I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 18 06:41:07 -12 2023 I: pbuilder-time-stamp: 1681843267 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libstatgen_1.0.15-6.dsc] I: copying [./libstatgen_1.0.15.orig.tar.gz] I: copying [./libstatgen_1.0.15-6.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 4 01:05:37 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libstatgen_1.0.15-6.dsc: no acceptable signature found dpkg-source: info: extracting libstatgen in libstatgen-1.0.15 dpkg-source: info: unpacking libstatgen_1.0.15.orig.tar.gz dpkg-source: info: unpacking libstatgen_1.0.15-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying Fix_compilation_flags.patch dpkg-source: info: applying spelling.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1026975/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='0da5daf7ed4948d2878d212a476b7f6b' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1026975' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.G6KBP8vg/pbuilderrc_odhm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.G6KBP8vg/b1 --logfile b1/build.log libstatgen_1.0.15-6.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos1-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash -rwxr-xr-x 1 root root 121904 Sep 20 2022 date -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd -rwxr-xr-x 1 root root 102200 Sep 20 2022 df -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 35664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/1026975/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), doxygen, libssl-dev, zlib1g-dev, d-shlibs dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} doxygen{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libclang-cpp14{a} libclang1-14{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libllvm14{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libz3-4{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 73.2 MB of archives. After unpacking 329 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 d-shlibs all 0.104 [18.6 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libllvm14 amd64 1:14.0.6-12 [21.8 MB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libclang-cpp14 amd64 1:14.0.6-12 [11.1 MB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libclang1-14 amd64 1:14.0.6-12 [6157 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 doxygen amd64 1.9.4-4 [4611 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.8-1 [2427 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Fetched 73.2 MB in 1s (71.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (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 ... 19596 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.104_all.deb ... Unpacking d-shlibs (0.104) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../31-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../32-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../33-libz3-4_4.8.12-3.1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-3.1) ... Selecting previously unselected package libllvm14:amd64. Preparing to unpack .../34-libllvm14_1%3a14.0.6-12_amd64.deb ... Unpacking libllvm14:amd64 (1:14.0.6-12) ... Selecting previously unselected package libclang-cpp14. Preparing to unpack .../35-libclang-cpp14_1%3a14.0.6-12_amd64.deb ... Unpacking libclang-cpp14 (1:14.0.6-12) ... Selecting previously unselected package libclang1-14. Preparing to unpack .../36-libclang1-14_1%3a14.0.6-12_amd64.deb ... Unpacking libclang1-14 (1:14.0.6-12) ... Selecting previously unselected package doxygen. Preparing to unpack .../37-doxygen_1.9.4-4_amd64.deb ... Unpacking doxygen (1.9.4-4) ... Selecting previously unselected package libssl-dev:amd64. Preparing to unpack .../38-libssl-dev_3.0.8-1_amd64.deb ... Unpacking libssl-dev:amd64 (3.0.8-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../39-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libssl-dev:amd64 (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up d-shlibs (0.104) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libllvm14:amd64 (1:14.0.6-12) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libclang1-14 (1:14.0.6-12) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libclang-cpp14 (1:14.0.6-12) ... Setting up debhelper (13.11.4) ... Setting up doxygen (1.9.4-4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/libstatgen-1.0.15/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libstatgen_1.0.15-6_source.changes dpkg-buildpackage: info: source package libstatgen dpkg-buildpackage: info: source version 1.0.15-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/build/libstatgen-1.0.15' make[2]: Entering directory '/build/libstatgen-1.0.15/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-1.0.15/samtools' make[2]: Entering directory '/build/libstatgen-1.0.15/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 baseUtilitiesTest *~ results/* rm -rf obj trimSequence *~ results/* rm -rf obj reusableVectorTest *~ results/* # clean current directory rm -f *.o *~ rm -f phiX-bs.umfa phiX-cs.umfa gtest make[2]: Leaving directory '/build/libstatgen-1.0.15/general' make[2]: Entering directory '/build/libstatgen-1.0.15/bam' rm -f ../include/SamFileHeader.h ../include/SamFile.h ../include/GenericSamInterface.h ../include/SamInterface.h ../include/BamInterface.h ../include/SamRecord.h ../include/BamIndex.h ../include/SamHeaderHD.h ../include/SamHeaderPG.h ../include/SamHeaderRecord.h ../include/SamHeaderSQ.h ../include/SamHeaderRG.h ../include/SamHeaderTag.h ../include/SamValidation.h ../include/SamStatistics.h ../include/SamQuerySeqWithRefHelper.h ../include/SamFilter.h ../include/PileupElement.h ../include/PileupElementBaseQual.h ../include/SamReferenceInfo.h ../include/SamTags.h ../include/PosList.h ../include/CigarHelper.h ../include/SamRecordPool.h ../include/SamCoordOutput.h ../include/SamRecordHelper.h ../include/Pileup.h ../include/SamHelper.h ../include/SamFlag.h ../include/SamStatus.h ar d ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/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_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 ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj samTest *~ results/* make[2]: Leaving directory '/build/libstatgen-1.0.15/bam' make[2]: Entering directory '/build/libstatgen-1.0.15/fastq' 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 ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o ranlib ../libStatGen_debug.a ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o ranlib ../libStatGen_profile.a rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj fastqTest *~ results/* make[2]: Leaving directory '/build/libstatgen-1.0.15/fastq' make[2]: Entering directory '/build/libstatgen-1.0.15/glf' 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 ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o ranlib ../libStatGen_debug.a 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 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-1.0.15/glf' make[2]: Entering directory '/build/libstatgen-1.0.15/vcf' rm -f ../include/VcfFile.h ../include/VcfFileReader.h ../include/VcfFileWriter.h ../include/VcfGenotypeField.h ../include/VcfGenotypeFormat.h ../include/VcfGenotypeSample.h ../include/VcfHeader.h ../include/VcfHelper.h ../include/VcfRecord.h ../include/VcfRecordField.h ../include/VcfRecordFilter.h ../include/VcfRecordGenotype.h ../include/VcfRecordInfo.h ../include/VcfSubsetSamples.h ../include/VcfRecordDiscardRules.h ar d ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o ranlib ../libStatGen.a ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o ranlib ../libStatGen_debug.a ar d ../libStatGen_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 rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ rm -rf obj vcfTest *~ results/* make[2]: Leaving directory '/build/libstatgen-1.0.15/vcf' rm -f libStatGen.a rm -f