I: pbuilder: network access will be disabled during build 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 I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libstatgen_1.0.14-5.dsc] I: copying [./libstatgen_1.0.14.orig.tar.gz] I: copying [./libstatgen_1.0.14-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error 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 dpkg-source: warning: failed to verify signature on ./libstatgen_1.0.14-5.dsc dpkg-source: info: extracting libstatgen in libstatgen-1.0.14 dpkg-source: info: unpacking libstatgen_1.0.14.orig.tar.gz dpkg-source: info: unpacking libstatgen_1.0.14-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_compilation_error.patch dpkg-source: info: applying Fix_compilation_flags.patch dpkg-source: info: applying Remove_erroneous_deletes_in_Chromosome_constructor.patch I: using fakeroot in build. I: Installing the build-deps 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 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=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 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 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 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 Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11), doxygen, libssl-dev, zlib1g-dev, d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libclang1-6.0{a} libcroco3{a} libedit2{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libllvm6.0{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libssl-dev{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 48.3 MB of archives. After unpacking 188 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 d-shlibs all 0.84 [17.2 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libllvm6.0 amd64 1:6.0.1-10 [14.7 MB] Get: 37 http://deb.debian.org/debian buster/main amd64 libclang1-6.0 amd64 1:6.0.1-10 [6951 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 doxygen amd64 1.8.13-10 [3985 kB] 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 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.) Preparing to unpack .../00-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3+deb10u1_amd64.deb ... Unpacking groff-base (1.22.4-3+deb10u1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.1-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_amd64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking libmagic1:amd64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../09-file_1%3a5.35-4+deb10u2_amd64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../10-gettext-base_0.19.8.1-9_amd64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../11-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.18-2_amd64.deb ... Unpacking m4 (1.4.18-2) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.69-11_all.deb ... Unpacking autoconf (2.69-11) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20180224.1_all.deb ... Unpacking autotools-dev (20180224.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.1-4_all.deb ... Unpacking automake (1:1.16.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.19.8.1-9_all.deb ... Unpacking autopoint (0.19.8.1-9) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../17-d-shlibs_0.84_all.deb ... Unpacking d-shlibs (0.84) ... Selecting previously unselected package libtool. Preparing to unpack .../18-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../19-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../20-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../25-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../26-libicu63_63.1-6+deb10u1_amd64.deb ... Unpacking libicu63:amd64 (63.1-6+deb10u1) ... 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Reading state information... 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:/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 dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_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 ar d ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: creating ../libStatGen.a ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o ar: creating ../libStatGen_debug.a ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: creating ../libStatGen_profile.a ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ make[2]: Leaving directory '/build/libstatgen-1.0.14/samtools' make[2]: Entering directory '/build/libstatgen-1.0.14/general' rm -f ../include/BaseAsciiMap.h ../include/BaseQualityHelper.h ../include/BaseUtilities.h ../include/BasicHash.h ../include/BgzfFileType.h ../include/BgzfFileTypeRecovery.h ../include/CharBuffer.h ../include/Chromosome.h ../include/Cigar.h ../include/CigarRoller.h ../include/Error.h ../include/ErrorHandler.h ../include/FileType.h ../include/FortranFormat.h ../include/GenomeSequence.h ../include/GenotypeLists.h ../include/glfHandler.h ../include/GzipFileType.h ../include/GzipHeader.h ../include/Hash.h ../include/IndexBase.h ../include/Input.h ../include/InputFile.h ../include/IntArray.h ../include/IntHash.h ../include/LongLongCounter.h ../include/MapFunction.h ../include/MathMatrix.h ../include/MathVector.h ../include/MemoryAllocators.h ../include/MemoryInfo.h ../include/MemoryMapArray.h ../include/MemoryMap.h ../include/MiniDeflate.h ../include/NonOverlapRegions.h ../include/Parameters.h ../include/PedigreeAlleleFreq.h ../include/Pedigree.h ../include/PedigreeDescription.h ../include/PedigreeFamily.h ../include/PedigreeGlobals.h ../include/PedigreePerson.h ../include/PhoneHome.h ../include/QuickIndex.h ../include/Random.h ../include/ReferenceSequence.h ../include/SmithWaterman.h ../include/Sort.h ../include/STLUtilities.h ../include/StatGenStatus.h ../include/StringAlias.h ../include/StringArray.h ../include/StringBasics.h ../include/StringHash.h ../include/StringMap.h ../include/Tabix.h ../include/UncompressedFileType.h ../include/Constant.h ../include/CSG_MD5.h ../include/Generic.h ../include/GenomeSequenceHelpers.h ../include/GreedyTupleAligner.h ../include/InplaceMerge.h ../include/LongHash.h ../include/LongInt.h ../include/MathConstant.h ../include/PackedVector.h ../include/PedigreeAlleles.h ../include/Performance.h ../include/ReusableVector.h ../include/SimpleStats.h ../include/TrimSequence.h ../include/UnitTest.h ar d ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj inputFileTest *~ results/* rm -rf obj cigarRollerTest *~ results/* rm -rf obj stringTest *~ results/* rm -rf obj memoryMapArrayTest *~ results/* rm -rf obj packedVectorTest *~ results/* rm -rf obj referenceSequenceTest *~ results/* rm -rf obj nonOverlapRegionsTest *~ 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 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' make[2]: Entering directory '/build/libstatgen-1.0.14/glf' make[2]: Entering directory '/build/libstatgen-1.0.14/vcf' 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 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/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.