I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 8 02:27:26 +14 2024 I: pbuilder-time-stamp: 1704630446 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [libstatgen_1.0.14-7.dsc] I: copying [./libstatgen_1.0.14.orig.tar.gz] I: copying [./libstatgen_1.0.14-7.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.n1Kg0emI/trustedkeys.kbx': General error gpgv: Signature made Mon Aug 3 20:38:42 2020 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libstatgen_1.0.14-7.dsc dpkg-source: info: extracting libstatgen in libstatgen-1.0.14 dpkg-source: info: unpacking libstatgen_1.0.14.orig.tar.gz dpkg-source: info: unpacking libstatgen_1.0.14-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_compilation_error.patch dpkg-source: info: applying Fix_compilation_flags.patch dpkg-source: info: applying Remove_erroneous_deletes_in_Chromosome_constructor.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/964465/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 Jan 7 12:28 /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/964465/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/964465/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=15 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=cc83173c7ca24eeea2f1c7da3822b936 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=964465 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.u0ODuzyT/pbuilderrc_y7bK --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.u0ODuzyT/b2 --logfile b2/build.log libstatgen_1.0.14-7.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 27 2022 bash -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 20 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 7 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 7 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 20 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount -rwxr-xr-x 1 root root 203072 Jan 25 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 7 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 7 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 20 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 20 2022 more -rwsr-xr-x 1 root root 55528 Jan 20 2022 mount -rwxr-xr-x 1 root root 18664 Jan 20 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 7 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 16 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 27 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed lrwxrwxrwx 1 root root 9 Jan 7 12:28 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 20 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 20 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 20 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 7 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 5898 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8049 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/964465/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), doxygen, libssl-dev, zlib1g-dev, d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 17743 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 doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs 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} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libclang-cpp11{a} libclang1-11{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libllvm11{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libpipeline1{a} libsigsegv2{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libz3-4{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 42 newly installed, 0 to remove and 0 not upgraded. Need to get 64.8 MB of archives. After unpacking 275 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3+deb11u1 [69.2 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 d-shlibs all 0.98 [17.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 32 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Get: 33 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get: 34 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get: 35 http://deb.debian.org/debian bullseye/main amd64 libedit2 amd64 3.1-20191231-2+b1 [96.7 kB] Get: 36 http://deb.debian.org/debian bullseye/main amd64 libz3-4 amd64 4.8.10-1 [6949 kB] Get: 37 http://deb.debian.org/debian bullseye/main amd64 libllvm11 amd64 1:11.0.1-2 [17.9 MB] Get: 38 http://deb.debian.org/debian bullseye/main amd64 libclang-cpp11 amd64 1:11.0.1-2 [9632 kB] Get: 39 http://deb.debian.org/debian bullseye/main amd64 libclang1-11 amd64 1:11.0.1-2 [5521 kB] Get: 40 http://deb.debian.org/debian bullseye/main amd64 doxygen amd64 1.9.1-1 [4232 kB] Get: 41 http://deb.debian.org/debian bullseye/main amd64 libssl-dev amd64 1.1.1w-0+deb11u1 [1820 kB] Get: 42 http://deb.debian.org/debian bullseye/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2+deb11u2 [191 kB] Fetched 64.8 MB in 5s (14.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17743 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3+deb11u1) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking file (1:5.39-3+deb11u1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../16-d-shlibs_0.98_all.deb ... Unpacking d-shlibs (0.98) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../17-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-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 .../21-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../22-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../23-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../24-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../25-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../26-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../28-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../29-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../30-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../31-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Selecting previously unselected package libmd0:amd64. Preparing to unpack .../32-libmd0_1.0.3-3_amd64.deb ... Unpacking libmd0:amd64 (1.0.3-3) ... Selecting previously unselected package libbsd0:amd64. 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Setting up libz3-4:amd64 (4.8.10-1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up libssl-dev:amd64 (1.1.1w-0+deb11u1) ... Setting up autopoint (0.21-4) ... Setting up d-shlibs (0.98) ... Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2+deb11u2) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up libedit2:amd64 (3.1-20191231-2+b1) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libllvm11:amd64 (1:11.0.1-2) ... Setting up libclang1-11 (1:11.0.1-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp11 (1:11.0.1-2) ... Setting up dh-autoreconf (20) ... Setting up doxygen (1.9.1-1) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 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/964465/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/964465/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libstatgen-1.0.14/ && 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 > ../libstatgen_1.0.14-7_source.changes dpkg-buildpackage: info: source package libstatgen dpkg-buildpackage: info: source version 1.0.14-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_auto_clean make -j15 clean make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/samtools' rm -f ../include/bgzf.h ../include/knetfile.h ../include/khash.h ../include/bam.h ar d ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: creating ../libStatGen.a ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o ar: creating ../libStatGen_debug.a ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: creating ../libStatGen_profile.a ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/samtools' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/general' rm -f ../include/BaseAsciiMap.h ../include/BaseQualityHelper.h ../include/BaseUtilities.h ../include/BasicHash.h ../include/BgzfFileType.h ../include/BgzfFileTypeRecovery.h ../include/CharBuffer.h ../include/Chromosome.h ../include/Cigar.h ../include/CigarRoller.h ../include/Error.h ../include/ErrorHandler.h ../include/FileType.h ../include/FortranFormat.h ../include/GenomeSequence.h ../include/GenotypeLists.h ../include/glfHandler.h ../include/GzipFileType.h ../include/GzipHeader.h ../include/Hash.h ../include/IndexBase.h ../include/Input.h ../include/InputFile.h ../include/IntArray.h ../include/IntHash.h ../include/LongLongCounter.h ../include/MapFunction.h ../include/MathMatrix.h ../include/MathVector.h ../include/MemoryAllocators.h ../include/MemoryInfo.h ../include/MemoryMapArray.h ../include/MemoryMap.h ../include/MiniDeflate.h ../include/NonOverlapRegions.h ../include/Parameters.h ../include/PedigreeAlleleFreq.h ../include/Pedigree.h ../include/PedigreeDescription.h ../include/PedigreeFamily.h ../include/PedigreeGlobals.h ../include/PedigreePerson.h ../include/PhoneHome.h ../include/QuickIndex.h ../include/Random.h ../include/ReferenceSequence.h ../include/SmithWaterman.h ../include/Sort.h ../include/STLUtilities.h ../include/StatGenStatus.h ../include/StringAlias.h ../include/StringArray.h ../include/StringBasics.h ../include/StringHash.h ../include/StringMap.h ../include/Tabix.h ../include/UncompressedFileType.h ../include/Constant.h ../include/CSG_MD5.h ../include/Generic.h ../include/GenomeSequenceHelpers.h ../include/GreedyTupleAligner.h ../include/InplaceMerge.h ../include/LongHash.h ../include/LongInt.h ../include/MathConstant.h ../include/PackedVector.h ../include/PedigreeAlleles.h ../include/Performance.h ../include/ReusableVector.h ../include/SimpleStats.h ../include/TrimSequence.h ../include/UnitTest.h ar d ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj inputFileTest *~ results/* rm -rf obj stringTest *~ results/* rm -rf obj cigarRollerTest *~ results/* rm -rf obj trimSequence *~ results/* rm -rf obj packedVectorTest *~ results/* rm -rf obj memoryMapArrayTest *~ results/* rm -rf obj baseUtilitiesTest *~ results/* rm -rf obj referenceSequenceTest *~ results/* rm -rf obj nonOverlapRegionsTest *~ results/* rm -rf obj reusableVectorTest *~ results/* # clean current directory rm -f *.o *~ rm -f phiX-bs.umfa phiX-cs.umfa gtest make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/general' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/bam' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/glf' rm -f ../include/GlfException.h ../include/GlfFile.h ../include/GlfHeader.h ../include/GlfRecord.h ../include/GlfRefSection.h ../include/GlfStatus.h make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' ar d ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o