libStatGen_debug.a rm -f libStatGen_profile.a make[1]: Leaving directory '/build/libstatgen-1.0.15' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary dh binary --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/build/libstatgen-1.0.15' dh_auto_build make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/libstatgen-1.0.15' make[3]: Entering directory '/build/libstatgen-1.0.15/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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15/samtools' make[3]: Entering directory '/build/libstatgen-1.0.15/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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\"" Sort.cpp: In function 'void QuickSort(void*, size_t, size_t, int (*)(const void*, const void*))': Sort.cpp:158:31: warning: array subscript 128 is outside array bounds of 'QuickSort(void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 158 | stack[stackIdx].left = scanl + 1; | ~~~~~~~~~~~~~~^ Sort.cpp:50:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 50 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp:159:31: warning: array subscript 128 is outside array bounds of 'QuickSort(void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 159 | stack[stackIdx].right = r; | ~~~~~~~~~~~~~~^ Sort.cpp:50:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 50 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp:142:31: warning: array subscript 128 is outside array bounds of 'QuickSort(void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 142 | stack[stackIdx].left = l; | ~~~~~~~~~~~~~~^ Sort.cpp:50:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 50 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp:143:31: warning: array subscript 128 is outside array bounds of 'QuickSort(void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 143 | stack[stackIdx].right = scanl - 1; | ~~~~~~~~~~~~~~^ Sort.cpp:50:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 50 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp: In function 'void QuickSort2(void*, void*, size_t, size_t, int (*)(const void*, const void*))': Sort.cpp:320:31: warning: array subscript 128 is outside array bounds of 'QuickSort2(void*, void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 320 | stack[stackIdx].left = scanl + 1; | ~~~~~~~~~~~~~~^ Sort.cpp:212:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 212 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp:321:31: warning: array subscript 128 is outside array bounds of 'QuickSort2(void*, void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 321 | stack[stackIdx].right = r; | ~~~~~~~~~~~~~~^ Sort.cpp:212:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 212 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp:304:31: warning: array subscript 128 is outside array bounds of 'QuickSort2(void*, void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 304 | stack[stackIdx].left = l; | ~~~~~~~~~~~~~~^ Sort.cpp:212:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 212 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ Sort.cpp:305:31: warning: array subscript 128 is outside array bounds of 'QuickSort2(void*, void*, size_t, size_t, int (*)(const void*, const void*))::__QuickSortStack [128]' [-Warray-bounds] 305 | stack[stackIdx].right = scanl - 1; | ~~~~~~~~~~~~~~^ Sort.cpp:212:62: note: at offset 2048 into object of size 2048 allocated by 'operator new []' 212 | __QuickSortStack * stack = new __QuickSortStack[stackSize]; | ^ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wno-format-truncation -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\"" ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/libstatgen-1.0.15/general' make[3]: Entering directory '/build/libstatgen-1.0.15/bam' ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h ln -s ../bam/SamFile.h ../include/SamFile.h ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h ln -s ../bam/SamInterface.h ../include/SamInterface.h ln -s ../bam/BamInterface.h ../include/BamInterface.h ln -s ../bam/SamRecord.h ../include/SamRecord.h ln -s ../bam/BamIndex.h ../include/BamIndex.h ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h ln -s ../bam/SamValidation.h ../include/SamValidation.h ln -s ../bam/SamStatistics.h ../include/SamStatistics.h ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h ln -s ../bam/SamFilter.h ../include/SamFilter.h ln -s ../bam/PileupElement.h ../include/PileupElement.h ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h ln -s ../bam/SamTags.h ../include/SamTags.h ln -s ../bam/PosList.h ../include/PosList.h ln -s ../bam/CigarHelper.h ../include/CigarHelper.h 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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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/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-1.0.15/bam' make[3]: Entering directory '/build/libstatgen-1.0.15/fastq' ln -s ../fastq/FastQFile.h ../include/FastQFile.h ln -s ../fastq/BaseCount.h ../include/BaseCount.h ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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\"" 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-1.0.15/fastq' make[3]: Entering directory '/build/libstatgen-1.0.15/glf' ln -s ../glf/GlfException.h ../include/GlfException.h ln -s ../glf/GlfFile.h ../include/GlfFile.h ln -s ../glf/GlfHeader.h ../include/GlfHeader.h ln -s ../glf/GlfRecord.h ../include/GlfRecord.h ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h ln -s ../glf/GlfStatus.h ../include/GlfStatus.h mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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\"" 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-1.0.15/glf' make[3]: Entering directory '/build/libstatgen-1.0.15/vcf' ln -s ../vcf/VcfFile.h ../include/VcfFile.h ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.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 mkdir -p obj g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\"" g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/libstatgen-1.0.15=. -fstack-protector-strong -Wformat -Werror=format-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\"" 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-1.0.15/vcf' make[2]: Leaving directory '/build/libstatgen-1.0.15' # Build the shared library x86_64-linux-gnu-g++ -shared -o libStatGen.so.1 */obj/*.o -fPIC -Wl,-soname,libStatGen.so.1 -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 'COLS_IN_ALPHA_INDEX' at line 755 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 'LATEX_SOURCE_CODE' at line 1064 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: Tag 'PERL_PATH' at line 1327 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 'CLASS_DIAGRAMS' at line 1340 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 'MSCGEN_PATH' at line 1349 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++' Doxygen version used: 1.9.4 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-1.0.15/include Searching for files in directory /build/libstatgen-1.0.15/copyrights Searching for files in directory /build/libstatgen-1.0.15/dox Searching for files in directory /build/libstatgen-1.0.15/dox/man Searching for files in directory /build/libstatgen-1.0.15/dox/html Searching INPUT for files to process... Searching for files in directory /build/libstatgen-1.0.15/bam Searching for files in directory /build/libstatgen-1.0.15/bam/obj Searching for files in directory /build/libstatgen-1.0.15/bam/test Searching for files in directory /build/libstatgen-1.0.15/bam/test/testFiles Searching for files in directory /build/libstatgen-1.0.15/bam/test/results Searching for files in directory /build/libstatgen-1.0.15/bam/test/expected Searching for files in directory /build/libstatgen-1.0.15/bam/test/expected/noZlib Searching for files in directory /build/libstatgen-1.0.15/bam/examples Searching