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 ranlib ../libStatGen_debug.a ranlib ../libStatGen_debug.a ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o 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 *~ ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 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/glf' rm -f libStatGen.a rm -f libStatGen_debug.a rm -f libStatGen_profile.a make[1]: Leaving directory '/build/libstatgen-1.0.14' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/libstatgen-1.0.14' dh_auto_build 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 ln -s ../samtools/knetfile.h ../include/knetfile.h ln -s ../samtools/khash.h ../include/khash.h ln -s ../samtools/bam.h ../include/bam.h mkdir -p obj gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/bgzf.o -c bgzf.c gcc -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/knetfile.o -c knetfile.c ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/libstatgen-1.0.14/samtools' make[3]: Entering directory '/build/libstatgen-1.0.14/general' ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h ln -s ../general/BasicHash.h ../include/BasicHash.h ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h ln -s ../general/CharBuffer.h ../include/CharBuffer.h ln -s ../general/Chromosome.h ../include/Chromosome.h ln -s ../general/Cigar.h ../include/Cigar.h ln -s ../general/CigarRoller.h ../include/CigarRoller.h ln -s ../general/Error.h ../include/Error.h ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h ln -s ../general/FileType.h ../include/FileType.h ln -s ../general/FortranFormat.h ../include/FortranFormat.h ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h ln -s ../general/glfHandler.h ../include/glfHandler.h ln -s ../general/GzipFileType.h ../include/GzipFileType.h ln -s ../general/GzipHeader.h ../include/GzipHeader.h ln -s ../general/Hash.h ../include/Hash.h ln -s ../general/IndexBase.h ../include/IndexBase.h ln -s ../general/Input.h ../include/Input.h ln -s ../general/InputFile.h ../include/InputFile.h ln -s ../general/IntArray.h ../include/IntArray.h ln -s ../general/IntHash.h ../include/IntHash.h ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h ln -s ../general/MapFunction.h ../include/MapFunction.h ln -s ../general/MathMatrix.h ../include/MathMatrix.h ln -s ../general/MathVector.h ../include/MathVector.h ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h ln -s ../general/MemoryMap.h ../include/MemoryMap.h ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h ln -s ../general/Parameters.h ../include/Parameters.h ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h ln -s ../general/Pedigree.h ../include/Pedigree.h ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h ln -s ../general/PhoneHome.h ../include/PhoneHome.h ln -s ../general/QuickIndex.h ../include/QuickIndex.h ln -s ../general/Random.h ../include/Random.h ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h ln -s ../general/Sort.h ../include/Sort.h ln -s ../general/STLUtilities.h ../include/STLUtilities.h ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h ln -s ../general/StringAlias.h ../include/StringAlias.h ln -s ../general/StringArray.h ../include/StringArray.h ln -s ../general/StringBasics.h ../include/StringBasics.h ln -s ../general/StringHash.h ../include/StringHash.h ln -s ../general/StringMap.h ../include/StringMap.h ln -s ../general/Tabix.h ../include/Tabix.h ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h ln -s ../general/Constant.h ../include/Constant.h ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h ln -s ../general/Generic.h ../include/Generic.h ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h ln -s ../general/LongHash.h ../include/LongHash.h ln -s ../general/LongInt.h ../include/LongInt.h ln -s ../general/MathConstant.h ../include/MathConstant.h ln -s ../general/PackedVector.h ../include/PackedVector.h ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h ln -s ../general/Performance.h ../include/Performance.h ln -s ../general/ReusableVector.h ../include/ReusableVector.h ln -s ../general/SimpleStats.h ../include/SimpleStats.h ln -s ../general/TrimSequence.h ../include/TrimSequence.h ln -s ../general/UnitTest.h ../include/UnitTest.h g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/BaseAsciiMap.o -c BaseAsciiMap.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/BaseUtilities.o -c BaseUtilities.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/BgzfFileType.o -c BgzfFileType.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/CharBuffer.o -c CharBuffer.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/Cigar.o -c Cigar.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/Error.o -c Error.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/FileType.o -c FileType.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/GenomeSequence.o -c GenomeSequence.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/glfHandler.o -c glfHandler.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/GzipHeader.o -c GzipHeader.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/IndexBase.o -c IndexBase.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/InputFile.o -c InputFile.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/IntHash.o -c IntHash.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/MapFunction.o -c MapFunction.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/MathVector.o -c MathVector.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/MemoryInfo.o -c MemoryInfo.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/MemoryMap.o -c MemoryMap.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/NonOverlapRegions.o -c NonOverlapRegions.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/PedigreeDescription.o -c PedigreeDescription.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/PedigreeGlobals.o -c PedigreeGlobals.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/PhoneHome.o -c PhoneHome.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/Random.o -c Random.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/SmithWaterman.o -c SmithWaterman.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/STLUtilities.o -c STLUtilities.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/StringAlias.o -c StringAlias.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/StringBasics.o -c StringBasics.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/StringMap.o -c StringMap.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/UncompressedFileType.o -c UncompressedFileType.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/PedigreeTrim.o -c PedigreeTrim.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/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 ../fastq/FastQFile.h ../include/FastQFile.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 ../vcf/VcfFileReader.h ../include/VcfFileReader.h ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.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 ../fastq/FastQStatus.h ../include/FastQStatus.h ln -s ../glf/GlfRecord.h ../include/GlfRecord.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\"" 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 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 ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h ln -s ../bam/SamValidation.h ../include/SamValidation.h ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h ln -s ../bam/SamStatistics.h ../include/SamStatistics.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h ln -s ../bam/SamFilter.h ../include/SamFilter.h ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h ln -s ../bam/PileupElement.h ../include/PileupElement.h mkdir -p obj 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/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h ln -s ../bam/Pileup.h ../include/Pileup.h ln -s ../bam/SamHelper.h ../include/SamHelper.h ln -s ../bam/SamFlag.h ../include/SamFlag.h ln -s ../bam/SamStatus.h ../include/SamStatus.h mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/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/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/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\"" 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/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\"" 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/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.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/SamFilter.o -c SamFilter.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/PileupElement.o -c PileupElement.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/PileupElementBaseQual.o -c PileupElementBaseQual.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/SamReferenceInfo.o -c SamReferenceInfo.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/SamTags.o -c SamTags.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/PosList.o -c PosList.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/CigarHelper.o -c CigarHelper.