Diff of the two buildlogs: -- --- b1/build.log 2021-06-19 16:17:26.374906112 +0000 +++ b2/build.log 2021-06-19 16:30:52.468584540 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jun 19 04:12:46 -12 2021 -I: pbuilder-time-stamp: 1624119166 +I: Current time: Sat Jul 23 12:40:32 +14 2022 +I: pbuilder-time-stamp: 1658529632 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sun Mar 17 20:36:11 2019 -12 +gpgv: Signature made Mon Mar 18 22:36:11 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -31,136 +31,170 @@ dpkg-source: info: applying Remove_erroneous_deletes_in_Chromosome_constructor.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/58868/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/9546/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/9546/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/9546/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + 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]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + 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 parallel=16' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='44f9615863c146c69c1842d5f81b0127' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='58868' - PS1='# ' - PS2='> ' + INVOCATION_ID=5a0ad26d445a4a06bc8908243e781a24 + 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=9546 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.iI372YmQnl/pbuilderrc_Lic5 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.iI372YmQnl/b1 --logfile b1/build.log libstatgen_1.0.14-5.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.iI372YmQnl/pbuilderrc_0Fvs --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.iI372YmQnl/b2 --logfile b2/build.log libstatgen_1.0.14-5.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.5-amd64 #1 SMP Debian 5.10.24-1~bpo10+1 (2021-03-29) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jun 6 20:25 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/58868/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 23 12:41 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 11 04:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/9546/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -245,7 +279,7 @@ Get: 39 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libssl-dev amd64 1.1.1d-0+deb10u6 [1794 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 48.3 MB in 1s (54.2 MB/s) +Fetched 48.3 MB in 2s (27.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -432,7 +466,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libstatgen-1.0.14/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/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 dpkg-buildpackage: info: source package libstatgen dpkg-buildpackage: info: source version 1.0.14-5 dpkg-buildpackage: info: source distribution unstable @@ -442,7 +476,7 @@ fakeroot debian/rules clean dh clean dh_auto_clean - make -j15 clean + make -j16 clean make[1]: Entering directory '/build/libstatgen-1.0.14' make[2]: Entering directory '/build/libstatgen-1.0.14/samtools' rm -f ../include/bgzf.h ../include/knetfile.h ../include/khash.h ../include/bam.h @@ -472,10 +506,10 @@ rm -rf obj memoryMapArrayTest *~ results/* rm -rf obj packedVectorTest *~ results/* rm -rf obj referenceSequenceTest *~ results/* -rm -rf obj baseUtilitiesTest *~ results/* rm -rf obj nonOverlapRegionsTest *~ results/* -rm -rf obj trimSequence *~ results/* rm -rf obj reusableVectorTest *~ results/* +rm -rf obj baseUtilitiesTest *~ results/* +rm -rf obj trimSequence *~ results/* # clean current directory rm -f *.o *~ rm -f phiX-bs.umfa phiX-cs.umfa gtest @@ -484,45 +518,45 @@ make[2]: Entering directory '/build/libstatgen-1.0.14/fastq' make[2]: Entering directory '/build/libstatgen-1.0.14/glf' make[2]: Entering directory '/build/libstatgen-1.0.14/vcf' -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.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 ../include/GlfException.h ../include/GlfFile.h ../include/GlfHeader.h ../include/GlfRecord.h ../include/GlfRefSection.h ../include/GlfStatus.h 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 rm -f ../include/FastQFile.h ../include/BaseCount.h ../include/BaseComposition.h ../include/FastQStatus.h ar d ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o ranlib ../libStatGen.a +rm -f ../include/GlfException.h ../include/GlfFile.h ../include/GlfHeader.h ../include/GlfRecord.h ../include/GlfRefSection.h ../include/GlfStatus.h ar d ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o -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 +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 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 ranlib ../libStatGen.a +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 ranlib ../libStatGen.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 -ranlib ../libStatGen_debug.a ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o -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_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 -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 ranlib ../libStatGen_debug.a ranlib ../libStatGen_debug.a -ranlib ../libStatGen_profile.a -ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o +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 +ranlib ../libStatGen_debug.a 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 +ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o +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 ranlib ../libStatGen_profile.a ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ -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 obj/*.o obj/debug/*.o obj/profile/*.