for files in directory /build/libstatgen-1.0.15/bam/examples/printRefPositions Searching for files in directory /build/libstatgen-1.0.15/bam/examples/printRefPositions/expected Searching for files in directory /build/libstatgen-1.0.15/bam/examples/pileup Searching for files in directory /build/libstatgen-1.0.15/fastq Searching for files in directory /build/libstatgen-1.0.15/fastq/obj Searching for files in directory /build/libstatgen-1.0.15/fastq/test Searching for files in directory /build/libstatgen-1.0.15/fastq/test/expectedResults Searching for files in directory /build/libstatgen-1.0.15/general Searching for files in directory /build/libstatgen-1.0.15/general/test Searching for files in directory /build/libstatgen-1.0.15/general/test/trimSequence Searching for files in directory /build/libstatgen-1.0.15/general/test/string Searching for files in directory /build/libstatgen-1.0.15/general/test/string/testFiles Searching for files in directory /build/libstatgen-1.0.15/general/test/reusableVector Searching for files in directory /build/libstatgen-1.0.15/general/test/referenceSequenceTest Searching for files in directory /build/libstatgen-1.0.15/general/test/packedVectorTest Searching for files in directory /build/libstatgen-1.0.15/general/test/nonOverlapRegions Searching for files in directory /build/libstatgen-1.0.15/general/test/nonOverlapRegions/results Searching for files in directory /build/libstatgen-1.0.15/general/test/memoryMapArrayTest Searching for files in directory /build/libstatgen-1.0.15/general/test/inputFileTest Searching for files in directory /build/libstatgen-1.0.15/general/test/inputFileTest/expected Searching for files in directory /build/libstatgen-1.0.15/general/test/inputFileTest/data Searching for files in directory /build/libstatgen-1.0.15/general/test/dbsnp Searching for files in directory /build/libstatgen-1.0.15/general/test/dbsnp/testFiles Searching for files in directory /build/libstatgen-1.0.15/general/test/dbsnp/expected Searching for files in directory /build/libstatgen-1.0.15/general/test/cigar Searching for files in directory /build/libstatgen-1.0.15/general/test/baseUtilitiesTest Searching for files in directory /build/libstatgen-1.0.15/general/obj Searching for files in directory /build/libstatgen-1.0.15/glf Searching for files in directory /build/libstatgen-1.0.15/glf/obj Searching for files in directory /build/libstatgen-1.0.15/glf/test Searching for files in directory /build/libstatgen-1.0.15/glf/test/testFiles Searching for files in directory /build/libstatgen-1.0.15/glf/test/results Searching for files in directory /build/libstatgen-1.0.15/samtools Searching for files in directory /build/libstatgen-1.0.15/samtools/obj Searching for files in directory /build/libstatgen-1.0.15/Makefiles Reading and parsing tag files Parsing files Preprocessing /build/libstatgen-1.0.15/bam/BamIndex.cpp... Parsing file /build/libstatgen-1.0.15/bam/BamIndex.cpp... Preprocessing /build/libstatgen-1.0.15/bam/BamIndex.h... Parsing file /build/libstatgen-1.0.15/bam/BamIndex.h... Preprocessing /build/libstatgen-1.0.15/bam/BamInterface.cpp... Parsing file /build/libstatgen-1.0.15/bam/BamInterface.cpp... Preprocessing /build/libstatgen-1.0.15/bam/BamInterface.h... Parsing file /build/libstatgen-1.0.15/bam/BamInterface.h... Preprocessing /build/libstatgen-1.0.15/bam/CigarHelper.cpp... Parsing file /build/libstatgen-1.0.15/bam/CigarHelper.cpp... Preprocessing /build/libstatgen-1.0.15/bam/CigarHelper.h... Parsing file /build/libstatgen-1.0.15/bam/CigarHelper.h... Preprocessing /build/libstatgen-1.0.15/bam/examples/pileup/Main.cpp... Parsing file /build/libstatgen-1.0.15/bam/examples/pileup/Main.cpp... Preprocessing /build/libstatgen-1.0.15/bam/examples/printRefPositions/Main.cpp... Parsing file /build/libstatgen-1.0.15/bam/examples/printRefPositions/Main.cpp... Preprocessing /build/libstatgen-1.0.15/bam/examples/printRefPositions/PrintRefPositions.cpp... Parsing file /build/libstatgen-1.0.15/bam/examples/printRefPositions/PrintRefPositions.cpp... Preprocessing /build/libstatgen-1.0.15/bam/examples/printRefPositions/PrintRefPositions.h... Parsing file /build/libstatgen-1.0.15/bam/examples/printRefPositions/PrintRefPositions.h... Preprocessing /build/libstatgen-1.0.15/bam/GenericSamInterface.cpp... Parsing file /build/libstatgen-1.0.15/bam/GenericSamInterface.cpp... Preprocessing /build/libstatgen-1.0.15/bam/GenericSamInterface.h... Parsing file /build/libstatgen-1.0.15/bam/GenericSamInterface.h... Preprocessing /build/libstatgen-1.0.15/bam/Pileup.h... Parsing file /build/libstatgen-1.0.15/bam/Pileup.h... Preprocessing /build/libstatgen-1.0.15/bam/PileupElement.cpp... Parsing file /build/libstatgen-1.0.15/bam/PileupElement.cpp... Preprocessing /build/libstatgen-1.0.15/bam/PileupElement.h... Parsing file /build/libstatgen-1.0.15/bam/PileupElement.h... Preprocessing /build/libstatgen-1.0.15/bam/PileupElementBaseQual.cpp... Parsing file /build/libstatgen-1.0.15/bam/PileupElementBaseQual.cpp... Preprocessing /build/libstatgen-1.0.15/bam/PileupElementBaseQual.h... Parsing file /build/libstatgen-1.0.15/bam/PileupElementBaseQual.h... Preprocessing /build/libstatgen-1.0.15/bam/PosList.cpp... Parsing file /build/libstatgen-1.0.15/bam/PosList.cpp... Preprocessing /build/libstatgen-1.0.15/bam/PosList.h... Parsing file /build/libstatgen-1.0.15/bam/PosList.h... Preprocessing /build/libstatgen-1.0.15/bam/SamCoordOutput.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamCoordOutput.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamCoordOutput.h... Parsing file /build/libstatgen-1.0.15/bam/SamCoordOutput.h... Preprocessing /build/libstatgen-1.0.15/bam/SamFile.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamFile.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamFile.h... Parsing file /build/libstatgen-1.0.15/bam/SamFile.h... Preprocessing /build/libstatgen-1.0.15/bam/SamFileHeader.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamFileHeader.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamFileHeader.h... Parsing file /build/libstatgen-1.0.15/bam/SamFileHeader.h... Preprocessing /build/libstatgen-1.0.15/bam/SamFilter.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamFilter.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamFilter.h... Parsing file /build/libstatgen-1.0.15/bam/SamFilter.h... Preprocessing /build/libstatgen-1.0.15/bam/SamFlag.h... Parsing file /build/libstatgen-1.0.15/bam/SamFlag.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderHD.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderHD.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderHD.h... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderHD.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderPG.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderPG.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderPG.h... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderPG.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderRecord.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderRecord.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderRecord.h... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderRecord.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderRG.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderRG.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderRG.h... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderRG.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderSQ.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderSQ.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderSQ.h... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderSQ.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderTag.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderTag.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamHeaderTag.h... Parsing file /build/libstatgen-1.0.15/bam/SamHeaderTag.h... Preprocessing /build/libstatgen-1.0.15/bam/SamHelper.h... Parsing file /build/libstatgen-1.0.15/bam/SamHelper.h... Preprocessing /build/libstatgen-1.0.15/bam/SamInterface.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamInterface.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamInterface.h... Parsing file /build/libstatgen-1.0.15/bam/SamInterface.h... Preprocessing /build/libstatgen-1.0.15/bam/SamQuerySeqWithRefHelper.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamQuerySeqWithRefHelper.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamQuerySeqWithRefHelper.h... Parsing file /build/libstatgen-1.0.15/bam/SamQuerySeqWithRefHelper.h... Preprocessing /build/libstatgen-1.0.15/bam/SamRecord.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamRecord.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamRecord.h... Parsing file /build/libstatgen-1.0.15/bam/SamRecord.h... Preprocessing /build/libstatgen-1.0.15/bam/SamRecordHelper.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamRecordHelper.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamRecordHelper.h... Parsing file /build/libstatgen-1.0.15/bam/SamRecordHelper.h... Preprocessing /build/libstatgen-1.0.15/bam/SamRecordPool.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamRecordPool.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamRecordPool.h... Parsing file /build/libstatgen-1.0.15/bam/SamRecordPool.h... Preprocessing /build/libstatgen-1.0.15/bam/SamReferenceInfo.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamReferenceInfo.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamReferenceInfo.h... Parsing file /build/libstatgen-1.0.15/bam/SamReferenceInfo.h... Preprocessing /build/libstatgen-1.0.15/bam/SamStatistics.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamStatistics.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamStatistics.h... Parsing file /build/libstatgen-1.0.15/bam/SamStatistics.h... Preprocessing /build/libstatgen-1.0.15/bam/SamStatus.h... Parsing file /build/libstatgen-1.0.15/bam/SamStatus.h... Preprocessing /build/libstatgen-1.0.15/bam/SamTags.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamTags.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamTags.h... Parsing file /build/libstatgen-1.0.15/bam/SamTags.h... Preprocessing /build/libstatgen-1.0.15/bam/SamValidation.cpp... Parsing file /build/libstatgen-1.0.15/bam/SamValidation.cpp... Preprocessing /build/libstatgen-1.0.15/bam/SamValidation.h... Parsing file /build/libstatgen-1.0.15/bam/SamValidation.h... Preprocessing /build/libstatgen-1.0.15/bam/test/BamIndexTest.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/BamIndexTest.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/BamIndexTest.h... Parsing file /build/libstatgen-1.0.15/bam/test/BamIndexTest.h... Preprocessing /build/libstatgen-1.0.15/bam/test/Main.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/Main.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/Modify.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/Modify.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/Modify.h... Parsing file /build/libstatgen-1.0.15/bam/test/Modify.h... Preprocessing /build/libstatgen-1.0.15/bam/test/ModifyVar.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/ModifyVar.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/ModifyVar.h... Parsing file /build/libstatgen-1.0.15/bam/test/ModifyVar.h... Preprocessing /build/libstatgen-1.0.15/bam/test/ReadFiles.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/ReadFiles.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/ReadFiles.h... Parsing file /build/libstatgen-1.0.15/bam/test/ReadFiles.h... Preprocessing /build/libstatgen-1.0.15/bam/test/SamFileTest.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/SamFileTest.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/SamFileTest.h... Parsing file /build/libstatgen-1.0.15/bam/test/SamFileTest.h... Preprocessing /build/libstatgen-1.0.15/bam/test/ShiftIndels.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/ShiftIndels.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/ShiftIndels.h... Parsing file /build/libstatgen-1.0.15/bam/test/ShiftIndels.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestCigarHelper.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestCigarHelper.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestCigarHelper.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestCigarHelper.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestEquals.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestEquals.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestEquals.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestEquals.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestFilter.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestFilter.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestFilter.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestFilter.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestPileup.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestPileup.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestPileup.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestPileup.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestPosList.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestPosList.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestPosList.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestPosList.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestSamCoordOutput.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestSamCoordOutput.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestSamCoordOutput.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestSamCoordOutput.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestSamRecordHelper.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestSamRecordHelper.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestSamRecordHelper.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestSamRecordHelper.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestSamRecordPool.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestSamRecordPool.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestSamRecordPool.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestSamRecordPool.h... Preprocessing /build/libstatgen-1.0.15/bam/test/TestValidate.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/TestValidate.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/TestValidate.h... Parsing file /build/libstatgen-1.0.15/bam/test/TestValidate.h... Preprocessing /build/libstatgen-1.0.15/bam/test/ValidationTest.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/ValidationTest.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/ValidationTest.h... Parsing file /build/libstatgen-1.0.15/bam/test/ValidationTest.h... Preprocessing /build/libstatgen-1.0.15/bam/test/WriteFiles.cpp... Parsing file /build/libstatgen-1.0.15/bam/test/WriteFiles.cpp... Preprocessing /build/libstatgen-1.0.15/bam/test/WriteFiles.h... Parsing file /build/libstatgen-1.0.15/bam/test/WriteFiles.h... Preprocessing /build/libstatgen-1.0.15/fastq/BaseComposition.cpp... Parsing file /build/libstatgen-1.0.15/fastq/BaseComposition.cpp... Preprocessing /build/libstatgen-1.0.15/fastq/BaseComposition.h... Parsing file /build/libstatgen-1.0.15/fastq/BaseComposition.h... Preprocessing /build/libstatgen-1.0.15/fastq/BaseCount.cpp... Parsing file /build/libstatgen-1.0.15/fastq/BaseCount.cpp... Preprocessing /build/libstatgen-1.0.15/fastq/BaseCount.h... Parsing file /build/libstatgen-1.0.15/fastq/BaseCount.h... Preprocessing /build/libstatgen-1.0.15/fastq/FastQFile.cpp... Parsing file /build/libstatgen-1.0.15/fastq/FastQFile.cpp... Preprocessing /build/libstatgen-1.0.15/fastq/FastQFile.h... Parsing file /build/libstatgen-1.0.15/fastq/FastQFile.h... Preprocessing /build/libstatgen-1.0.15/fastq/FastQStatus.cpp... Parsing