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/SamRecordPool.o -c SamRecordPool.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/SamCoordOutput.o -c SamCoordOutput.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/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/libstatgen-1.0.14/vcf' ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/libstatgen-1.0.14/bam' make[2]: Leaving directory '/build/libstatgen-1.0.14' # Build the shared library g++ -shared -o libStatGen.so.0 */obj/*.o -fPIC -Wl,-soname,libStatGen.so.0 -Wl,-z,relro -Wl,-z,now # Build doxygen doc doxygen warning: Tag `DETAILS_AT_TOP' at line 163 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `SYMBOL_CACHE_SIZE' at line 296 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `SHOW_DIRECTORIES' at line 484 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `HTML_ALIGN_MEMBERS' at line 810 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `USE_INLINE_TREES' at line 963 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `XML_SCHEMA' at line 1156 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag `XML_DTD' at line 1162 of file `Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: doxygen no longer ships with the FreeSans font. You may want to clear or change DOT_FONTNAME. Otherwise you run the risk that the wrong font is being used for dot generated graphs. Adding custom extension mapping: .h will be treated as language c++ Notice: Output directory `dox' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /build/libstatgen-1.0.14/include Searching for files in directory /build/libstatgen-1.0.14/copyrights Searching for files in directory /build/libstatgen-1.0.14/dox Searching for files in directory /build/libstatgen-1.0.14/dox/html Searching for files in directory /build/libstatgen-1.0.14/dox/man Searching INPUT for files to process... 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Parsing file /build/libstatgen-1.0.14/bam/BamIndex.cpp... Preprocessing /build/libstatgen-1.0.14/bam/BamIndex.h... Parsing file /build/libstatgen-1.0.14/bam/BamIndex.h... Preprocessing /build/libstatgen-1.0.14/bam/BamInterface.cpp... Parsing file /build/libstatgen-1.0.14/bam/BamInterface.cpp... Preprocessing /build/libstatgen-1.0.14/bam/BamInterface.h... Parsing file /build/libstatgen-1.0.14/bam/BamInterface.h... Preprocessing /build/libstatgen-1.0.14/bam/CigarHelper.cpp... Parsing file /build/libstatgen-1.0.14/bam/CigarHelper.cpp... Preprocessing /build/libstatgen-1.0.14/bam/CigarHelper.h... Parsing file /build/libstatgen-1.0.14/bam/CigarHelper.h... Preprocessing /build/libstatgen-1.0.14/bam/examples/pileup/Main.cpp... Parsing file /build/libstatgen-1.0.14/bam/examples/pileup/Main.cpp... Preprocessing /build/libstatgen-1.0.14/bam/examples/printRefPositions/Main.cpp... Parsing file /build/libstatgen-1.0.14/bam/examples/printRefPositions/Main.cpp... 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Parsing file /build/libstatgen-1.0.14/bam/SamStatistics.cpp... Preprocessing /build/libstatgen-1.0.14/bam/SamStatistics.h... Parsing file /build/libstatgen-1.0.14/bam/SamStatistics.h... Preprocessing /build/libstatgen-1.0.14/bam/SamStatus.h... Parsing file /build/libstatgen-1.0.14/bam/SamStatus.h... Preprocessing /build/libstatgen-1.0.14/bam/SamTags.cpp... Parsing file /build/libstatgen-1.0.14/bam/SamTags.cpp... Preprocessing /build/libstatgen-1.0.14/bam/SamTags.h... Parsing file /build/libstatgen-1.0.14/bam/SamTags.h... Preprocessing /build/libstatgen-1.0.14/bam/SamValidation.cpp... Parsing file /build/libstatgen-1.0.14/bam/SamValidation.cpp... Preprocessing /build/libstatgen-1.0.14/bam/SamValidation.h... Parsing file /build/libstatgen-1.0.14/bam/SamValidation.h... Preprocessing /build/libstatgen-1.0.14/bam/test/BamIndexTest.cpp... Parsing file /build/libstatgen-1.0.14/bam/test/BamIndexTest.cpp... Preprocessing /build/libstatgen-1.0.14/bam/test/BamIndexTest.h... 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Parsing file /build/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.h... Parsing file /build/libstatgen-1.0.14/general/test/cigar/CigarRollerTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/dbsnp/Main.cpp... Parsing file /build/libstatgen-1.0.14/general/test/dbsnp/Main.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/GenomeSequence_test.cpp... Parsing file /build/libstatgen-1.0.14/general/test/GenomeSequence_test.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/GreedyTupleAligner_test.cpp... Parsing file /build/libstatgen-1.0.14/general/test/GreedyTupleAligner_test.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/gtest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/gtest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.h... Parsing file /build/libstatgen-1.0.14/general/test/inputFileTest/InputFileTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Parsing file /build/libstatgen-1.0.14/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Parsing file /build/libstatgen-1.0.14/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.h... Parsing file /build/libstatgen-1.0.14/general/test/packedVectorTest/PackedVectorTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Parsing file /build/libstatgen-1.0.14/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.h... Parsing file /build/libstatgen-1.0.14/general/test/reusableVector/ReusableVectorTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/STLUtilities_test.cpp... Parsing file /build/libstatgen-1.0.14/general/test/STLUtilities_test.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/string/StringTest.cpp... Parsing file /build/libstatgen-1.0.14/general/test/string/StringTest.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/string/StringTest.h... Parsing file /build/libstatgen-1.0.14/general/test/string/StringTest.h... Preprocessing /build/libstatgen-1.0.14/general/test/trimSequence/TrimSequence.cpp... Parsing file /build/libstatgen-1.0.14/general/test/trimSequence/TrimSequence.cpp... Preprocessing /build/libstatgen-1.0.14/general/test/TrimSequence_test.cpp... Parsing file /build/libstatgen-1.0.14/general/test/TrimSequence_test.cpp... Preprocessing /build/libstatgen-1.0.14/general/TrimSequence.h... Parsing file /build/libstatgen-1.0.14/general/TrimSequence.h... Preprocessing /build/libstatgen-1.0.14/general/UncompressedFileType.cpp... Parsing file /build/libstatgen-1.0.14/general/UncompressedFileType.cpp... Preprocessing /build/libstatgen-1.0.14/general/UncompressedFileType.h... Parsing file /build/libstatgen-1.0.14/general/UncompressedFileType.h... Preprocessing /build/libstatgen-1.0.14/general/UnitTest.h... Parsing file /build/libstatgen-1.0.14/general/UnitTest.h... Preprocessing /build/libstatgen-1.0.14/glf/GlfException.cpp... Parsing file /build/libstatgen-1.0.14/glf/GlfException.cpp... Preprocessing /build/libstatgen-1.0.14/glf/GlfException.h... Parsing file /build/libstatgen-1.0.14/glf/GlfException.h... Preprocessing /build/libstatgen-1.0.14/glf/GlfFile.cpp... Parsing file /build/libstatgen-1.0.14/glf/GlfFile.cpp... Preprocessing /build/libstatgen-1.0.14/glf/GlfFile.h... Parsing file /build/libstatgen-1.0.14/glf/GlfFile.h... Preprocessing /build/libstatgen-1.0.14/glf/GlfHeader.cpp... Parsing file /build/libstatgen-1.0.14/glf/GlfHeader.cpp... Preprocessing /build/libstatgen-1.0.14/glf/GlfHeader.h... Parsing file /build/libstatgen-1.0.14/glf/GlfHeader.h... Preprocessing /build/libstatgen-1.0.14/glf/GlfRecord.cpp... Parsing file /build/libstatgen-1.0.14/glf/GlfRecord.cpp... Preprocessing /build/libstatgen-1.0.14/glf/GlfRecord.h... Parsing file /build/libstatgen-1.0.14/glf/GlfRecord.h... Preprocessing /build/libstatgen-1.0.14/glf/GlfRefSection.cpp... Parsing file /build/libstatgen-1.0.14/glf/GlfRefSection.cpp... Preprocessing /build/libstatgen-1.0.14/glf/GlfRefSection.h... Parsing file /build/libstatgen-1.0.14/glf/GlfRefSection.h... Preprocessing /build/libstatgen-1.0.14/glf/GlfStatus.cpp... Parsing file /build/libstatgen-1.0.14/glf/GlfStatus.cpp... Preprocessing /build/libstatgen-1.0.14/glf/GlfStatus.h... Parsing