rm -f ../include/SamFileHeader.h ../include/SamFile.h ../include/GenericSamInterface.h ../include/SamInterface.h ../include/BamInterface.h ../include/SamRecord.h ../include/BamIndex.h ../include/SamHeaderHD.h ../include/SamHeaderPG.h ../include/SamHeaderRecord.h ../include/SamHeaderSQ.h ../include/SamHeaderRG.h ../include/SamHeaderTag.h ../include/SamValidation.h ../include/SamStatistics.h ../include/SamQuerySeqWithRefHelper.h ../include/SamFilter.h ../include/PileupElement.h ../include/PileupElementBaseQual.h ../include/SamReferenceInfo.h ../include/SamTags.h ../include/PosList.h ../include/CigarHelper.h ../include/SamRecordPool.h ../include/SamCoordOutput.h ../include/SamRecordHelper.h ../include/Pileup.h ../include/SamHelper.h ../include/SamFlag.h ../include/SamStatus.h ar d ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ranlib ../libStatGen_debug.a ranlib ../libStatGen.a rm -f ../include/FastQFile.h ../include/BaseCount.h ../include/BaseComposition.h ../include/FastQStatus.h ar d ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o rm -f ../include/VcfFile.h ../include/VcfFileReader.h ../include/VcfFileWriter.h ../include/VcfGenotypeField.h ../include/VcfGenotypeFormat.h ../include/VcfGenotypeSample.h ../include/VcfHeader.h ../include/VcfHelper.h ../include/VcfRecord.h ../include/VcfRecordField.h ../include/VcfRecordFilter.h ../include/VcfRecordGenotype.h ../include/VcfRecordInfo.h ../include/VcfSubsetSamples.h ../include/VcfRecordDiscardRules.h ar d ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o ar d ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ranlib ../libStatGen_profile.a ranlib ../libStatGen_debug.a ranlib ../libStatGen.a ar d ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o ar d ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o ranlib ../libStatGen.a ranlib ../libStatGen_profile.a ranlib ../libStatGen_debug.a ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o ranlib ../libStatGen_profile.a ar d ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj samTest *~ results/* rm -rf obj glfTest *~ results/* make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/bam' make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' rm -rf obj fastqTest *~ results/* rm -rf obj vcfTest *~ results/* make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/vcf' rm -f libStatGen.a rm -f libStatGen_debug.a rm -f libStatGen_profile.a make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' dh_auto_build make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/samtools' ln -s ../samtools/bgzf.h ../include/bgzf.h ln -s ../samtools/knetfile.h ../include/knetfile.h ln -s ../samtools/khash.h ../include/khash.h ln -s ../samtools/bam.h ../include/bam.h mkdir -p obj gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/bgzf.o -c bgzf.c gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/knetfile.o -c knetfile.c ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/samtools' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/general' ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h ln -s ../general/BasicHash.h ../include/BasicHash.h ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h ln -s ../general/CharBuffer.h ../include/CharBuffer.h ln -s ../general/Chromosome.h ../include/Chromosome.h ln -s ../general/Cigar.h ../include/Cigar.h ln -s ../general/CigarRoller.h ../include/CigarRoller.h ln -s ../general/Error.h ../include/Error.h ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h ln -s ../general/FileType.h ../include/FileType.h ln -s ../general/FortranFormat.h ../include/FortranFormat.h ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h ln -s ../general/glfHandler.h ../include/glfHandler.h ln -s ../general/GzipFileType.h ../include/GzipFileType.h ln -s ../general/GzipHeader.h ../include/GzipHeader.h ln -s ../general/Hash.h ../include/Hash.h ln -s ../general/IndexBase.h ../include/IndexBase.h ln -s ../general/Input.h ../include/Input.h ln -s ../general/InputFile.h ../include/InputFile.h ln -s ../general/IntArray.h ../include/IntArray.h ln -s ../general/IntHash.h ../include/IntHash.h ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h ln -s ../general/MapFunction.h ../include/MapFunction.h ln -s ../general/MathMatrix.h ../include/MathMatrix.h ln -s ../general/MathVector.h ../include/MathVector.h ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h ln -s ../general/MemoryMap.h ../include/MemoryMap.h ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h ln -s ../general/Parameters.h ../include/Parameters.h ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h ln -s ../general/Pedigree.h ../include/Pedigree.h ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h ln -s ../general/PhoneHome.h ../include/PhoneHome.h ln -s ../general/QuickIndex.h ../include/QuickIndex.h ln -s ../general/Random.h ../include/Random.h ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h ln -s ../general/Sort.h ../include/Sort.h ln -s ../general/STLUtilities.h ../include/STLUtilities.h ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h ln -s ../general/StringAlias.h ../include/StringAlias.h ln -s ../general/StringArray.h ../include/StringArray.h ln -s ../general/StringBasics.h ../include/StringBasics.h ln -s ../general/StringHash.h ../include/StringHash.h ln -s ../general/StringMap.h ../include/StringMap.h ln -s ../general/Tabix.h ../include/Tabix.h ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h ln -s ../general/Constant.h ../include/Constant.h ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h ln -s ../general/Generic.h ../include/Generic.h ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h ln -s ../general/LongHash.h ../include/LongHash.h ln -s ../general/LongInt.h ../include/LongInt.h ln -s ../general/MathConstant.h ../include/MathConstant.h ln -s ../general/PackedVector.h ../include/PackedVector.h ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h ln -s ../general/Performance.h ../include/Performance.h ln -s ../general/ReusableVector.h ../include/ReusableVector.h ln -s ../general/SimpleStats.h ../include/SimpleStats.h ln -s ../general/TrimSequence.h ../include/TrimSequence.h ln -s ../general/UnitTest.h ../include/UnitTest.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/general' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/bam' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/glf' make[3]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' ln -s ../fastq/FastQFile.h ../include/FastQFile.h ln -s ../fastq/BaseCount.h ../include/BaseCount.h ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h ln -s ../glf/GlfException.h ../include/GlfException.h ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h mkdir -p obj ln -s ../bam/SamFile.h ../include/SamFile.h ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h ln -s ../vcf/VcfFile.h ../include/VcfFile.h ln -s ../glf/GlfFile.h ../include/GlfFile.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamInterface.h ../include/SamInterface.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" ln -s ../glf/GlfHeader.h ../include/GlfHeader.h ln -s ../glf/GlfRecord.h ../include/GlfRecord.h ln -s ../bam/BamInterface.h ../include/BamInterface.h ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamRecord.h ../include/SamRecord.h ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/BamIndex.h ../include/BamIndex.h ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h ln -s ../glf/GlfStatus.h ../include/GlfStatus.h ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h mkdir -p obj ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h ln -s ../bam/SamValidation.h ../include/SamValidation.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h ln -s ../bam/SamStatistics.h ../include/SamStatistics.h ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h ln -s ../bam/SamFilter.h ../include/SamFilter.h ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h ln -s ../bam/PileupElement.h ../include/PileupElement.h ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h mkdir -p obj ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h ln -s ../bam/SamTags.h ../include/SamTags.h ln -s ../bam/PosList.h ../include/PosList.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/CigarHelper.h ../include/CigarHelper.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h ln -s ../bam/Pileup.h ../include/Pileup.h ln -s ../bam/SamHelper.h ../include/SamHelper.h ln -s ../bam/SamFlag.h ../include/SamFlag.h ln -s ../bam/SamStatus.h ../include/SamStatus.h mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/vcf' ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/bam' make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14' # Build the shared library g++ -shared -o libStatGen.so.0 */obj/*.o -fPIC -Wl,-soname,libStatGen.so.0 -Wl,-z,relro -Wl,-z,now # Build doxygen doc doxygen warning: Tag 'DETAILS_AT_TOP' at line 163 of file 'Doxyfile' has become obsolete. 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Otherwise you run the risk that the wrong font is being used for dot generated graphs. Adding custom extension mapping: 'h' will be treated as language 'c++' Doxygen version used: 1.9.1 Notice: Output directory 'dox' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /build/reproducible-path/libstatgen-1.0.14/include Searching for files in directory /build/reproducible-path/libstatgen-1.0.14/copyrights Searching for files in directory /build/reproducible-path/libstatgen-1.0.14/dox Searching for files in directory /build/reproducible-path/libstatgen-1.0.14/dox/html Searching for files in directory /build/reproducible-path/libstatgen-1.0.14/dox/man Searching INPUT for files to process... 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Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/BamIndex.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/BamIndex.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/BamIndex.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/BamInterface.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/BamInterface.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/BamInterface.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/BamInterface.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/CigarHelper.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/CigarHelper.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/CigarHelper.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/CigarHelper.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/examples/pileup/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/examples/pileup/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/examples/printRefPositions/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/examples/printRefPositions/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/examples/printRefPositions/PrintRefPositions.