file /build/libstatgen-1.0.15/fastq/FastQStatus.cpp... Preprocessing /build/libstatgen-1.0.15/fastq/FastQStatus.h... Parsing file /build/libstatgen-1.0.15/fastq/FastQStatus.h... Preprocessing /build/libstatgen-1.0.15/fastq/test/FastQFileTest.cpp... Parsing file /build/libstatgen-1.0.15/fastq/test/FastQFileTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/BaseAsciiMap.cpp... Parsing file /build/libstatgen-1.0.15/general/BaseAsciiMap.cpp... Preprocessing /build/libstatgen-1.0.15/general/BaseAsciiMap.h... Parsing file /build/libstatgen-1.0.15/general/BaseAsciiMap.h... Preprocessing /build/libstatgen-1.0.15/general/BaseQualityHelper.cpp... Parsing file /build/libstatgen-1.0.15/general/BaseQualityHelper.cpp... Preprocessing /build/libstatgen-1.0.15/general/BaseQualityHelper.h... Parsing file /build/libstatgen-1.0.15/general/BaseQualityHelper.h... Preprocessing /build/libstatgen-1.0.15/general/BaseUtilities.cpp... Parsing file /build/libstatgen-1.0.15/general/BaseUtilities.cpp... Preprocessing /build/libstatgen-1.0.15/general/BaseUtilities.h... Parsing file /build/libstatgen-1.0.15/general/BaseUtilities.h... Preprocessing /build/libstatgen-1.0.15/general/BasicHash.cpp... Parsing file /build/libstatgen-1.0.15/general/BasicHash.cpp... Preprocessing /build/libstatgen-1.0.15/general/BasicHash.h... Parsing file /build/libstatgen-1.0.15/general/BasicHash.h... Preprocessing /build/libstatgen-1.0.15/general/BgzfFileType.cpp... Parsing file /build/libstatgen-1.0.15/general/BgzfFileType.cpp... Preprocessing /build/libstatgen-1.0.15/general/BgzfFileType.h... Parsing file /build/libstatgen-1.0.15/general/BgzfFileType.h... Preprocessing /build/libstatgen-1.0.15/general/BgzfFileTypeRecovery.cpp... Parsing file /build/libstatgen-1.0.15/general/BgzfFileTypeRecovery.cpp... Preprocessing /build/libstatgen-1.0.15/general/BgzfFileTypeRecovery.h... Parsing file /build/libstatgen-1.0.15/general/BgzfFileTypeRecovery.h... Preprocessing /build/libstatgen-1.0.15/general/CharBuffer.cpp... Parsing file /build/libstatgen-1.0.15/general/CharBuffer.cpp... Preprocessing /build/libstatgen-1.0.15/general/CharBuffer.h... Parsing file /build/libstatgen-1.0.15/general/CharBuffer.h... Preprocessing /build/libstatgen-1.0.15/general/Chromosome.cpp... Parsing file /build/libstatgen-1.0.15/general/Chromosome.cpp... Preprocessing /build/libstatgen-1.0.15/general/Chromosome.h... Parsing file /build/libstatgen-1.0.15/general/Chromosome.h... Preprocessing /build/libstatgen-1.0.15/general/Cigar.cpp... Parsing file /build/libstatgen-1.0.15/general/Cigar.cpp... Preprocessing /build/libstatgen-1.0.15/general/Cigar.h... Parsing file /build/libstatgen-1.0.15/general/Cigar.h... Preprocessing /build/libstatgen-1.0.15/general/CigarRoller.cpp... Parsing file /build/libstatgen-1.0.15/general/CigarRoller.cpp... Preprocessing /build/libstatgen-1.0.15/general/CigarRoller.h... Parsing file /build/libstatgen-1.0.15/general/CigarRoller.h... Preprocessing /build/libstatgen-1.0.15/general/Constant.h... Parsing file /build/libstatgen-1.0.15/general/Constant.h... Preprocessing /build/libstatgen-1.0.15/general/CSG_MD5.h... Parsing file /build/libstatgen-1.0.15/general/CSG_MD5.h... Preprocessing /build/libstatgen-1.0.15/general/Error.cpp... Parsing file /build/libstatgen-1.0.15/general/Error.cpp... Preprocessing /build/libstatgen-1.0.15/general/Error.h... Parsing file /build/libstatgen-1.0.15/general/Error.h... Preprocessing /build/libstatgen-1.0.15/general/ErrorHandler.cpp... Parsing file /build/libstatgen-1.0.15/general/ErrorHandler.cpp... Preprocessing /build/libstatgen-1.0.15/general/ErrorHandler.h... Parsing file /build/libstatgen-1.0.15/general/ErrorHandler.h... Preprocessing /build/libstatgen-1.0.15/general/FileType.cpp... Parsing file /build/libstatgen-1.0.15/general/FileType.cpp... Preprocessing /build/libstatgen-1.0.15/general/FileType.h... Parsing file /build/libstatgen-1.0.15/general/FileType.h... Preprocessing /build/libstatgen-1.0.15/general/FortranFormat.cpp... Parsing file /build/libstatgen-1.0.15/general/FortranFormat.cpp... Preprocessing /build/libstatgen-1.0.15/general/FortranFormat.h... Parsing file /build/libstatgen-1.0.15/general/FortranFormat.h... Preprocessing /build/libstatgen-1.0.15/general/Generic.cpp... Parsing file /build/libstatgen-1.0.15/general/Generic.cpp... Preprocessing /build/libstatgen-1.0.15/general/Generic.h... Parsing file /build/libstatgen-1.0.15/general/Generic.h... Preprocessing /build/libstatgen-1.0.15/general/GenomeSequence.cpp... Parsing file /build/libstatgen-1.0.15/general/GenomeSequence.cpp... Preprocessing /build/libstatgen-1.0.15/general/GenomeSequence.h... Parsing file /build/libstatgen-1.0.15/general/GenomeSequence.h... Preprocessing /build/libstatgen-1.0.15/general/GenomeSequenceHelpers.h... Parsing file /build/libstatgen-1.0.15/general/GenomeSequenceHelpers.h... Preprocessing /build/libstatgen-1.0.15/general/GenotypeLists.cpp... Parsing file /build/libstatgen-1.0.15/general/GenotypeLists.cpp... Preprocessing /build/libstatgen-1.0.15/general/GenotypeLists.h... Parsing file /build/libstatgen-1.0.15/general/GenotypeLists.h... Preprocessing /build/libstatgen-1.0.15/general/glfHandler.cpp... Parsing file /build/libstatgen-1.0.15/general/glfHandler.cpp... Preprocessing /build/libstatgen-1.0.15/general/glfHandler.h... Parsing file /build/libstatgen-1.0.15/general/glfHandler.h... Preprocessing /build/libstatgen-1.0.15/general/GreedyTupleAligner.h... Parsing file /build/libstatgen-1.0.15/general/GreedyTupleAligner.h... Preprocessing /build/libstatgen-1.0.15/general/GzipFileType.cpp... Parsing file /build/libstatgen-1.0.15/general/GzipFileType.cpp... Preprocessing /build/libstatgen-1.0.15/general/GzipFileType.h... Parsing file /build/libstatgen-1.0.15/general/GzipFileType.h... Preprocessing /build/libstatgen-1.0.15/general/GzipHeader.cpp... Parsing file /build/libstatgen-1.0.15/general/GzipHeader.cpp... Preprocessing /build/libstatgen-1.0.15/general/GzipHeader.h... Parsing file /build/libstatgen-1.0.15/general/GzipHeader.h... Preprocessing /build/libstatgen-1.0.15/general/Hash.cpp... Parsing file /build/libstatgen-1.0.15/general/Hash.cpp... Preprocessing /build/libstatgen-1.0.15/general/Hash.h... Parsing file /build/libstatgen-1.0.15/general/Hash.h... Preprocessing /build/libstatgen-1.0.15/general/IndexBase.cpp... Parsing file /build/libstatgen-1.0.15/general/IndexBase.cpp... Preprocessing /build/libstatgen-1.0.15/general/IndexBase.h... Parsing file /build/libstatgen-1.0.15/general/IndexBase.h... Preprocessing /build/libstatgen-1.0.15/general/InplaceMerge.cpp... Parsing file /build/libstatgen-1.0.15/general/InplaceMerge.cpp... Preprocessing /build/libstatgen-1.0.15/general/InplaceMerge.h... Parsing file /build/libstatgen-1.0.15/general/InplaceMerge.h... Preprocessing /build/libstatgen-1.0.15/general/Input.cpp... Parsing file /build/libstatgen-1.0.15/general/Input.cpp... Preprocessing /build/libstatgen-1.0.15/general/Input.h... Parsing file /build/libstatgen-1.0.15/general/Input.h... Preprocessing /build/libstatgen-1.0.15/general/InputFile.cpp... Parsing file /build/libstatgen-1.0.15/general/InputFile.cpp... Preprocessing /build/libstatgen-1.0.15/general/InputFile.h... Parsing file /build/libstatgen-1.0.15/general/InputFile.h... Preprocessing /build/libstatgen-1.0.15/general/IntArray.cpp... Parsing file /build/libstatgen-1.0.15/general/IntArray.cpp... Preprocessing /build/libstatgen-1.0.15/general/IntArray.h... Parsing file /build/libstatgen-1.0.15/general/IntArray.h... Preprocessing /build/libstatgen-1.0.15/general/IntHash.cpp... Parsing file /build/libstatgen-1.0.15/general/IntHash.cpp... Preprocessing /build/libstatgen-1.0.15/general/IntHash.h... Parsing file /build/libstatgen-1.0.15/general/IntHash.h... Preprocessing /build/libstatgen-1.0.15/general/LongHash.h... Parsing file /build/libstatgen-1.0.15/general/LongHash.h... Preprocessing /build/libstatgen-1.0.15/general/LongInt.h... Parsing