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 vcfTest *~ results/* rm -rf obj fastqTest *~ results/* +make[2]: Leaving directory '/build/libstatgen-1.0.14/fastq' +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 -rf obj samTest *~ results/* +make[2]: Leaving directory '/build/libstatgen-1.0.14/bam' +rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ +rm -rf obj vcfTest *~ results/* make[2]: Leaving directory '/build/libstatgen-1.0.14/vcf' +ranlib ../libStatGen_profile.a +rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj glfTest *~ results/* -make[2]: Leaving directory '/build/libstatgen-1.0.14/bam' -make[2]: Leaving directory '/build/libstatgen-1.0.14/fastq' make[2]: Leaving directory '/build/libstatgen-1.0.14/glf' rm -f libStatGen.a rm -f libStatGen_debug.a @@ -537,7 +571,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/libstatgen-1.0.14' dh_auto_build - make -j15 "INSTALL=install --strip-program=true" + make -j16 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/libstatgen-1.0.14' make[3]: Entering directory '/build/libstatgen-1.0.14/samtools' ln -s ../samtools/bgzf.h ../include/bgzf.h @@ -689,75 +723,76 @@ make[3]: Leaving directory '/build/libstatgen-1.0.14/general' make[3]: Entering directory '/build/libstatgen-1.0.14/bam' make[3]: Entering directory '/build/libstatgen-1.0.14/fastq' +make[3]: Entering directory '/build/libstatgen-1.0.14/glf' make[3]: Entering directory '/build/libstatgen-1.0.14/vcf' -ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../fastq/FastQFile.h ../include/FastQFile.h -make[3]: Entering directory '/build/libstatgen-1.0.14/glf' -ln -s ../bam/SamFile.h ../include/SamFile.h -ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h +ln -s ../glf/GlfException.h ../include/GlfException.h +ln -s ../glf/GlfFile.h ../include/GlfFile.h ln -s ../fastq/BaseCount.h ../include/BaseCount.h ln -s ../vcf/VcfFile.h ../include/VcfFile.h -ln -s ../bam/SamInterface.h ../include/SamInterface.h -ln -s ../bam/BamInterface.h ../include/BamInterface.h -ln -s ../bam/SamRecord.h ../include/SamRecord.h ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h -ln -s ../bam/BamIndex.h ../include/BamIndex.h -ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h +ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h -ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h -ln -s ../glf/GlfException.h ../include/GlfException.h +ln -s ../bam/SamFile.h ../include/SamFile.h +ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h +ln -s ../glf/GlfHeader.h ../include/GlfHeader.h +ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h -ln -s ../glf/GlfFile.h ../include/GlfFile.h -ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h -ln -s ../glf/GlfHeader.h ../include/GlfHeader.h -mkdir -p obj -ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../glf/GlfRecord.h ../include/GlfRecord.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h +ln -s ../bam/SamInterface.h ../include/SamInterface.h ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h +ln -s ../glf/GlfStatus.h ../include/GlfStatus.h +mkdir -p obj +ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h +mkdir -p obj +ln -s ../bam/BamInterface.h ../include/BamInterface.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/SamRecord.h ../include/SamRecord.h +ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h -ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 ../bam/BamIndex.h ../include/BamIndex.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 ../vcf/VcfHeader.h ../include/VcfHeader.h -ln -s ../glf/GlfStatus.h ../include/GlfStatus.h -ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 ../bam/SamHeaderHD.h ../include/SamHeaderHD.h ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h +ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h +ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h -mkdir -p obj +ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h +ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h ln -s ../bam/SamValidation.h ../include/SamValidation.h -ln -s ../bam/SamStatistics.h ../include/SamStatistics.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/VcfRecordFilter.h ../include/VcfRecordFilter.h +ln -s ../bam/SamStatistics.h ../include/SamStatistics.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/VcfRecordGenotype.h ../include/VcfRecordGenotype.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ln -s ../bam/SamFilter.h ../include/SamFilter.h ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h -ln -s ../bam/PileupElement.h ../include/PileupElement.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/VcfSubsetSamples.h ../include/VcfSubsetSamples.h -ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h -ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h +ln -s ../bam/PileupElement.h ../include/PileupElement.h mkdir -p obj -ln -s ../bam/SamTags.h ../include/SamTags.h +ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/SamTags.h ../include/SamTags.h +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ln -s ../bam/PosList.h ../include/PosList.h ln -s ../bam/CigarHelper.h ../include/CigarHelper.