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/examples/printRefPositions/PrintRefPositions.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/examples/printRefPositions/PrintRefPositions.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/examples/printRefPositions/PrintRefPositions.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/GenericSamInterface.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/GenericSamInterface.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/GenericSamInterface.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/GenericSamInterface.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/Pileup.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/Pileup.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/PileupElement.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/PileupElement.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/PileupElement.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/PileupElement.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/PileupElementBaseQual.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/PileupElementBaseQual.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/PileupElementBaseQual.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/PileupElementBaseQual.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/PosList.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/PosList.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/PosList.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/PosList.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamCoordOutput.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamCoordOutput.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamCoordOutput.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamCoordOutput.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFile.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFile.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFile.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFile.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFileHeader.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFileHeader.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFileHeader.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFileHeader.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFilter.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFilter.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFilter.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFilter.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamFlag.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamFlag.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderHD.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderHD.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderHD.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderHD.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderPG.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderPG.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderPG.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderPG.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRecord.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRecord.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRecord.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRecord.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRG.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRG.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRG.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderRG.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderSQ.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderSQ.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderSQ.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderSQ.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderTag.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderTag.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderTag.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHeaderTag.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamHelper.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamHelper.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamInterface.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamInterface.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamInterface.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamInterface.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamQuerySeqWithRefHelper.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamQuerySeqWithRefHelper.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamQuerySeqWithRefHelper.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamQuerySeqWithRefHelper.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamRecord.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamRecord.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamRecord.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamRecord.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordHelper.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordHelper.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordHelper.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordHelper.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordPool.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordPool.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordPool.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamRecordPool.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamReferenceInfo.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamReferenceInfo.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamReferenceInfo.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamReferenceInfo.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamStatistics.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamStatistics.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamStatistics.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamStatistics.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamStatus.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamStatus.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamTags.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamTags.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamTags.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamTags.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamValidation.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamValidation.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/SamValidation.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/SamValidation.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/BamIndexTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/BamIndexTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/BamIndexTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/BamIndexTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/Modify.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/Modify.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/Modify.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/Modify.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ModifyVar.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ModifyVar.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ModifyVar.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ModifyVar.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ReadFiles.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ReadFiles.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ReadFiles.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ReadFiles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/SamFileTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/SamFileTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/SamFileTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/SamFileTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ShiftIndels.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ShiftIndels.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ShiftIndels.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ShiftIndels.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestCigarHelper.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestCigarHelper.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestCigarHelper.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestCigarHelper.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestEquals.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestEquals.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestEquals.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestEquals.h... 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Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamCoordOutput.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamCoordOutput.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamCoordOutput.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamCoordOutput.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordHelper.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordHelper.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordHelper.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordHelper.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordPool.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordPool.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordPool.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestSamRecordPool.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestValidate.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestValidate.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/TestValidate.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/TestValidate.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ValidationTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ValidationTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/ValidationTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/ValidationTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/WriteFiles.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/WriteFiles.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/bam/test/WriteFiles.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/bam/test/WriteFiles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/fastq/BaseComposition.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/fastq/BaseComposition.