file /build/libstatgen-1.0.15/general/LongInt.h... Preprocessing /build/libstatgen-1.0.15/general/LongLongCounter.cpp... Parsing file /build/libstatgen-1.0.15/general/LongLongCounter.cpp... Preprocessing /build/libstatgen-1.0.15/general/LongLongCounter.h... Parsing file /build/libstatgen-1.0.15/general/LongLongCounter.h... Preprocessing /build/libstatgen-1.0.15/general/MapFunction.cpp... Parsing file /build/libstatgen-1.0.15/general/MapFunction.cpp... Preprocessing /build/libstatgen-1.0.15/general/MapFunction.h... Parsing file /build/libstatgen-1.0.15/general/MapFunction.h... Preprocessing /build/libstatgen-1.0.15/general/MathConstant.h... Parsing file /build/libstatgen-1.0.15/general/MathConstant.h... Preprocessing /build/libstatgen-1.0.15/general/MathMatrix.cpp... Parsing file /build/libstatgen-1.0.15/general/MathMatrix.cpp... Preprocessing /build/libstatgen-1.0.15/general/MathMatrix.h... Parsing file /build/libstatgen-1.0.15/general/MathMatrix.h... Preprocessing /build/libstatgen-1.0.15/general/MathVector.cpp... Parsing file /build/libstatgen-1.0.15/general/MathVector.cpp... Preprocessing /build/libstatgen-1.0.15/general/MathVector.h... Parsing file /build/libstatgen-1.0.15/general/MathVector.h... Preprocessing /build/libstatgen-1.0.15/general/MemoryAllocators.cpp... Parsing file /build/libstatgen-1.0.15/general/MemoryAllocators.cpp... Preprocessing /build/libstatgen-1.0.15/general/MemoryAllocators.h... Parsing file /build/libstatgen-1.0.15/general/MemoryAllocators.h... Preprocessing /build/libstatgen-1.0.15/general/MemoryInfo.cpp... Parsing file /build/libstatgen-1.0.15/general/MemoryInfo.cpp... Preprocessing /build/libstatgen-1.0.15/general/MemoryInfo.h... Parsing file /build/libstatgen-1.0.15/general/MemoryInfo.h... Preprocessing /build/libstatgen-1.0.15/general/MemoryMap.cpp... Parsing file /build/libstatgen-1.0.15/general/MemoryMap.cpp... Preprocessing /build/libstatgen-1.0.15/general/MemoryMap.h... Parsing file /build/libstatgen-1.0.15/general/MemoryMap.h... Preprocessing /build/libstatgen-1.0.15/general/MemoryMapArray.cpp... Parsing file /build/libstatgen-1.0.15/general/MemoryMapArray.cpp... Preprocessing /build/libstatgen-1.0.15/general/MemoryMapArray.h... Parsing file /build/libstatgen-1.0.15/general/MemoryMapArray.h... Preprocessing /build/libstatgen-1.0.15/general/MiniDeflate.cpp... Parsing file /build/libstatgen-1.0.15/general/MiniDeflate.cpp... Preprocessing /build/libstatgen-1.0.15/general/MiniDeflate.h... Parsing file /build/libstatgen-1.0.15/general/MiniDeflate.h... Preprocessing /build/libstatgen-1.0.15/general/NonOverlapRegions.cpp... Parsing file /build/libstatgen-1.0.15/general/NonOverlapRegions.cpp... Preprocessing /build/libstatgen-1.0.15/general/NonOverlapRegions.h... Parsing file /build/libstatgen-1.0.15/general/NonOverlapRegions.h... Preprocessing /build/libstatgen-1.0.15/general/PackedVector.h... Parsing file /build/libstatgen-1.0.15/general/PackedVector.h... Preprocessing /build/libstatgen-1.0.15/general/Parameters.cpp... Parsing file /build/libstatgen-1.0.15/general/Parameters.cpp... Preprocessing /build/libstatgen-1.0.15/general/Parameters.h... Parsing file /build/libstatgen-1.0.15/general/Parameters.h... Preprocessing /build/libstatgen-1.0.15/general/Pedigree.cpp... Parsing file /build/libstatgen-1.0.15/general/Pedigree.cpp... Preprocessing /build/libstatgen-1.0.15/general/Pedigree.h... Parsing file /build/libstatgen-1.0.15/general/Pedigree.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeAlleleFreq.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeAlleleFreq.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreeAlleleFreq.h... Parsing file /build/libstatgen-1.0.15/general/PedigreeAlleleFreq.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeAlleles.h... Parsing file /build/libstatgen-1.0.15/general/PedigreeAlleles.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeDescription.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeDescription.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreeDescription.h... Parsing file /build/libstatgen-1.0.15/general/PedigreeDescription.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeFamily.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeFamily.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreeFamily.h... Parsing file /build/libstatgen-1.0.15/general/PedigreeFamily.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeGlobals.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeGlobals.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreeGlobals.h... Parsing file /build/libstatgen-1.0.15/general/PedigreeGlobals.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeLoader.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeLoader.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreePerson.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreePerson.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreePerson.h... Parsing file /build/libstatgen-1.0.15/general/PedigreePerson.h... Preprocessing /build/libstatgen-1.0.15/general/PedigreeTrim.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeTrim.cpp... Preprocessing /build/libstatgen-1.0.15/general/PedigreeTwin.cpp... Parsing file /build/libstatgen-1.0.15/general/PedigreeTwin.cpp... Preprocessing /build/libstatgen-1.0.15/general/Performance.h... Parsing file /build/libstatgen-1.0.15/general/Performance.h... Preprocessing /build/libstatgen-1.0.15/general/PhoneHome.cpp... Parsing file /build/libstatgen-1.0.15/general/PhoneHome.cpp... Preprocessing /build/libstatgen-1.0.15/general/PhoneHome.h... Parsing file /build/libstatgen-1.0.15/general/PhoneHome.h... Preprocessing /build/libstatgen-1.0.15/general/QuickIndex.cpp... Parsing file /build/libstatgen-1.0.15/general/QuickIndex.cpp... Preprocessing /build/libstatgen-1.0.15/general/QuickIndex.h... Parsing file /build/libstatgen-1.0.15/general/QuickIndex.h... Preprocessing /build/libstatgen-1.0.15/general/Random.cpp... Parsing file /build/libstatgen-1.0.15/general/Random.cpp... Preprocessing /build/libstatgen-1.0.15/general/Random.h... Parsing file /build/libstatgen-1.0.15/general/Random.h... Preprocessing /build/libstatgen-1.0.15/general/ReferenceSequence.cpp... Parsing file /build/libstatgen-1.0.15/general/ReferenceSequence.cpp... Preprocessing /build/libstatgen-1.0.15/general/ReferenceSequence.h... Parsing file /build/libstatgen-1.0.15/general/ReferenceSequence.h... Preprocessing /build/libstatgen-1.0.15/general/ReusableVector.h... Parsing file /build/libstatgen-1.0.15/general/ReusableVector.h... Preprocessing /build/libstatgen-1.0.15/general/SimpleStats.h... Parsing file /build/libstatgen-1.0.15/general/SimpleStats.h... Preprocessing /build/libstatgen-1.0.15/general/SmithWaterman.cpp... Parsing file /build/libstatgen-1.0.15/general/SmithWaterman.cpp... Preprocessing /build/libstatgen-1.0.15/general/SmithWaterman.h... Parsing file /build/libstatgen-1.0.15/general/SmithWaterman.h... Preprocessing /build/libstatgen-1.0.15/general/Sort.cpp... Parsing file /build/libstatgen-1.0.15/general/Sort.cpp... Preprocessing /build/libstatgen-1.0.15/general/Sort.h... Parsing file /build/libstatgen-1.0.15/general/Sort.h... Preprocessing /build/libstatgen-1.0.15/general/StatGenStatus.cpp... Parsing file /build/libstatgen-1.0.15/general/StatGenStatus.cpp... Preprocessing /build/libstatgen-1.0.15/general/StatGenStatus.h... Parsing file /build/libstatgen-1.0.15/general/StatGenStatus.h... Preprocessing /build/libstatgen-1.0.15/general/STLUtilities.cpp... Parsing file /build/libstatgen-1.0.15/general/STLUtilities.cpp... Preprocessing /build/libstatgen-1.0.15/general/STLUtilities.h... Parsing file /build/libstatgen-1.0.15/general/STLUtilities.h... Preprocessing /build/libstatgen-1.0.15/general/String.cpp... Parsing file /build/libstatgen-1.0.15/general/String.cpp... Preprocessing /build/libstatgen-1.0.15/general/StringAlias.cpp... Parsing file /build/libstatgen-1.0.15/general/StringAlias.cpp... Preprocessing /build/libstatgen-1.0.15/general/StringAlias.h... Parsing file /build/libstatgen-1.0.15/general/StringAlias.h... Preprocessing /build/libstatgen-1.0.15/general/StringArray.cpp... Parsing file /build/libstatgen-1.0.15/general/StringArray.cpp... Preprocessing /build/libstatgen-1.0.15/general/StringArray.h... Parsing file /build/libstatgen-1.0.15/general/StringArray.h... Preprocessing /build/libstatgen-1.0.15/general/StringBasics.cpp... Parsing file /build/libstatgen-1.0.15/general/StringBasics.cpp... Preprocessing /build/libstatgen-1.0.15/general/StringBasics.h... Parsing file /build/libstatgen-1.0.15/general/StringBasics.h... Preprocessing /build/libstatgen-1.0.15/general/StringHash.cpp... Parsing file /build/libstatgen-1.0.15/general/StringHash.cpp... Preprocessing /build/libstatgen-1.0.15/general/StringHash.h... Parsing file /build/libstatgen-1.0.15/general/StringHash.h... Preprocessing /build/libstatgen-1.0.15/general/StringMap.cpp... Parsing file /build/libstatgen-1.0.15/general/StringMap.cpp... Preprocessing /build/libstatgen-1.0.15/general/StringMap.h... Parsing file /build/libstatgen-1.0.15/general/StringMap.h... Preprocessing /build/libstatgen-1.0.15/general/Tabix.cpp... Parsing file /build/libstatgen-1.0.15/general/Tabix.cpp... Preprocessing /build/libstatgen-1.0.15/general/Tabix.h... Parsing file /build/libstatgen-1.0.15/general/Tabix.h... Preprocessing /build/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Parsing file /build/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/Chromosome_test.cpp... Parsing file /build/libstatgen-1.0.15/general/test/Chromosome_test.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.h... Parsing file /build/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/dbsnp/Main.cpp... Parsing file /build/libstatgen-1.0.15/general/test/dbsnp/Main.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/GenomeSequence_test.cpp... Parsing file /build/libstatgen-1.0.15/general/test/GenomeSequence_test.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/GreedyTupleAligner_test.cpp... Parsing file /build/libstatgen-1.0.15/general/test/GreedyTupleAligner_test.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/gtest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/gtest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.h... Parsing file /build/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Parsing file /build/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Parsing file /build/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.h... Parsing file /build/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Parsing file /build/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.h... Parsing file /build/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/STLUtilities_test.cpp... Parsing file /build/libstatgen-1.0.15/general/test/STLUtilities_test.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/string/StringTest.cpp... Parsing file /build/libstatgen-1.0.15/general/test/string/StringTest.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/string/StringTest.h... Parsing file /build/libstatgen-1.0.15/general/test/string/StringTest.h... Preprocessing /build/libstatgen-1.0.15/general/test/trimSequence/TrimSequence.cpp... Parsing file /build/libstatgen-1.0.15/general/test/trimSequence/TrimSequence.cpp... Preprocessing /build/libstatgen-1.0.15/general/test/TrimSequence_test.cpp... Parsing file /build/libstatgen-1.0.15/general/test/TrimSequence_test.cpp... Preprocessing /build/libstatgen-1.0.15/general/TrimSequence.h... Parsing file /build/libstatgen-1.0.15/general/TrimSequence.h... Preprocessing /build/libstatgen-1.0.15/general/UncompressedFileType.cpp... Parsing file /build/libstatgen-1.0.15/general/UncompressedFileType.cpp... Preprocessing /build/libstatgen-1.0.15/general/UncompressedFileType.h... Parsing file /build/libstatgen-1.0.15/general/UncompressedFileType.h... Preprocessing /build/libstatgen-1.0.15/general/UnitTest.h... Parsing file /build/libstatgen-1.0.15/general/UnitTest.h... Preprocessing /build/libstatgen-1.0.15/glf/GlfException.cpp... Parsing file /build/libstatgen-1.0.15/glf/GlfException.cpp... Preprocessing /build/libstatgen-1.0.15/glf/GlfException.h... Parsing file /build/libstatgen-1.0.15/glf/GlfException.h... Preprocessing /build/libstatgen-1.0.15/glf/GlfFile.cpp... Parsing file /build/libstatgen-1.0.15/glf/GlfFile.cpp... Preprocessing /build/libstatgen-1.0.15/glf/GlfFile.h... Parsing file /build/libstatgen-1.0.15/glf/GlfFile.h... Preprocessing /build/libstatgen-1.0.15/glf/GlfHeader.cpp... Parsing file /build/libstatgen-1.0.15/glf/GlfHeader.cpp... Preprocessing /build/libstatgen-1.0.15/glf/GlfHeader.h... Parsing file /build/libstatgen-1.0.15/glf/GlfHeader.h... Preprocessing /build/libstatgen-1.0.15/glf/GlfRecord.cpp... Parsing file /build/libstatgen-1.0.15/glf/GlfRecord.cpp... Preprocessing /build/libstatgen-1.0.15/glf/GlfRecord.h... Parsing file /build/libstatgen-1.0.15/glf/GlfRecord.h... Preprocessing /build/libstatgen-1.0.15/glf/GlfRefSection.cpp... Parsing file /build/libstatgen-1.0.15/glf/GlfRefSection.cpp... Preprocessing /build/libstatgen-1.0.15/glf/GlfRefSection.h... Parsing file /build/libstatgen-1.0.15/glf/GlfRefSection.h... Preprocessing /build/libstatgen-1.0.15/glf/GlfStatus.cpp... Parsing file /build/libstatgen-1.0.15/glf/GlfStatus.cpp... Preprocessing /build/libstatgen-1.0.15/glf/GlfStatus.h... Parsing file /build/libstatgen-1.0.15/glf/GlfStatus.h... Preprocessing /build/libstatgen-1.0.15/glf/test/Main.cpp... Parsing file /build/libstatgen-1.0.15/glf/test/Main.cpp... Preprocessing /build/libstatgen-1.0.15/glf/test/ReadFiles.cpp... Parsing file /build/libstatgen-1.0.15/glf/test/ReadFiles.cpp... Preprocessing /build/libstatgen-1.0.15/glf/test/ReadFiles.h... Parsing file /build/libstatgen-1.0.15/glf/test/ReadFiles.h... Preprocessing /build/libstatgen-1.0.15/glf/test/Validate.cpp... Parsing file /build/libstatgen-1.0.15/glf/test/Validate.cpp... Preprocessing /build/libstatgen-1.0.15/glf/test/Validate.h... Parsing file /build/libstatgen-1.0.15/glf/test/Validate.h... Preprocessing /build/libstatgen-1.0.15/glf/test/WriteFiles.cpp... Parsing file /build/libstatgen-1.0.15/glf/test/WriteFiles.cpp... Preprocessing /build/libstatgen-1.0.15/glf/test/WriteFiles.h... Parsing file /build/libstatgen-1.0.15/glf/test/WriteFiles.h... Preprocessing /build/libstatgen-1.0.15/samtools/bam.h... Parsing file /build/libstatgen-1.0.15/samtools/bam.h... Preprocessing /build/libstatgen-1.0.15/samtools/bgzf.c... Parsing file /build/libstatgen-1.0.15/samtools/bgzf.c... Preprocessing /build/libstatgen-1.0.15/samtools/bgzf.h... Parsing file /build/libstatgen-1.0.15/samtools/bgzf.h... Preprocessing /build/libstatgen-1.0.15/samtools/khash.h... Parsing file /build/libstatgen-1.0.15/samtools/khash.h... Preprocessing /build/libstatgen-1.0.15/samtools/knetfile.c... Parsing file /build/libstatgen-1.0.15/samtools/knetfile.c... Preprocessing /build/libstatgen-1.0.15/samtools/knetfile.h... Parsing file /build/libstatgen-1.0.15/samtools/knetfile.