates.1 programs/bammarkduplicatesopt.1 programs/bammaskflags.1 programs/bamrecompress.1 programs/bamadapterfind.1 programs/bamfilteraux.1 programs/bamauxsort.1 programs/bamadapterclip.1 programs/bamcollate2.1 programs/bam12auxmerge.1 programs/bam12split.1 programs/bam12strip.1 programs/bamreset.1 programs/bamrank.1 programs/bamclipreinsert.1 programs/bamzztoname.1 programs/bamindex.1 programs/bamfilterflags.1 programs/bamfilterrg.1 programs/bamdownsamplerandom.1 programs/bammarkduplicates2.1 programs/bamcat.1 programs/bammerge.1 programs/bamsplit.1 programs/bamsplitdiv.1 programs/bamchecksort.1 programs/fastqtobam.1 programs/bamfixmateinformation.1 programs/normalisefasta.1 programs/bamfilterheader.1 programs/bamfilterheader2.1 programs/bammdnm.1 programs/bamseqchksum.1 programs/bamvalidate.1 programs/bamflagsplit.1 programs/bamintervalcomment.1 programs/bamstreamingmarkduplicates.1 programs/bamsormadup.1 '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' /usr/bin/install -c -m 644 programs/fastaexplod.1 programs/bamrecalculatecigar.1 programs/bamfiltermc.1 programs/bamfillquery.1 programs/bamalignfrac.1 programs/bamauxmerge.1 programs/bamauxmerge2.1 programs/bambisect.1 programs/bamclipXT.1 programs/bamconsensus.1 programs/filtergtf.1 programs/bamfeaturecount.1 '/build/reproducible-path/biobambam2-2.0.185+ds/debian/biobambam2/usr/share/man/man1' make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/src' Making install in test make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds/test' make[2]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Entering directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[2]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' make[1]: Leaving directory '/build/reproducible-path/biobambam2-2.0.185+ds' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'biobambam2' in '../biobambam2_2.0.185+ds-2_arm64.deb'. dpkg-deb: building package 'biobambam2-dbgsym' in '../biobambam2-dbgsym_2.0.185+ds-2_arm64.deb'. dpkg-genbuildinfo --build=binary -O../biobambam2_2.0.185+ds-2_arm64.buildinfo dpkg-genchanges --build=binary -O../biobambam2_2.0.185+ds-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/50043/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/50043/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/50043 and its subdirectories I: Current time: Mon May 13 21:46:37 +14 2024 I: pbuilder-time-stamp: 1715586397