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/fastq/BaseComposition.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/fastq/BaseComposition.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/fastq/BaseCount.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/fastq/BaseCount.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/fastq/BaseCount.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/fastq/BaseCount.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/fastq/FastQFile.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/fastq/FastQFile.cpp... 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Parsing file /build/reproducible-path/libstatgen-1.0.14/general/BasicHash.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileType.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileType.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileType.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileType.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileTypeRecovery.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileTypeRecovery.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileTypeRecovery.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/BgzfFileTypeRecovery.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/CharBuffer.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/CharBuffer.cpp... 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Parsing file /build/reproducible-path/libstatgen-1.0.14/general/GenotypeLists.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/glfHandler.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/glfHandler.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/glfHandler.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/glfHandler.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/GreedyTupleAligner.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/GreedyTupleAligner.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/GzipFileType.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/GzipFileType.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/GzipFileType.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/GzipFileType.h... 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Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MemoryInfo.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MemoryInfo.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MemoryInfo.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MemoryInfo.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MemoryMap.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MemoryMap.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MemoryMap.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MemoryMap.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MemoryMapArray.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MemoryMapArray.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MemoryMapArray.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MemoryMapArray.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MiniDeflate.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MiniDeflate.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/MiniDeflate.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/MiniDeflate.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/NonOverlapRegions.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/NonOverlapRegions.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/NonOverlapRegions.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/NonOverlapRegions.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PackedVector.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PackedVector.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Parameters.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Parameters.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Parameters.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Parameters.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Pedigree.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Pedigree.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Pedigree.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Pedigree.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeAlleleFreq.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeAlleleFreq.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeAlleleFreq.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeAlleleFreq.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeAlleles.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeAlleles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeDescription.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeDescription.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeDescription.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeDescription.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeFamily.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeFamily.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeFamily.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeFamily.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeGlobals.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeGlobals.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeGlobals.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeGlobals.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeLoader.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeLoader.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreePerson.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreePerson.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreePerson.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreePerson.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeTrim.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeTrim.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PedigreeTwin.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PedigreeTwin.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Performance.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Performance.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PhoneHome.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PhoneHome.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/PhoneHome.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/PhoneHome.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/QuickIndex.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/QuickIndex.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/QuickIndex.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/QuickIndex.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Random.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Random.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Random.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Random.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/ReferenceSequence.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/ReferenceSequence.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/ReferenceSequence.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/ReferenceSequence.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/ReusableVector.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/ReusableVector.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/SimpleStats.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/SimpleStats.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/SmithWaterman.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/SmithWaterman.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/SmithWaterman.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/SmithWaterman.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Sort.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Sort.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Sort.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Sort.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StatGenStatus.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StatGenStatus.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StatGenStatus.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StatGenStatus.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/STLUtilities.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/STLUtilities.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/STLUtilities.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/STLUtilities.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/String.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/String.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringAlias.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringAlias.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringAlias.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringAlias.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringArray.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringArray.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringArray.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringArray.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringBasics.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringBasics.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringBasics.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringBasics.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringHash.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringHash.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringHash.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringHash.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringMap.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringMap.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/StringMap.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/StringMap.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Tabix.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Tabix.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/Tabix.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/Tabix.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/Chromosome_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/Chromosome_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/dbsnp/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/dbsnp/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/GenomeSequence_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/GenomeSequence_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/GreedyTupleAligner_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/GreedyTupleAligner_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/gtest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/gtest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/STLUtilities_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/STLUtilities_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/string/StringTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/string/StringTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/string/StringTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/string/StringTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/trimSequence/TrimSequence.