file /build/libstatgen-1.0.14/glf/GlfStatus.h... Preprocessing /build/libstatgen-1.0.14/glf/test/Main.cpp... Parsing file /build/libstatgen-1.0.14/glf/test/Main.cpp... Preprocessing /build/libstatgen-1.0.14/glf/test/ReadFiles.cpp... Parsing file /build/libstatgen-1.0.14/glf/test/ReadFiles.cpp... Preprocessing /build/libstatgen-1.0.14/glf/test/ReadFiles.h... Parsing file /build/libstatgen-1.0.14/glf/test/ReadFiles.h... Preprocessing /build/libstatgen-1.0.14/glf/test/Validate.cpp... Parsing file /build/libstatgen-1.0.14/glf/test/Validate.cpp... Preprocessing /build/libstatgen-1.0.14/glf/test/Validate.h... Parsing file /build/libstatgen-1.0.14/glf/test/Validate.h... Preprocessing /build/libstatgen-1.0.14/glf/test/WriteFiles.cpp... Parsing file /build/libstatgen-1.0.14/glf/test/WriteFiles.cpp... Preprocessing /build/libstatgen-1.0.14/glf/test/WriteFiles.h... Parsing file /build/libstatgen-1.0.14/glf/test/WriteFiles.h... Preprocessing /build/libstatgen-1.0.14/samtools/bam.h... Parsing file /build/libstatgen-1.0.14/samtools/bam.h... Preprocessing /build/libstatgen-1.0.14/samtools/bgzf.c... Parsing file /build/libstatgen-1.0.14/samtools/bgzf.c... Preprocessing /build/libstatgen-1.0.14/samtools/bgzf.h... Parsing file /build/libstatgen-1.0.14/samtools/bgzf.h... Preprocessing /build/libstatgen-1.0.14/samtools/khash.h... Parsing file /build/libstatgen-1.0.14/samtools/khash.h... Preprocessing /build/libstatgen-1.0.14/samtools/knetfile.c... Parsing file /build/libstatgen-1.0.14/samtools/knetfile.c... Preprocessing /build/libstatgen-1.0.14/samtools/knetfile.h... Parsing file /build/libstatgen-1.0.14/samtools/knetfile.h... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Associating documentation with classes... Computing nesting relations for classes... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Freeing entry tree Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Computing dependencies between directories... Generating citations page... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file bam/BamIndex.cpp... Generating code for file bam/BamIndex.h... Generating code for file bam/BamInterface.cpp... Generating code for file bam/BamInterface.h... Generating code for file bam/CigarHelper.cpp... Generating code for file bam/CigarHelper.h... Generating code for file bam/examples/pileup/Main.cpp... Generating code for file bam/examples/printRefPositions/Main.cpp... Generating code for file bam/test/Main.cpp... Generating code for file general/test/dbsnp/Main.cpp... Generating code for file glf/test/Main.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.h... Generating code for file bam/GenericSamInterface.cpp... Generating code for file bam/GenericSamInterface.h... Generating code for file bam/Pileup.h... Generating code for file bam/PileupElement.cpp... Generating code for file bam/PileupElement.h... Generating code for file bam/PileupElementBaseQual.cpp... Generating code for file bam/PileupElementBaseQual.h... Generating code for file bam/PosList.cpp... Generating code for file bam/PosList.h... Generating code for file bam/SamCoordOutput.cpp... Generating code for file bam/SamCoordOutput.h... Generating code for file bam/SamFile.cpp... Generating code for file bam/SamFile.h... Generating code for file bam/SamFileHeader.cpp... Generating code for file bam/SamFileHeader.h... Generating code for file bam/SamFilter.cpp... Generating code for file bam/SamFilter.h... Generating code for file bam/SamFlag.h... Generating code for file bam/SamHeaderHD.cpp... Generating code for file bam/SamHeaderHD.h... Generating code for file bam/SamHeaderPG.cpp... Generating code for file bam/SamHeaderPG.h... Generating code for file bam/SamHeaderRecord.cpp... Generating code for file bam/SamHeaderRecord.h... Generating code for file bam/SamHeaderRG.cpp... Generating code for file bam/SamHeaderRG.h... Generating code for file bam/SamHeaderSQ.cpp... Generating code for file bam/SamHeaderSQ.h... Generating code for file bam/SamHeaderTag.cpp... Generating code for file bam/SamHeaderTag.h... Generating code for file bam/SamHelper.h... Generating code for file bam/SamInterface.cpp... Generating code for file bam/SamInterface.h... Generating code for file bam/SamQuerySeqWithRefHelper.cpp... Generating code for file bam/SamQuerySeqWithRefHelper.h... Generating code for file bam/SamRecord.cpp... Generating code for file bam/SamRecord.h... Generating code for file bam/SamRecordHelper.cpp... Generating code for file bam/SamRecordHelper.h... Generating code for file bam/SamRecordPool.cpp... Generating code for file bam/SamRecordPool.h... Generating code for file bam/SamReferenceInfo.cpp... Generating code for file bam/SamReferenceInfo.h... Generating code for file bam/SamStatistics.cpp... Generating code for file bam/SamStatistics.h... Generating code for file bam/SamStatus.h... Generating code for file bam/SamTags.cpp... Generating code for file bam/SamTags.h... Generating code for file bam/SamValidation.cpp... Generating code for file bam/SamValidation.h... Generating code for file bam/test/BamIndexTest.cpp... Generating code for file bam/test/BamIndexTest.h... Generating code for file bam/test/Modify.cpp... Generating code for file bam/test/Modify.h... Generating code for file bam/test/ModifyVar.cpp... Generating code for file bam/test/ModifyVar.h... Generating code for file bam/test/ReadFiles.cpp... Generating code for file glf/test/ReadFiles.cpp... Generating code for file bam/test/ReadFiles.h... Generating code for file glf/test/ReadFiles.h... Generating code for file bam/test/SamFileTest.cpp... Generating code for file bam/test/SamFileTest.h... Generating code for file bam/test/ShiftIndels.cpp... Generating code for file bam/test/ShiftIndels.h... Generating code for file bam/test/TestCigarHelper.cpp... Generating code for file bam/test/TestCigarHelper.h... Generating code for file bam/test/TestEquals.cpp... Generating code for file bam/test/TestEquals.h... Generating code for file bam/test/TestFilter.cpp... Generating code for file bam/test/TestFilter.h... Generating code for file bam/test/TestPileup.cpp... Generating code for file bam/test/TestPileup.h... Generating code for file bam/test/TestPosList.cpp... Generating code for file bam/test/TestPosList.h... Generating code for file bam/test/TestSamCoordOutput.cpp... Generating code for file bam/test/TestSamCoordOutput.h... Generating code for file bam/test/TestSamRecordHelper.cpp... Generating code for file bam/test/TestSamRecordHelper.h... Generating code for file bam/test/TestSamRecordPool.cpp... Generating code for file bam/test/TestSamRecordPool.h... Generating code for file bam/test/TestValidate.cpp... Generating code for file bam/test/TestValidate.h... Generating code for file bam/test/ValidationTest.cpp... Generating code for file bam/test/ValidationTest.h... Generating code for file bam/test/WriteFiles.cpp... Generating code for file glf/test/WriteFiles.cpp... Generating code for file bam/test/WriteFiles.h... Generating code for file glf/test/WriteFiles.h... Generating code for file fastq/BaseComposition.cpp... Generating code for file fastq/BaseComposition.h... Generating code for file fastq/BaseCount.cpp... Generating code for file fastq/BaseCount.h... Generating code for file fastq/FastQFile.cpp... Generating code for file fastq/FastQFile.h... Generating code for file fastq/FastQStatus.cpp... Generating code for file fastq/FastQStatus.h... Generating code for file fastq/test/FastQFileTest.cpp... Generating code for file general/BaseAsciiMap.cpp... Generating code for file general/BaseAsciiMap.h... Generating code for file general/BaseQualityHelper.cpp... Generating code for file general/BaseQualityHelper.h... Generating code for file general/BaseUtilities.cpp... Generating code for file general/BaseUtilities.h... Generating code for file general/BasicHash.cpp... Generating code for file general/BasicHash.h... Generating code for file general/BgzfFileType.cpp... Generating code for file general/BgzfFileType.h... Generating