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/SamCoordOutput.h ../include/SamCoordOutput.h -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h ln -s ../bam/Pileup.h ../include/Pileup.h ln -s ../bam/SamHelper.h ../include/SamHelper.h @@ -766,33 +801,32 @@ mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -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') -make[3]: Leaving directory '/build/libstatgen-1.0.14/fastq' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" 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') make[3]: Leaving directory '/build/libstatgen-1.0.14/glf' -g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +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') +make[3]: Leaving directory '/build/libstatgen-1.0.14/fastq' g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" @@ -1953,64 +1987,42 @@ Generating docs for compound SamHeaderSQ... Generating docs for compound SamHeaderTag... Generating docs for compound SamHelper... -Generatinsh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: sh: 1: dot: not founddot: not found - -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: g docs for compound SamInterface... +Generatinsh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +g docs for compound SamInterface... Generating docs for compound SamQuerySeqWithRef... Generating docs for compound SamQuerySeqWithRefIter... Generating docs for compound SamRecord... @@ -2080,7 +2092,7 @@ finalizing index lists... writing tag file... Running dot... -Generating dot graphs using 16 parallel threads... +Generating dot graphs using 17 parallel threads... 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dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found -sh: 1: dot: not found +Running dot forsh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command 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command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found +sh: dot: command not found ning dot for graph 177/287 Running dot for graph 178/287 Running dot for graph 179/287 @@ -2701,7 +2735,7 @@ finished... make[1]: Leaving directory '/build/libstatgen-1.0.14' dh_auto_test - make -j15 test + make -j16 test make[1]: Entering directory '/build/libstatgen-1.0.14' make[2]: Entering directory '/build/libstatgen-1.0.14/samtools' ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o @@ -2719,8 +2753,8 @@ make[2]: Leaving directory '/build/libstatgen-1.0.14/samtools' make[2]: Entering directory '/build/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/debug mkdir -p obj/profile g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -Wno-strict-overflow -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 -ffile-prefix-map=/build/libstatgen-1.0.14=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation -Wno-strict-overflow -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\"" @@ -2849,34 +2883,31 @@ mkdir obj mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +mkdir obj mkdir obj mkdir obj mkdir obj -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" mkdir obj -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" mkdir obj -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -mkdir -p results && ./stringTest -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -./trimSequence ./reusableVectorTest -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 ./baseUtilitiesTest -./packedVectorTest -PackedArrayTest PASS: 46 FAIL: 0 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +./trimSequence +mkdir -p results && ./stringTest In file included from /usr/include/string.h:494, from /usr/include/c++/8/cstring:42, from ../../../include/InputFile.h:23, @@ -2888,166 +2919,162 @@ /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:33: warning: 'void* __builtin___memcpy_chk(void*, const void*, long unsigned int, long unsigned int)' writing 196608 bytes into a region of size 65544 overflows the destination [-Wstringop-overflow=] return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 ./nonOverlapRegionsTest 2> results/NonOverlapRegionsTest.txt && diff results/NonOverlapRegionsTest.txt expectedNonOverlapRegionsTest.txt -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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; ./cigarRollerTest - -CigarRoller PASS: 646 FAIL: 0 -mkdir -p results; ./memoryMapArrayTest -MemoryMapArrayTest PASS: 108 FAIL: 0 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 +mkdir -p results; ./memoryMapArrayTest +MemoryMapArrayTest PASS: 108 FAIL: 0 +g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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/libstatgen-1.0.14/general' make[2]: Entering directory '/build/libstatgen-1.0.14/bam' make[2]: Entering directory '/build/libstatgen-1.0.14/fastq' +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') +mkdir -p obj/debug make[2]: Entering directory '/build/libstatgen-1.0.14/glf' make[2]: Entering directory '/build/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/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 -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o +mkdir -p obj/profile ar: `u' modifier ignored since `D' is the default (see `U') +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ar: `u' modifier ignored since `D' is the default (see `U') +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" mkdir -p obj/debug mkdir -p obj/debug -ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o +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 +mkdir -p obj/profile ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/debug +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" mkdir -p obj/profile mkdir -p obj/profile -mkdir -p obj/profile -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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -ar: `u' modifier ignored since `D' is the default (see `U') -mkdir -p obj/debug +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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/profile -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -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 -ffile-prefix-map=/build/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\"" 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') -mkdir obj -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -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 +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" ar: `u' modifier ignored since `D' is the default (see `U') +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -mkdir obj -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +mkdir obj +g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" +g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -ReadFiles.cpp: In function 'void testReadGlf()': -ReadFiles.cpp:45:24: warning: catching polymorphic type 'class GlfException' by value [-Wcatch-value=] - catch(GlfException e) - ^ -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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_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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -mkdir -p results; ./FastQValidatorTest.sh -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -make[2]: Leaving directory '/build/libstatgen-1.0.14/fastq' -g++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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\"" -./glfTest -make[2]: Leaving directory '/build/libstatgen-1.0.14/glf' -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" -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 -g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" +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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 +mkdir -p results; ./FastQValidatorTest.sh +ReadFiles.cpp: In function 'void testReadGlf()': +ReadFiles.cpp:45:24: warning: catching polymorphic type 'class GlfException' by value [-Wcatch-value=] + catch(GlfException e) + ^ +make[2]: Leaving directory '/build/libstatgen-1.0.14/fastq' g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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\"" @@ -3058,10 +3085,17 @@ g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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_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 -ffile-prefix-map=/build/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\"" 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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 -ffile-prefix-map=/build/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 +./glfTest +make[2]: Leaving directory '/build/libstatgen-1.0.14/glf' 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') mkdir obj @@ -3127,37 +3161,39 @@ dh_strip dh_makeshlibs dh_shlibdeps -dpkg-shlibdeps: warning: symbol gzeof used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries -dpkg-shlibdeps: warning: symbol gzdopen 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 inflate used by debian/libstatgen0/usr/lib/x86_64-linux-gnu/libStatGen.so.0 found in none of the libraries +dpkg-shlibdeps: warning: symbol deflateEnd 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 gzwrite 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 gzclose 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 inflateEnd 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 gzrewind 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 deflateEnd 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 gzeof 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: 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-dbgsym' in '../libstatgen0-dbgsym_1.0.14-5_amd64.deb'. -dpkg-deb: building package 'libstatgen-doc' in '../libstatgen-doc_1.0.14-5_all.deb'. -dpkg-deb: building package 'libstatgen-dev' in '../libstatgen-dev_1.0.14-5_amd64.deb'. dpkg-deb: building package 'libstatgen0' in '../libstatgen0_1.0.14-5_amd64.deb'. +dpkg-deb: building package 'libstatgen-dev' in '../libstatgen-dev_1.0.14-5_amd64.deb'. +dpkg-deb: building package 'libstatgen-doc' in '../libstatgen-doc_1.0.14-5_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libstatgen_1.0.14-5_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) I: copying local configuration +I: user script /srv/workspace/pbuilder/9546/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/9546/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/58868 and its subdirectories -I: Current time: Sat Jun 19 04:17:25 -12 2021 -I: pbuilder-time-stamp: 1624119445 +I: removing directory /srv/workspace/pbuilder/9546 and its subdirectories +I: Current time: Sat Jul 23 12:53:53 +14 2022 +I: pbuilder-time-stamp: 1658530433