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/trimSequence/TrimSequence.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/test/TrimSequence_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/test/TrimSequence_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/TrimSequence.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/TrimSequence.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/UncompressedFileType.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/UncompressedFileType.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/UncompressedFileType.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/UncompressedFileType.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/general/UnitTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/general/UnitTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfException.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfException.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfException.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfException.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfFile.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfFile.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfFile.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfFile.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfHeader.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfHeader.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfHeader.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfHeader.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfRecord.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfRecord.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfRecord.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfRecord.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfRefSection.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfRefSection.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfRefSection.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfRefSection.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfStatus.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfStatus.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/GlfStatus.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/GlfStatus.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/ReadFiles.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/ReadFiles.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/ReadFiles.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/ReadFiles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/Validate.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/Validate.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/Validate.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/Validate.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/WriteFiles.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/WriteFiles.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.14/glf/test/WriteFiles.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/glf/test/WriteFiles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/samtools/bam.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/samtools/bam.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/samtools/bgzf.c... Parsing file /build/reproducible-path/libstatgen-1.0.14/samtools/bgzf.c... Preprocessing /build/reproducible-path/libstatgen-1.0.14/samtools/bgzf.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/samtools/bgzf.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/samtools/khash.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/samtools/khash.h... Preprocessing /build/reproducible-path/libstatgen-1.0.14/samtools/knetfile.c... Parsing file /build/reproducible-path/libstatgen-1.0.14/samtools/knetfile.c... Preprocessing /build/reproducible-path/libstatgen-1.0.14/samtools/knetfile.h... Parsing file /build/reproducible-path/libstatgen-1.0.14/samtools/knetfile.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Computing nesting relations for classes... Associating documentation with classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file bam/BamIndex.cpp... Generating code for file bam/BamIndex.h... Generating code for file bam/BamInterface.cpp... Generating code for file bam/BamInterface.h... Generating code for file bam/CigarHelper.cpp... Generating code for file bam/CigarHelper.h... Generating code for file bam/examples/pileup/Main.cpp... Generating code for file bam/examples/printRefPositions/Main.cpp... Generating code for file bam/test/Main.cpp... Generating code for file general/test/dbsnp/Main.cpp... Generating code for file glf/test/Main.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.h... Generating code for file bam/GenericSamInterface.cpp... Generating code for file bam/GenericSamInterface.h... Generating code for file bam/Pileup.h... Generating code for file bam/PileupElement.cpp... Generating code for file bam/PileupElement.h... Generating code for file bam/PileupElementBaseQual.cpp... Generating code for file bam/PileupElementBaseQual.h... Generating code for file bam/PosList.cpp... Generating code for file bam/PosList.h... Generating code for file bam/SamCoordOutput.cpp... Generating code for file bam/SamCoordOutput.h... Generating code for file bam/SamFile.cpp... Generating code for file bam/SamFile.h... Generating code for file bam/SamFileHeader.cpp... Generating code for file bam/SamFileHeader.h... Generating code for file bam/SamFilter.cpp... Generating code for file bam/SamFilter.h... Generating code for file bam/SamFlag.h... Generating code for file bam/SamHeaderHD.cpp... Generating code for file bam/SamHeaderHD.h... Generating code for file bam/SamHeaderPG.cpp... Generating code for file bam/SamHeaderPG.h... Generating code for file bam/SamHeaderRecord.cpp... Generating code for file bam/SamHeaderRecord.h... Generating code for file bam/SamHeaderRG.cpp... Generating code for file bam/SamHeaderRG.h... Generating code for file bam/SamHeaderSQ.cpp... Generating code for file bam/SamHeaderSQ.h... Generating code for file bam/SamHeaderTag.cpp... Generating code for file bam/SamHeaderTag.h... Generating code for file bam/SamHelper.h... Generating code for file bam/SamInterface.cpp... Generating code for file bam/SamInterface.h... Generating code for file bam/SamQuerySeqWithRefHelper.cpp... Generating code for file bam/SamQuerySeqWithRefHelper.h... Generating code for file bam/SamRecord.cpp... Generating code for file bam/SamRecord.h... Generating code for file bam/SamRecordHelper.cpp... Generating code for file bam/SamRecordHelper.h... Generating code for file bam/SamRecordPool.cpp... Generating code for file bam/SamRecordPool.h... Generating code for file bam/SamReferenceInfo.cpp... Generating code for file bam/SamReferenceInfo.h... Generating code for file bam/SamStatistics.cpp... Generating code for file bam/SamStatistics.h... Generating code for file bam/SamStatus.h... Generating code for file bam/SamTags.cpp... Generating code for file bam/SamTags.h... Generating code for file bam/SamValidation.cpp... Generating code for file bam/SamValidation.h... Generating code for file bam/test/BamIndexTest.cpp... Generating code for file bam/test/BamIndexTest.h... Generating code for file bam/test/Modify.cpp... Generating code for file bam/test/Modify.h... Generating code for file bam/test/ModifyVar.cpp... Generating code for file bam/test/ModifyVar.h... Generating code for file bam/test/ReadFiles.cpp... Generating code for file glf/test/ReadFiles.cpp... Generating code for file bam/test/ReadFiles.h... Generating code for file glf/test/ReadFiles.h... Generating code for file bam/test/SamFileTest.cpp... Generating code for file bam/test/SamFileTest.h... Generating code for file bam/test/ShiftIndels.cpp... Generating code for file bam/test/ShiftIndels.h... Generating code for file bam/test/TestCigarHelper.cpp... Generating code for file bam/test/TestCigarHelper.h... Generating code for file bam/test/TestEquals.cpp... Generating code for file bam/test/TestEquals.h... Generating code for file bam/test/TestFilter.cpp... Generating code for file bam/test/TestFilter.h... Generating code for file bam/test/TestPileup.cpp... Generating code for file bam/test/TestPileup.h... Generating code for file bam/test/TestPosList.cpp... Generating code for file bam/test/TestPosList.h... Generating code for file bam/test/TestSamCoordOutput.cpp... Generating code for file bam/test/TestSamCoordOutput.h... Generating code for file bam/test/TestSamRecordHelper.cpp... Generating code for file bam/test/TestSamRecordHelper.h... Generating code for file bam/test/TestSamRecordPool.cpp... Generating code for file bam/test/TestSamRecordPool.h... Generating code for file bam/test/TestValidate.cpp... Generating code for file bam/test/TestValidate.h... Generating code for file bam/test/ValidationTest.cpp... Generating code for file bam/test/ValidationTest.h... Generating code for file bam/test/WriteFiles.cpp... Generating code for file glf/test/WriteFiles.cpp... Generating code for file bam/test/WriteFiles.h... Generating code for file glf/test/WriteFiles.h... Generating code for file fastq/BaseComposition.cpp... Generating code for file fastq/BaseComposition.h... Generating code for file fastq/BaseCount.cpp... Generating code for file fastq/BaseCount.h... Generating code for file fastq/FastQFile.cpp... Generating code for file fastq/FastQFile.h... Generating code for file fastq/FastQStatus.cpp... Generating code for file fastq/FastQStatus.h... Generating code for file fastq/test/FastQFileTest.cpp... Generating code for file general/BaseAsciiMap.cpp... Generating code for file general/BaseAsciiMap.h... Generating code for file general/BaseQualityHelper.cpp... Generating code for file general/BaseQualityHelper.h... Generating code for file general/BaseUtilities.cpp... Generating code for file general/BaseUtilities.h... Generating code for file general/BasicHash.cpp... Generating code for file general/BasicHash.h... Generating code for file general/BgzfFileType.cpp... Generating code for file general/BgzfFileType.h... Generating