code for file general/BgzfFileTypeRecovery.cpp... Generating code for file general/BgzfFileTypeRecovery.h... Generating code for file general/CharBuffer.cpp... Generating code for file general/CharBuffer.h... Generating code for file general/Chromosome.cpp... Generating code for file general/Chromosome.h... Generating code for file general/Cigar.cpp... Generating code for file general/Cigar.h... Generating code for file general/CigarRoller.cpp... Generating code for file general/CigarRoller.h... Generating code for file general/Constant.h... Generating code for file general/CSG_MD5.h... Generating code for file general/Error.cpp... Generating code for file general/Error.h... Generating code for file general/ErrorHandler.cpp... Generating code for file general/ErrorHandler.h... Generating code for file general/FileType.cpp... Generating code for file general/FileType.h... Generating code for file general/FortranFormat.cpp... Generating code for file general/FortranFormat.h... Generating code for file general/Generic.cpp... Generating code for file general/Generic.h... Generating code for file general/GenomeSequence.cpp... Generating code for file general/GenomeSequence.h... Generating code for file general/GenomeSequenceHelpers.h... Generating code for file general/GenotypeLists.cpp... Generating code for file general/GenotypeLists.h... Generating code for file general/glfHandler.cpp... Generating code for file general/glfHandler.h... Generating code for file general/GreedyTupleAligner.h... Generating code for file general/GzipFileType.cpp... Generating code for file general/GzipFileType.h... Generating code for file general/GzipHeader.cpp... Generating code for file general/GzipHeader.h... Generating code for file general/Hash.cpp... Generating code for file general/Hash.h... Generating code for file general/IndexBase.cpp... Generating code for file general/IndexBase.h... Generating code for file general/InplaceMerge.cpp... Generating code for file general/InplaceMerge.h... Generating code for file general/Input.cpp... Generating code for file general/Input.h... Generating code for file general/InputFile.cpp... Generating code for file general/InputFile.h... Generating code for file general/IntArray.cpp... Generating code for file general/IntArray.h... Generating code for file general/IntHash.cpp... Generating code for file general/IntHash.h... Generating code for file general/LongHash.h... Generating code for file general/LongInt.h... Generating code for file general/LongLongCounter.cpp... Generating code for file general/LongLongCounter.h... Generating code for file general/MapFunction.cpp... Generating code for file general/MapFunction.h... Generating code for file general/MathConstant.h... Generating code for file general/MathMatrix.cpp... Generating code for file general/MathMatrix.h... Generating code for file general/MathVector.cpp... Generating code for file general/MathVector.h... Generating code for file general/MemoryAllocators.cpp... Generating code for file general/MemoryAllocators.h... Generating code for file general/MemoryInfo.cpp... Generating code for file general/MemoryInfo.h... Generating code for file general/MemoryMap.cpp... Generating code for file general/MemoryMap.h... Generating code for file general/MemoryMapArray.cpp... Generating code for file general/MemoryMapArray.h... Generating code for file general/MiniDeflate.cpp... Generating code for file general/MiniDeflate.h... Generating code for file general/NonOverlapRegions.cpp... Generating code for file general/NonOverlapRegions.h... Generating code for file general/PackedVector.h... Generating code for file general/Parameters.cpp... Generating code for file general/Parameters.h... Generating code for file general/Pedigree.cpp... Generating code for file general/Pedigree.h... Generating code for file general/PedigreeAlleleFreq.cpp... Generating code for file general/PedigreeAlleleFreq.h... Generating code for file general/PedigreeAlleles.h... Generating code for file general/PedigreeDescription.cpp... Generating code for file general/PedigreeDescription.h... Generating code for file general/PedigreeFamily.cpp... Generating code for file general/PedigreeFamily.h... Generating code for file general/PedigreeGlobals.cpp... Generating code for file general/PedigreeGlobals.h... Generating code for file general/PedigreeLoader.cpp... Generating code for file general/PedigreePerson.cpp... Generating code for file general/PedigreePerson.h... Generating code for file general/PedigreeTrim.cpp... Generating code for file general/PedigreeTwin.cpp... Generating code for file general/Performance.h... Generating code for file general/PhoneHome.cpp... Generating code for file general/PhoneHome.h... Generating code for file general/QuickIndex.cpp... Generating code for file general/QuickIndex.h... Generating code for file general/Random.cpp... Generating code for file general/Random.h... Generating code for file general/ReferenceSequence.cpp... Generating code for file general/ReferenceSequence.h... Generating code for file general/ReusableVector.h... Generating code for file general/SimpleStats.h... Generating code for file general/SmithWaterman.cpp... Generating code for file general/SmithWaterman.h... Generating code for file general/Sort.cpp... Generating code for file general/Sort.h... Generating code for file general/StatGenStatus.cpp... Generating code for file general/StatGenStatus.h... Generating code for file general/STLUtilities.cpp... Generating code for file general/STLUtilities.h... Generating code for file general/String.cpp... Generating code for file general/StringAlias.cpp... Generating code for file general/StringAlias.h... Generating code for file general/StringArray.cpp... Generating code for file general/StringArray.h... Generating code for file general/StringBasics.cpp... Generating code for file general/StringBasics.h... Generating code for file general/StringHash.cpp... Generating code for file general/StringHash.h... Generating code for file general/StringMap.cpp... Generating code for file general/StringMap.h... Generating code for file general/Tabix.cpp... Generating code for file general/Tabix.h... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Generating code for file general/test/Chromosome_test.cpp... Generating code for file general/test/cigar/CigarRollerTest.cpp... Generating code for file general/test/cigar/CigarRollerTest.h... Generating code for file general/test/GenomeSequence_test.cpp... Generating code for file general/test/GreedyTupleAligner_test.cpp... Generating code for file general/test/gtest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.h... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Generating code for file general/test/packedVectorTest/PackedVectorTest.cpp... Generating code for file general/test/packedVectorTest/PackedVectorTest.h... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.h... Generating code for file general/test/reusableVector/ReusableVectorTest.cpp... Generating code for file general/test/reusableVector/ReusableVectorTest.h... Generating code for file general/test/STLUtilities_test.cpp... Generating code for file general/test/string/StringTest.cpp... Generating code for file general/test/string/StringTest.h... Generating code for file general/test/trimSequence/TrimSequence.cpp... Generating code for file general/test/TrimSequence_test.cpp... Generating code for file general/TrimSequence.h... Generating code for file general/UncompressedFileType.cpp... Generating code for file general/UncompressedFileType.h... Generating code for file general/UnitTest.h... Generating code for file glf/GlfException.cpp... Generating code for file glf/GlfException.h... Generating code for file glf/GlfFile.cpp... Generating code for file glf/GlfFile.h... Generating code for file glf/GlfHeader.cpp... Generating code for file glf/GlfHeader.h... Generating code for file glf/GlfRecord.cpp... Generating code for file glf/GlfRecord.h... Generating code for file glf/GlfRefSection.cpp... Generating code for file glf/GlfRefSection.h... Generating code for file glf/GlfStatus.cpp... Generating code for file glf/GlfStatus.h... Generating code for file glf/test/Validate.cpp... Generating code for file glf/test/Validate.h... Generating code for file samtools/bam.h... Generating code for file samtools/bgzf.c... Generating code for file samtools/bgzf.h... Generating code for file samtools/khash.h... Generating code for file samtools/knetfile.c... Generating code for file samtools/knetfile.h... Generating file documentation... Generating docs for file general/InputFile.