code for file general/BgzfFileTypeRecovery.cpp... Generating code for file general/BgzfFileTypeRecovery.h... Generating code for file general/CharBuffer.cpp... Generating code for file general/CharBuffer.h... Generating code for file general/Chromosome.cpp... Generating code for file general/Chromosome.h... Generating code for file general/Cigar.cpp... Generating code for file general/Cigar.h... Generating code for file general/CigarRoller.cpp... Generating code for file general/CigarRoller.h... Generating code for file general/Constant.h... Generating code for file general/CSG_MD5.h... Generating code for file general/Error.cpp... Generating code for file general/Error.h... Generating code for file general/ErrorHandler.cpp... Generating code for file general/ErrorHandler.h... Generating code for file general/FileType.cpp... Generating code for file general/FileType.h... Generating code for file general/FortranFormat.cpp... Generating code for file general/FortranFormat.h... Generating code for file general/Generic.cpp... Generating code for file general/Generic.h... Generating code for file general/GenomeSequence.cpp... Generating code for file general/GenomeSequence.h... Generating code for file general/GenomeSequenceHelpers.h... Generating code for file general/GenotypeLists.cpp... Generating code for file general/GenotypeLists.h... Generating code for file general/glfHandler.cpp... Generating code for file general/glfHandler.h... Generating code for file general/GreedyTupleAligner.h... Generating code for file general/GzipFileType.cpp... Generating code for file general/GzipFileType.h... Generating code for file general/GzipHeader.cpp... Generating code for file general/GzipHeader.h... Generating code for file general/Hash.cpp... Generating code for file general/Hash.h... Generating code for file general/IndexBase.cpp... Generating code for file general/IndexBase.h... Generating code for file general/InplaceMerge.cpp... Generating code for file general/InplaceMerge.h... Generating code for file general/Input.cpp... Generating code for file general/Input.h... Generating code for file general/InputFile.cpp... Generating code for file general/InputFile.h... Generating code for file general/IntArray.cpp... Generating code for file general/IntArray.h... Generating code for file general/IntHash.cpp... Generating code for file general/IntHash.h... Generating code for file general/LongHash.h... Generating code for file general/LongInt.h... Generating code for file general/LongLongCounter.cpp... Generating code for file general/LongLongCounter.h... Generating code for file general/MapFunction.cpp... Generating code for file general/MapFunction.h... Generating code for file general/MathConstant.h... Generating code for file general/MathMatrix.cpp... Generating code for file general/MathMatrix.h... Generating code for file general/MathVector.cpp... Generating code for file general/MathVector.h... Generating code for file general/MemoryAllocators.cpp... Generating code for file general/MemoryAllocators.h... Generating code for file general/MemoryInfo.cpp... Generating code for file general/MemoryInfo.h... Generating code for file general/MemoryMap.cpp... Generating code for file general/MemoryMap.h... Generating code for file general/MemoryMapArray.cpp... Generating code for file general/MemoryMapArray.h... Generating code for file general/MiniDeflate.cpp... Generating code for file general/MiniDeflate.h... Generating code for file general/NonOverlapRegions.cpp... Generating code for file general/NonOverlapRegions.h... Generating code for file general/PackedVector.h... Generating code for file general/Parameters.cpp... Generating code for file general/Parameters.h... Generating code for file general/Pedigree.cpp... Generating code for file general/Pedigree.h... Generating code for file general/PedigreeAlleleFreq.cpp... Generating code for file general/PedigreeAlleleFreq.h... Generating code for file general/PedigreeAlleles.h... Generating code for file general/PedigreeDescription.cpp... Generating code for file general/PedigreeDescription.h... Generating code for file general/PedigreeFamily.cpp... Generating code for file general/PedigreeFamily.h... Generating code for file general/PedigreeGlobals.cpp... Generating code for file general/PedigreeGlobals.h... Generating code for file general/PedigreeLoader.cpp... Generating code for file general/PedigreePerson.cpp... Generating code for file general/PedigreePerson.h... Generating code for file general/PedigreeTrim.cpp... Generating code for file general/PedigreeTwin.cpp... Generating code for file general/Performance.h... Generating code for file general/PhoneHome.cpp... Generating code for file general/PhoneHome.h... Generating code for file general/QuickIndex.cpp... Generating code for file general/QuickIndex.h... Generating code for file general/Random.cpp... Generating code for file general/Random.h... Generating code for file general/ReferenceSequence.cpp... Generating code for file general/ReferenceSequence.h... Generating code for file general/ReusableVector.h... Generating code for file general/SimpleStats.h... Generating code for file general/SmithWaterman.cpp... Generating code for file general/SmithWaterman.h... Generating code for file general/Sort.cpp... Generating code for file general/Sort.h... Generating code for file general/StatGenStatus.cpp... Generating code for file general/StatGenStatus.h... Generating code for file general/STLUtilities.cpp... Generating code for file general/STLUtilities.h... Generating code for file general/String.cpp... Generating code for file general/StringAlias.cpp... Generating code for file general/StringAlias.h... Generating code for file general/StringArray.cpp... Generating code for file general/StringArray.h... Generating code for file general/StringBasics.cpp... Generating code for file general/StringBasics.h... Generating code for file general/StringHash.cpp... Generating code for file general/StringHash.h... Generating code for file general/StringMap.cpp... Generating code for file general/StringMap.h... Generating code for file general/Tabix.cpp... Generating code for file general/Tabix.h... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Generating code for file general/test/Chromosome_test.cpp... Generating code for file general/test/cigar/CigarRollerTest.cpp... Generating code for file general/test/cigar/CigarRollerTest.h... Generating code for file general/test/GenomeSequence_test.cpp... Generating code for file general/test/GreedyTupleAligner_test.cpp... Generating code for file general/test/gtest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.h... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Generating code for file general/test/packedVectorTest/PackedVectorTest.cpp... Generating code for file general/test/packedVectorTest/PackedVectorTest.h... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.h... Generating code for file general/test/reusableVector/ReusableVectorTest.cpp... Generating code for file general/test/reusableVector/ReusableVectorTest.h... Generating code for file general/test/STLUtilities_test.cpp... Generating code for file general/test/string/StringTest.cpp... Generating code for file general/test/string/StringTest.h... Generating code for file general/test/trimSequence/TrimSequence.cpp... Generating code for file general/test/TrimSequence_test.cpp... Generating code for file general/TrimSequence.h... Generating code for file general/UncompressedFileType.cpp... Generating code for file general/UncompressedFileType.h... Generating code for file general/UnitTest.h... Generating code for file glf/GlfException.cpp... Generating code for file glf/GlfException.h... Generating code for file glf/GlfFile.cpp... Generating code for file glf/GlfFile.h... Generating code for file glf/GlfHeader.cpp... Generating code for file glf/GlfHeader.h... Generating code for file glf/GlfRecord.cpp... Generating code for file glf/GlfRecord.h... Generating code for file glf/GlfRefSection.cpp... Generating code for file glf/GlfRefSection.h... Generating code for file glf/GlfStatus.cpp... Generating code for file glf/GlfStatus.h... Generating code for file glf/test/Validate.cpp... Generating code for file glf/test/Validate.h... Generating code for file samtools/bam.h... Generating code for file samtools/bgzf.c... Generating code for file samtools/bgzf.h... Generating code for file samtools/khash.h... Generating code for file samtools/knetfile.c... Generating code for file samtools/knetfile.h... Generating file documentation... Generating docs for file general/InputFile.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound __kstring_t... Generating docs for compound Alleles... Generating docs for compound AnalyzeClass... Generating docs for compound BamIndex... Generating docs for compound BamIndexFileTest... Generating docs for compound BamInterface... Generating docs for compound bamRecordStruct... Generating docs for compound BaseAsciiMap... Generating docs for compound BaseComposition... Generating docs for compound BaseCount... Generating docs for compound baseQualityConvertor... Generating docs for compound BaseUtilities... Generating docs for compound BasicHash... Generating docs for compound BGZF... Generating docs for compound CharBuffer... Generating docs for compound Chromosome... Generating docs for compound ChromosomeInfo... Generating docs for compound Chunk... Generating docs for compound Cigar... Generating docs for nested compound Cigar::CigarOperator... Generating docs for compound CigarHelper... Generating docs for compound CigarHelperTest... Generating docs for compound CigarRoller... Generating docs for compound CigarRollerTest... Generating docs for compound ColumnExtras... Generating docs for compound defaultPileup... Generating docs for compound DoubleParameter... Generating docs for compound emptyGenericHeader... Generating docs for compound EqualsTest... Generating docs for compound ErrorHandler... Generating docs for compound Family... Generating docs for compound FastQFile... Generating docs for compound FastQStatus... Generating docs for compound FileType... Generating docs for compound FilterTest... Generating docs for compound FortranFormat... Generating docs for compound GenericSamInterface... Generating docs for compound GenomeSequence... Generating docs for compound genomeSequenceMmapHeader... Generating docs for compound GenotypeList... Generating docs for compound glfEntry... Generating docs for compound GlfException... Generating docs for compound GlfFile... Generating docs for compound GlfFileReader... Generating docs for compound GlfFileWriter... Generating docs for compound glfHandler... Generating docs for compound GlfHeader... Generating docs for compound glfIndel... Generating docs for compound GlfRecord... Generating docs for compound GlfRefSection... Generating docs for compound GlfStatus... Generating docs for compound GlobalTestEnvironment... Generating docs for compound GreedyTupleAligner... Generating docs for compound GzipHeader... Generating docs for compound HiddenDouble... Generating docs for compound HiddenInteger... Generating docs for compound HiddenString... Generating docs for compound HiddenSwitch... Generating docs for compound IFILE_Test... Generating docs for compound IndexBase... Generating docs for nested compound IndexBase::Bin... Generating docs for nested compound IndexBase::Reference... Generating docs for compound InputFile... Generating docs for compound IntArray... Generating docs for compound IntHash... Generating docs for compound IntParameter... Generating docs for compound knetFile_s... Generating docs for compound ListParameter... Generating docs for compound LongCounter... Generating docs for compound LongHash... Generating docs for compound LongParamContainer... Generating docs for compound LongParameterList... Generating docs for compound LongParameters... Generating docs for compound MarkerInfo... Generating docs for compound Matrix... Generating docs for compound MD5_CTX... Generating docs for compound MemoryMap... Generating docs for compound MemoryMapArray... Generating docs for compound MemoryMapArrayHeader... Generating docs for compound MemoryMapArrayTest... Generating docs for compound MemoryMapGenericHeader... Generating docs for compound MiniDeflate... Generating docs for compound MockGenomeSequence... Generating docs for compound modify... Generating docs for compound modifyVar... Generating docs for compound NonOverlapRegionPos... Generating docs for compound NonOverlapRegions... Generating docs for compound NonOverlapRegionsTest... Generating docs for compound OptionList... Generating docs for compound PackedArrayTest... Generating docs for compound PackedRead... Generating docs for compound PackedSequenceData... Generating docs for compound PackedVector... Generating docs for compound Parameter... Generating docs for compound ParameterList... Generating docs for compound Pedigree... Generating docs for compound PedigreeDescription... Generating docs for compound PedigreeGlobals... Generating docs for compound PedigreeKey... Generating docs for compound Person... Generating docs for compound PhoneHome... Generating docs for compound Pileup... Generating docs for compound PileupElement... Generating docs for compound PileupElementBaseQual... Generating docs for compound PileupHelper... Generating docs for compound PosList... Generating docs for compound QuickIndex... Generating docs for compound Random... Generating docs for compound ReferenceSequenceTest... Generating docs for compound ReusableVector... Generating docs for compound ReusableVectorTest... Generating docs for compound ReusableVectorTestDataType... Generating docs for compound RunningStat... Generating docs for compound SamCoordOutput... Generating docs for compound SamCoordOutputTest... Generating docs for compound SamFile... Generating docs for compound SamFileHeader... Generating docs for compound SamFileReader... Generating docs for compound SamFileWriter... Generating docs for compound SamFilter... Generating docs for compound SamFlag... Generating docs for compound SamHeaderHD... Generating docs for compound SamHeaderPG... Generating docs for compound SamHeaderRecord... Generating docs for compound SamHeaderRG... Generating docs for compound SamHeaderSQ... Generating docs for compound SamHeaderTag... Generating docs for compound SamHelper... Generating docs for compound SamInterface... Generating docs for compound SamQuerySeqWithRef... Generating docs for compound SamQuerySeqWithRefIter... Generating docs for compound SamRecord... Generating docs for compound SamRecordHelper... Generating docs for compound SamRecordHelperTest... Generating docs for compound SamRecordPool... Generating docs for compound SamRecordPoolTest... Generating docs for compound SamReferenceInfo... Generating docs for compound SamSingleBaseMatchInfo... Generating docs for compound SamStatistics... Generating docs for compound SamTags... Generating docs for compound SamValidationError... Generating docs for compound SamValidationErrors... Generating docs for compound SamValidator... Generating docs for compound SetParameter... Generating docs for compound Ssh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found sh: line 1: dot: command not found hiftIndelsTest... Generating docs for compound SmithWaterman... Generating docs for nested compound SmithWaterman::weight... Generating docs for compound SortedChunkList... Generating docs for compound StatGenStatus... Generating docs for compound String... Generating docs for compound StringAlias... Generating docs for compound StringArray... Generating docs for compound StringDoubleHash... Generating docs for compound StringHash... Generating docs for compound StringHashBase... Generating docs for compound StringIntHash... Generating docs for compound StringIntMap... Generating docs for compound StringMap... Generating docs for compound StringParameter... Generating docs for compound SwitchParameter... Generating docs for compound Tabix... Generating docs for compound TestPileup... Generating docs for compound TestPileupElement... Generating docs for compound TestPosList... Generating docs for compound TestValidate... Generating docs for compound TestWrite... Generating docs for compound Timing... Generating docs for compound UncompressedFileType... Generating docs for compound UnitTest... Generating docs for compound Vector... Generating docs for compound VectorFunc... Generating docs for compound Weight... Generating namespace index... Generating docs for namespace STLUtilities Generating graph info page... Generating directory documentation... Generating dependency graph for directory bam Generating dependency graph for directory general/test/dbsnp Generating dependency graph for directory fastq Generating dependency graph for directory glf Generating dependency graph for directory general/test/inputFileTest Generating dependency graph for directory general/test Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 16 parallel threads... 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Patching output file 18/98 Patching output file 19/98 Patching output file 20/98 Patching output file 21/98 Patching output file 22/98 Patching output file 23/98 Patching output file 24/98 Patching output file 25/98 Patching output file 26/98 Patching output file 27/98 Patching output file 28/98 Patching output file 29/98 Patching output file 30/98 Patching output file 31/98 Patching output file 32/98 Patching output file 33/98 Patching output file 34/98 Patching output file 35/98 Patching output file 36/98 Patching output file 37/98 Patching output file 38/98 Patching output file 39/98 Patching output file 40/98 Patching output file 41/98 Patching output file 42/98 Patching output file 43/98 Patching output file 44/98 Patching output file 45/98 Patching output file 46/98 Patching output file 47/98 Patching output file 48/98 Patching output file 49/98 Patching output file 50/98 Patching output file 51/98 Patching output file 52/98 Patching output file 53/98 Patching output file 54/98 Patching output file 55/98 Patching output file 56/98 Patching output file 57/98 Patching output file 58/98 Patching output file 59/98 Patching output file 60/98 Patching output file 61/98 Patching output file 62/98 Patching output file 63/98 Patching output file 64/98 Patching output file 65/98 Patching output file 66/98 Patching output file 67/98 Patching output file 68/98 Patching output file 69/98 Patching output file 70/98 Patching output file 71/98 Patching output file 72/98 Patching output file 73/98 Patching output file 74/98 Patching output file 75/98 Patching output file 76/98 Patching output file 77/98 Patching output file 78/98 Patching output file 79/98 Patching output file 80/98 Patching output file 81/98 Patching output file 82/98 Patching output file 83/98 Patching output file 84/98 Patching output file 85/98 Patching output file 86/98 Patching output file 87/98 Patching output file 88/98 Patching output file 89/98 Patching output file 90/98 Patching output file 91/98 Patching output file 92/98 Patching output file 93/98 Patching output file 94/98 Patching output file 95/98 Patching output file 96/98 Patching output file 97/98 Patching output file 98/98 lookup cache used 9549/65536 hits=87105 misses=10062 finished... make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14' dh_auto_test make -j15 test make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/samtools' ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o mkdir -p obj/debug ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/profile gcc -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/bgzf.o -c bgzf.c gcc -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/knetfile.o -c knetfile.c gcc -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/bgzf.o -c bgzf.c gcc -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/knetfile.o -c knetfile.c ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/samtools' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/general' ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o mkdir -p obj/debug ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/profile g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') ar -cru ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir obj mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRollerTest.o -c CigarRollerTest.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PackedVectorTest.o -c PackedVectorTest.cpp -DVERSION="\"0.0.1\"" mkdir obj mkdir obj mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringTest.o -c StringTest.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFileTest.o -c InputFileTest.cpp -DVERSION="\"0.0.1\"" mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArrayTest.o -c MemoryMapArrayTest.cpp -DVERSION="\"0.0.1\"" mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequenceTest.o -c ReferenceSequenceTest.cpp -DVERSION="\"0.0.1\"" mkdir obj mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilitiesTest.o -c BaseUtilitiesTest.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReusableVectorTest.o -c ReusableVectorTest.cpp -DVERSION="\"0.0.1\"" mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TrimSequence.o -c TrimSequence.