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound __kstring_t... Generating docs for compound Alleles... Generating docs for compound AnalyzeClass... Generating docs for compound BamIndex... Generating docs for compound BamIndexFileTest... Generating docs for compound BamInterface... Generating docs for compound bamRecordStruct... Generating docs for compound BaseAsciiMap... Generating docs for compound BaseComposition... Generating docs for compound BaseCount... Generating docs for compound baseQualityConvertor... Generating docs for compound BaseUtilities... Generating docs for compound BasicHash... Generating docs for compound BGZF... Generating docs for compound CharBuffer... Generating docs for compound Chromosome... Generating docs for compound ChromosomeInfo... Generating docs for compound Chunk... Generating docs for compound Cigar... Generating docs for nested compound Cigar::CigarOperator... Generating docs for compound CigarHelper... Generating docs for compound CigarHelperTest... Generating docs for compound CigarRoller... Generating docs for compound CigarRollerTest... Generating docs for compound ColumnExtras... Generating docs for compound defaultPileup... Generating docs for compound DoubleParameter... Generating docs for compound emptyGenericHeader... Generating docs for compound EqualsTest... Generating docs for compound ErrorHandler... Generating docs for compound Family... Generating docs for compound FastQFile... Generating docs for compound FastQStatus... Generating docs for compound FileType... Generating docs for compound FilterTest... Generating docs for compound FortranFormat... Generating docs for compound GenericSamInterface... Generating docs for compound GenomeSequence... Generating docs for compound genomeSequenceMmapHeader... Generating docs for compound GenotypeList... Generating docs for compound glfEntry... Generating docs for compound GlfException... Generating docs for compound GlfFile... Generating docs for compound GlfFileReader... Generating docs for compound GlfFileWriter... Generating docs for compound glfHandler... Generating docs for compound GlfHeader... Generating docs for compound glfIndel... Generating docs for compound GlfRecord... Generating docs for compound GlfRefSection... Generating docs for compound GlfStatus... Generating docs for compound GlobalTestEnvironment... Generating docs for compound GreedyTupleAligner... Generating docs for compound GzipHeader... Generating docs for compound HiddenDouble... Generating docs for compound HiddenInteger... Generating docs for compound HiddenString... Generating docs for compound HiddenSwitch... Generating docs for compound IFILE_Test... Generating docs for compound IndexBase... Generating docs for nested compound IndexBase::Bin... Generating docs for nested compound IndexBase::Reference... Generating docs for compound InputFile... Generating docs for compound IntArray... Generating docs for compound IntHash... Generating docs for compound IntParameter... Generating docs for compound knetFile_s... Generating docs for compound ListParameter... Generating docs for compound LongCounter... Generating docs for compound LongHash... Generating docs for compound LongParamContainer... Generating docs for compound LongParameterList... Generating docs for compound LongParameters... Generating docs for compound MarkerInfo... Generating docs for compound Matrix... Generating docs for compound MD5_CTX... Generating docs for compound MemoryMap... Generating docs for compound MemoryMapArray... Generating docs for compound MemoryMapArrayHeader... Generating docs for compound MemoryMapArrayTest... Generating docs for compound MemoryMapGenericHeader... Generating docs for compound MiniDeflate... Generating docs for compound MockGenomeSequence... Generating docs for compound modify... Generating docs for compound modifyVar... Generating docs for compound NonOverlapRegionPos... Generating docs for compound NonOverlapRegions... Generating docs for compound NonOverlapRegionsTest... Generating docs for compound OptionList... Generating docs for compound PackedArrayTest... Generating docs for compound PackedRead... Generating docs for compound PackedSequenceData... Generating docs for compound PackedVector... Generating docs for compound Parameter... Generating docs for compound ParameterList... Generating docs for compound Pedigree... Generating docs for compound PedigreeDescription... Generating docs for compound PedigreeGlobals... Generating docs for compound PedigreeKey... Generating docs for compound Person... Generating docs for compound PhoneHome... Generating docs for compound Pileup... Generating docs for compound PileupElement... Generating docs for compound PileupElementBaseQual... Generating docs for compound PileupHelper... Generating docs for compound PosList... Generating docs for compound QuickIndex... Generating docs for compound Random... Generating docs for compound ReferenceSequenceTest... Generating docs for compound ReusableVector... Generating docs for compound ReusableVectorTest... Generating docs for compound ReusableVectorTestDataType... Generating docs for compound RunningStat... Generating docs for compound SamCoordOutput... Generating docs for compound SamCoordOutputTest... Generating docs for compound SamFile... Generating docs for compound SamFileHeader... Generating docs for compound SamFileReader... Generating docs for compound SamFileWriter... Generating docs for compound SamFilter... Generating docs for compound SamFlag... Generating docs for compound SamHeaderHD... Generating docs for compound SamHeaderPG... Generating docs for compound SamHeaderRecord... Generating docs for compound SamHeaderRG... Generating docs for compound SamHeaderSQ... Generating docs for compound SamHeaderTag... Generating docs for compound SamHelper... 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... Generating docs for compound SamRecordHelper... Generating docs for compound SamRecordHelperTest... Generating docs for compound SamRecordPool... Generating docs for compound SamRecordPoolTest... Generating docs for compound SamReferenceInfo... Generating docs for compound SamSingleBaseMatchInfo... Generating docs for compound SamStatistics... Generating docs for compound SamTags... Generating docs for compound SamValidationError... Generating docs for compound SamValidationErrors... Generating docs for compound SamValidator... Generating docs for compound SetParameter... Generating docs for compound ShiftIndelsTest... Generating docs for compound SmithWaterman... Generating docs for nested compound SmithWaterman::weight... Generating docs for compound SortedChunkList... Generating docs for compound StatGenStatus... Generating docs for compound String... Generating docs for compound StringAlias... Generating docs for compound StringArray... Generating docs for compound StringDoubleHash... Generating docs for compound StringHash... Generating docs for compound StringHashBase... Generating docs for compound StringIntHash... Generating docs for compound StringIntMap... Generating docs for compound StringMap... Generating docs for compound StringParameter... Generating docs for compound SwitchParameter... Generating docs for compound Tabix... Generating docs for compound TestPileup... Generating docs for compound TestPileupElement... Generating docs for compound TestPosList... Generating docs for compound TestValidate... Generating docs for compound TestWrite... Generating docs for compound Timing... Generating docs for compound UncompressedFileType... Generating docs for compound UnitTest... Generating docs for compound Vector... Generating docs for compound VectorFunc... Generating docs for compound Weight... Generating namespace index... Generating docs for namespace STLUtilities Generating graph info page... Generating directory documentation... Generating dependency graph for directory bam Generating dependency graph for directory general/test/dbsnp Generating dependency graph for directory fastq Generating dependency graph for directory glf Generating dependency graph for directory general/test/inputFileTest Generating dependency graph for directory general/test Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running dot... Generating dot graphs using 17 parallel threads... 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cache used 10216/65536 hits=89187 misses=10500 finished... make[1]: Leaving directory '/build/libstatgen-1.0.14' dh_auto_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 ar: `u' modifier ignored since `D' is the default (see `U') mkdir -p obj/debug mkdir -p obj/profile gcc -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/bgzf.o -c bgzf.c gcc -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/knetfile.o -c knetfile.c gcc -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/bgzf.o -c bgzf.c gcc -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/knetfile.o -c knetfile.c ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[2]: Leaving directory '/build/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 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\"" 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/BaseUtilities.o -c BaseUtilities.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/BasicHash.o -c BasicHash.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/BgzfFileType.o -c BgzfFileType.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/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.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/CharBuffer.o -c CharBuffer.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/Chromosome.o -c Chromosome.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/Cigar.o -c Cigar.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/CigarRoller.o -c CigarRoller.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/Error.o -c Error.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/ErrorHandler.o -c ErrorHandler.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/FileType.o -c FileType.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/FortranFormat.o -c FortranFormat.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/GenomeSequence.o -c GenomeSequence.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/GenotypeLists.o -c GenotypeLists.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/glfHandler.o -c glfHandler.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/GzipFileType.o -c GzipFileType.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/GzipHeader.o -c GzipHeader.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/Hash.o -c Hash.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/IndexBase.o -c IndexBase.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/Input.o -c Input.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/InputFile.o -c InputFile.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/IntArray.o -c IntArray.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/IntHash.o -c IntHash.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/LongLongCounter.o -c LongLongCounter.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/MapFunction.o -c MapFunction.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/MathMatrix.o -c MathMatrix.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/MathVector.o -c MathVector.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/MemoryAllocators.o -c MemoryAllocators.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/MemoryInfo.o -c MemoryInfo.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/MemoryMapArray.o -c MemoryMapArray.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/MemoryMap.o -c MemoryMap.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/MiniDeflate.o -c MiniDeflate.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/NonOverlapRegions.o -c NonOverlapRegions.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/Parameters.o -c Parameters.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/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.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/Pedigree.o -c Pedigree.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/PedigreeDescription.o -c PedigreeDescription.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/PedigreeFamily.o -c PedigreeFamily.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/PedigreeGlobals.o -c PedigreeGlobals.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/PedigreePerson.o -c PedigreePerson.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/PhoneHome.o -c PhoneHome.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/QuickIndex.o -c QuickIndex.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/Random.o -c Random.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/ReferenceSequence.o -c ReferenceSequence.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/SmithWaterman.o -c SmithWaterman.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/Sort.o -c Sort.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/STLUtilities.o -c STLUtilities.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/StatGenStatus.o -c StatGenStatus.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/StringAlias.o -c StringAlias.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/StringArray.o -c StringArray.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/StringBasics.o -c StringBasics.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/StringHash.o -c StringHash.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/StringMap.o -c StringMap.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/Tabix.o -c Tabix.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/UncompressedFileType.o -c UncompressedFileType.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/PedigreeLoader.o -c PedigreeLoader.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/PedigreeTrim.o -c PedigreeTrim.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/PedigreeTwin.o -c PedigreeTwin.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/BaseQualityHelper.o -c BaseQualityHelper.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/BasicHash.o -c BasicHash.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Chromosome.o -c Chromosome.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/CigarRoller.o -c CigarRoller.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/ErrorHandler.o -c ErrorHandler.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/FortranFormat.o -c FortranFormat.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/GenotypeLists.o -c GenotypeLists.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/GzipFileType.o -c GzipFileType.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Hash.o -c Hash.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Input.o -c Input.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/IntArray.o -c IntArray.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/LongLongCounter.o -c LongLongCounter.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/MathMatrix.o -c MathMatrix.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/MemoryAllocators.o -c MemoryAllocators.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/MemoryMapArray.o -c MemoryMapArray.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/MiniDeflate.o -c MiniDeflate.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Parameters.o -c Parameters.