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegionsTest.o -c NonOverlapRegionsTest.cpp -DVERSION="\"0.0.1\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o stringTest obj/StringTest.o ../../../libStatGen_debug.a -lm -lz g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o reusableVectorTest obj/ReusableVectorTest.o ../../../libStatGen_debug.a -lm -lz g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o nonOverlapRegionsTest obj/NonOverlapRegionsTest.o ../../../libStatGen_debug.a -lm -lz g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o baseUtilitiesTest obj/BaseUtilitiesTest.o ../../../libStatGen_debug.a -lm -lz ./reusableVectorTest mkdir -p results && ./stringTest ./baseUtilitiesTest ./nonOverlapRegionsTest 2> results/NonOverlapRegionsTest.txt && diff results/NonOverlapRegionsTest.txt expectedNonOverlapRegionsTest.txt g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o trimSequence obj/TrimSequence.o ../../../libStatGen_debug.a -lm -lz ./trimSequence g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o packedVectorTest obj/PackedVectorTest.o ../../../libStatGen_debug.a -lm -lz ./packedVectorTest PackedArrayTest PASS: 46 FAIL: 0 In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from ../../../include/InputFile.h:23, from InputFileTest.h:18, from InputFileTest.cpp:17: In function 'void* memcpy(void*, const void*, size_t)', inlined from 'int InputFile::ifread(void*, unsigned int)' at ../../../include/InputFile.h:167:19, inlined from 'void IFILE_Test::test_ifread_ifgetc(const char*)' at InputFileTest.cpp:696:25: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:33: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' forming offset [65546, 196609] is out of the bounds [0, 65546] [-Warray-bounds] 34 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o cigarRollerTest obj/CigarRollerTest.o ../../../libStatGen_debug.a -lm -lz mkdir -p results; ./cigarRollerTest CigarRoller PASS: 646 FAIL: 0 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o memoryMapArrayTest obj/MemoryMapArrayTest.o ../../../libStatGen_debug.a -lm -lz mkdir -p results; ./memoryMapArrayTest MemoryMapArrayTest PASS: 108 FAIL: 0 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o referenceSequenceTest obj/ReferenceSequenceTest.o ../../../libStatGen_debug.a -lm -lz ./referenceSequenceTest test2 sequence utilization is 6.25% - expect around 6.25% phiX reference utilization is 96.8357% - expect around 96.8% ReferenceSequenceTest PASS: 13 FAIL: 0 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o inputFileTest obj/InputFileTest.o ../../../libStatGen_debug.a -lm -lz mkdir -p results && ./inputFileTest > results/results.log && diff data/InputFileTest.bam results/bgzfFile.glf && diff data/InputFileTest.txt results/defaultFile.glf && diff data/InputFileTest.gz results/defaultFile.gz && diff data/InputFileTest.gz results/gzipFile.glf && diff data/InputFileTest.txt results/InputFileTest.glf && diff data/InputFileTest.txt results/uncompressedFile.glf && diff data/textFile.gz results/textFile.gz && diff data/textFile.gz results/textFile1.gz && diff results/results.log expected/results.log make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/general' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/bam' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/fastq' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/glf' make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.14/vcf' ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o mkdir -p obj/debug ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/debug mkdir -p obj/profile ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/profile g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" mkdir -p obj/debug ar: `u' modifier ignored since `D' is the default (see `U') g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" mkdir -p obj/profile ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/debug mkdir -p obj/profile g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" mkdir obj g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FastQFileTest.o -c FastQFileTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir obj g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReadFiles.o -c ReadFiles.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\"" ReadFiles.cpp: In function 'void testReadGlf()': ReadFiles.cpp:45:24: warning: catching polymorphic type 'class GlfException' by value [-Wcatch-value=] 45 | catch(GlfException e) | ^ g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Validate.o -c Validate.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/WriteFiles.o -c WriteFiles.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o fastqTest obj/FastQFileTest.o ../../libStatGen_debug.a -lm -lz g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\"" mkdir -p results; ./FastQValidatorTest.sh make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/fastq' g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o glfTest obj/ReadFiles.o obj/Validate.o obj/WriteFiles.o obj/Main.o ../../libStatGen_debug.a -lm -lz g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/debug/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" ./glfTest make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/glf' g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\"" mkdir obj g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/WriteFiles.o -c WriteFiles.cpp -DVERSION="\"0.0.1\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ValidationTest.o -c ValidationTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReadFiles.o -c ReadFiles.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BamIndexTest.o -c BamIndexTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ModifyVar.o -c ModifyVar.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Modify.o -c Modify.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamFileTest.o -c SamFileTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestValidate.o -c TestValidate.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestEquals.o -c TestEquals.cpp -DVERSION="\"0.0.1\"" ar -cru ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o ar: `u' modifier ignored since `D' is the default (see `U') g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestFilter.o -c TestFilter.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ShiftIndels.o -c ShiftIndels.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestPileup.o -c TestPileup.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestPosList.o -c TestPosList.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestCigarHelper.o -c TestCigarHelper.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestSamRecordPool.o -c TestSamRecordPool.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestSamCoordOutput.o -c TestSamCoordOutput.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/TestSamRecordHelper.o -c TestSamRecordHelper.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" ar -cru ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir obj g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileTest.o -c VcfFileTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfHeaderTest.o -c VcfHeaderTest.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Main.o -c Main.cpp -DVERSION="\"0.0.1\"" g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o samTest obj/WriteFiles.o obj/ValidationTest.o obj/ReadFiles.o obj/BamIndexTest.o obj/ModifyVar.o obj/Modify.o obj/SamFileTest.o obj/TestValidate.o obj/TestEquals.o obj/TestFilter.o obj/ShiftIndels.o obj/TestPileup.o obj/TestPosList.o obj/TestCigarHelper.o obj/TestSamRecordPool.o obj/TestSamCoordOutput.o obj/TestSamRecordHelper.o obj/Main.o ../../libStatGen_debug.a -lm -lz ./test.sh make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/bam' g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o vcfTest obj/VcfFileTest.o obj/VcfHeaderTest.o obj/Main.o ../../libStatGen_debug.a -lm -lz ./vcfTest && diff results/vcfHeader.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedFirst.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedLast.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedMiddle.vcf expected/vcfHeader.vcf && diff results/vcfFile.vcf testFiles/vcfFile.vcf && diff results/vcfFileNoInfo.vcf expected/vcfFileNoInfo.vcf && diff results/vcfFileNoInfoBGZF.vcf expected/vcfFileNoInfoBGZF.vcf && diff results/vcfFileNoInfoKeepGT.vcf expected/vcfFileNoInfoKeepGT.vcf && diff results/vcfFileNoInfoKeepGQHQ.vcf expected/vcfFileNoInfoKeepGQHQ.vcf make[2]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14/vcf' make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.14' mkdir -p debian/libstatgen-dev/usr/include/libStatGen/ cp -L include/* debian/libstatgen-dev/usr/include/libStatGen/ ln -s libStatGen.so.0 libStatGen.so d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ libStatGen.so Library package automatic movement utility set -e install -d -m 755 debian/libstatgen-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstatgen0/usr/lib/x86_64-linux-gnu mv ./libStatGen.la debian/libstatgen-dev/usr/lib/x86_64-linux-gnu || true mv ./libStatGen.so debian/libstatgen-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libstatgen-1.0.14/libStatGen.so.0 debian/libstatgen0/usr/lib/x86_64-linux-gnu PKGDEV=libstatgen-dev PKGSHL=libstatgen0 mv: cannot stat './libStatGen.la': No such file or directory make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.14' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzclose used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateInit2_ used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzseek64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol deflate used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzwrite used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen64 used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libstatgen0' in '../libstatgen0_1.0.14-7_amd64.deb'. dpkg-deb: building package 'libstatgen0-dbgsym' in '../libstatgen0-dbgsym_1.0.14-7_amd64.deb'. dpkg-deb: building package 'libstatgen-dev' in '../libstatgen-dev_1.0.14-7_amd64.deb'. dpkg-deb: building package 'libstatgen-doc' in '../libstatgen-doc_1.0.14-7_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libstatgen_1.0.14-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/964465/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/964465/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/964465 and its subdirectories I: Current time: Mon Jan 8 02:39:33 +14 2024 I: pbuilder-time-stamp: 1704631173