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Pedigree.o -c Pedigree.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/PedigreeFamily.o -c PedigreeFamily.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/PedigreePerson.o -c PedigreePerson.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/QuickIndex.o -c QuickIndex.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/ReferenceSequence.o -c ReferenceSequence.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Sort.o -c Sort.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/StatGenStatus.o -c StatGenStatus.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/StringArray.o -c StringArray.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/StringHash.o -c StringHash.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/Tabix.o -c Tabix.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/PedigreeLoader.o -c PedigreeLoader.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 -Werror -Wno-format-truncation -Wno-strict-overflow -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" g++ -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') ar -cru ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') mkdir obj mkdir obj g++ -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -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/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/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\"" 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 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/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 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 ./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 trimSequence obj/TrimSequence.o ../../../libStatGen_debug.a -lm -lz ./baseUtilitiesTest 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, from InputFileTest.h:18, from InputFileTest.cpp:17: In function 'void* memcpy(void*, const void*, size_t)', inlined from 'int InputFile::ifread(void*, unsigned int)' at ../../../include/InputFile.h:167:19, inlined from 'void IFILE_Test::test_ifread_ifgetc(const char*)' at InputFileTest.cpp:696:25: /usr/include/x86_64-linux-gnu/bits/string_fortified.h:34:33: warning: 'void* __builtin___memcpy_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 memoryMapArrayTest obj/MemoryMapArrayTest.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 ./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/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/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 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/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/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/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\"" 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/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++ -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/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') 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/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/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\"" 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\"" 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++ -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\"" 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++ -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++ -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++ -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\"" 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/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\"" 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/SamReferenceInfo.o -c SamReferenceInfo.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/SamTags.o -c SamTags.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/PosList.o -c PosList.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/CigarHelper.o -c CigarHelper.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/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 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/ValidationTest.o -c ValidationTest.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/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/BamIndexTest.o -c BamIndexTest.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/ModifyVar.o -c ModifyVar.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/Modify.o -c Modify.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/SamFileTest.o -c SamFileTest.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/TestValidate.o -c TestValidate.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/TestEquals.o -c TestEquals.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/TestFilter.o -c TestFilter.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/ShiftIndels.o -c ShiftIndels.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/TestPileup.o -c TestPileup.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/TestPosList.o -c TestPosList.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/TestCigarHelper.o -c TestCigarHelper.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/TestSamRecordPool.o -c TestSamRecordPool.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/TestSamCoordOutput.o -c TestSamCoordOutput.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/TestSamRecordHelper.o -c TestSamRecordHelper.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 samTest obj/WriteFiles.o obj/ValidationTest.o obj/ReadFiles.o obj/BamIndexTest.o obj/ModifyVar.o obj/Modify.o obj/SamFileTest.o obj/TestValidate.o obj/TestEquals.o obj/TestFilter.o obj/ShiftIndels.o obj/TestPileup.o obj/TestPosList.o obj/TestCigarHelper.o obj/TestSamRecordPool.o obj/TestSamCoordOutput.o obj/TestSamRecordHelper.o obj/Main.o ../../libStatGen_debug.a -lm -lz ./test.sh make[2]: Leaving directory '/build/libstatgen-1.0.14/bam' 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 vcfTest obj/VcfFileTest.o obj/VcfHeaderTest.o obj/Main.o ../../libStatGen_debug.a -lm -lz ./vcfTest && diff results/vcfHeader.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedFirst.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedLast.vcf expected/vcfHeader.vcf && diff results/vcfHeaderAddedMiddle.vcf expected/vcfHeader.vcf && diff results/vcfFile.vcf testFiles/vcfFile.vcf && diff results/vcfFileNoInfo.vcf expected/vcfFileNoInfo.vcf && diff results/vcfFileNoInfoBGZF.vcf expected/vcfFileNoInfoBGZF.vcf && diff results/vcfFileNoInfoKeepGT.vcf expected/vcfFileNoInfoKeepGT.vcf && diff results/vcfFileNoInfoKeepGQHQ.vcf expected/vcfFileNoInfoKeepGQHQ.vcf make[2]: Leaving directory '/build/libstatgen-1.0.14/vcf' make[1]: Leaving directory '/build/libstatgen-1.0.14' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/libstatgen-1.0.14' mkdir -p debian/libstatgen-dev/usr/include/libStatGen/ cp -L include/* debian/libstatgen-dev/usr/include/libStatGen/ ln -s libStatGen.so.0 libStatGen.so d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ libStatGen.so Library package automatic movement utility set -e install -d -m 755 debian/libstatgen-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libstatgen0/usr/lib/x86_64-linux-gnu mv ./libStatGen.la debian/libstatgen-dev/usr/lib/x86_64-linux-gnu || true mv ./libStatGen.so debian/libstatgen-dev/usr/lib/x86_64-linux-gnu mv /build/libstatgen-1.0.14/libStatGen.so.0 debian/libstatgen0/usr/lib/x86_64-linux-gnu PKGDEV=libstatgen-dev PKGSHL=libstatgen0 mv: cannot stat './libStatGen.la': No such file or directory make[1]: Leaving directory '/build/libstatgen-1.0.14' dh_installdocs dh_installchangelogs dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps 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 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 '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/9546 and its subdirectories I: Current time: Sat Jul 23 12:53:53 +14 2022 I: pbuilder-time-stamp: 1658530433