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file bam/BamIndex.cpp... Generating code for file bam/BamIndex.h... Generating code for file bam/BamInterface.cpp... Generating code for file bam/BamInterface.h... Generating code for file bam/CigarHelper.cpp... Generating code for file bam/CigarHelper.h... Generating code for file bam/examples/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/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/test/Modify.cpp... Generating code for file bam/test/Modify.h... Generating code for file bam/test/ModifyVar.cpp... Generating code for file bam/test/ModifyVar.h... Generating code for file bam/test/ReadFiles.cpp... Generating code for file glf/test/ReadFiles.cpp... Generating code for file bam/test/ReadFiles.h... Generating code for file glf/test/ReadFiles.h... Generating code for file bam/test/SamFileTest.cpp... Generating code for file bam/test/SamFileTest.h... Generating code for file bam/test/ShiftIndels.cpp... Generating code for file bam/test/ShiftIndels.h... Generating code for file bam/test/TestCigarHelper.cpp... Generating code for file bam/test/TestCigarHelper.h... Generating code for file bam/test/TestEquals.cpp... Generating code for file bam/test/TestEquals.h... Generating code for file bam/test/TestFilter.cpp... Generating code for file bam/test/TestFilter.h... Generating code for file bam/test/TestPileup.cpp... Generating code for file bam/test/TestPileup.h... Generating code for file bam/test/TestPosList.cpp... Generating code for file bam/test/TestPosList.h... Generating code for file bam/test/TestSamCoordOutput.cpp... Generating code for file bam/test/TestSamCoordOutput.h... Generating code for file bam/test/TestSamRecordHelper.cpp... Generating code for file bam/test/TestSamRecordHelper.h... Generating code for file bam/test/TestSamRecordPool.cpp... Generating code for file bam/test/TestSamRecordPool.h... Generating code for file bam/test/TestValidate.cpp... Generating code for file bam/test/TestValidate.h... Generating code for file bam/test/ValidationTest.cpp... Generating code for file bam/test/ValidationTest.h... Generating code for file bam/test/WriteFiles.cpp... Generating code for file glf/test/WriteFiles.cpp... Generating code for file bam/test/WriteFiles.h... Generating code for file glf/test/WriteFiles.h... Generating code for file fastq/BaseComposition.cpp... Generating code for file fastq/BaseComposition.h... Generating code for file fastq/BaseCount.cpp... Generating code for file fastq/BaseCount.h... Generating code for file fastq/FastQFile.cpp... Generating code for file fastq/FastQFile.h... Generating code for file fastq/FastQStatus.cpp... Generating code for file fastq/FastQStatus.h... Generating code for file fastq/test/FastQFileTest.cpp... Generating code for file general/BaseAsciiMap.cpp... Generating code for file general/BaseAsciiMap.h... Generating code for file general/BaseQualityHelper.cpp... Generating code for file general/BaseQualityHelper.h... Generating code for file general/BaseUtilities.cpp... Generating code for file general/BaseUtilities.h... Generating code for file general/BasicHash.cpp... Generating code for file general/BasicHash.h... Generating code for file general/BgzfFileType.cpp... Generating code for file general/BgzfFileType.h... Generating code for file general/BgzfFileTypeRecovery.cpp... Generating code for file general/BgzfFileTypeRecovery.h... Generating code for file general/CharBuffer.cpp... Generating code for file general/CharBuffer.h... Generating code for file general/Chromosome.cpp... Generating code for file general/Chromosome.h... Generating code for file general/Cigar.cpp... Generating code for file general/Cigar.h... Generating code for file general/CigarRoller.cpp... Generating code for file general/CigarRoller.h... Generating code for file general/Constant.h... Generating code for file general/CSG_MD5.h... Generating code for file general/Error.cpp... Generating code for file general/Error.h... Generating code for file general/ErrorHandler.cpp... Generating code for file general/ErrorHandler.h... Generating code for file general/FileType.cpp... Generating code for file general/FileType.h... Generating code for file general/FortranFormat.cpp... Generating code for file general/FortranFormat.h... Generating code for file general/Generic.cpp... Generating code for file general/Generic.h... Generating code for file general/GenomeSequence.cpp... Generating code for file general/GenomeSequence.h... Generating code for file general/GenomeSequenceHelpers.h... Generating code for file general/GenotypeLists.cpp... Generating code for file general/GenotypeLists.h... Generating code for file general/glfHandler.cpp... Generating code for file general/glfHandler.h... Generating code for file general/GreedyTupleAligner.h... Generating code for file general/GzipFileType.cpp... Generating code for file general/GzipFileType.h... Generating code for file general/GzipHeader.cpp... Generating code for file general/GzipHeader.h... Generating code for file general/Hash.cpp... Generating code for file general/Hash.h... Generating code for file general/IndexBase.cpp... Generating code for file general/IndexBase.h... Generating code for file general/InplaceMerge.cpp... Generating code for file general/InplaceMerge.h... Generating code for file general/Input.cpp... Generating code for file general/Input.h... Generating code for file general/InputFile.cpp... Generating code for file general/InputFile.h... Generating code for file general/IntArray.cpp... Generating code for file general/IntArray.h... Generating code for file general/IntHash.cpp... Generating code for file general/IntHash.h... Generating code for file general/LongHash.h... Generating code for file general/LongInt.h... Generating code for file general/LongLongCounter.cpp... Generating code for file general/LongLongCounter.h... Generating code for file general/MapFunction.cpp... Generating code for file general/MapFunction.h... Generating code for file general/MathConstant.h... Generating code for file general/MathMatrix.cpp... Generating code for file general/MathMatrix.h... Generating code for file general/MathVector.cpp... Generating code for file general/MathVector.h... Generating code for file general/MemoryAllocators.cpp... Generating code for file general/MemoryAllocators.h... Generating code for file general/MemoryInfo.cpp... Generating code for file general/MemoryInfo.h... Generating code for file general/MemoryMap.cpp... Generating code for file general/MemoryMap.h... Generating code for file general/MemoryMapArray.cpp... Generating code for file general/MemoryMapArray.h... Generating code for file general/MiniDeflate.cpp... Generating code for file general/MiniDeflate.h... Generating code for file general/NonOverlapRegions.cpp... Generating code for file general/NonOverlapRegions.h... Generating code for file general/PackedVector.h... Generating code for file general/Parameters.cpp... Generating code for file general/Parameters.h... Generating code for file general/Pedigree.cpp... Generating code for file general/Pedigree.h... Generating code for file general/PedigreeAlleleFreq.cpp... Generating code for file general/PedigreeAlleleFreq.h... Generating code for file general/PedigreeAlleles.h... Generating code for file general/PedigreeDescription.cpp... Generating code for file general/PedigreeDescription.h... Generating code for file general/PedigreeFamily.cpp... Generating code for file general/PedigreeFamily.h... Generating code for file general/PedigreeGlobals.cpp... Generating code for file general/PedigreeGlobals.h... Generating code for file general/PedigreeLoader.cpp... Generating code for file general/PedigreePerson.cpp... Generating code for file general/PedigreePerson.h... Generating code for file general/PedigreeTrim.cpp... Generating code for file general/PedigreeTwin.cpp... Generating code for file general/Performance.h... Generating code for file general/PhoneHome.cpp... Generating code for file general/PhoneHome.h... Generating code for file general/QuickIndex.cpp... Generating code for file general/QuickIndex.h... Generating code for file general/Random.cpp... Generating code for file general/Random.h... Generating code for file general/ReferenceSequence.cpp... Generating code for file general/ReferenceSequence.h... Generating code for file general/ReusableVector.h... Generating code for file general/SimpleStats.h... Generating code for file general/SmithWaterman.cpp... Generating code for file general/SmithWaterman.h... Generating code for file general/Sort.cpp... Generating code for file general/Sort.h... Generating code for file general/StatGenStatus.cpp... Generating code for file general/StatGenStatus.h... Generating code for file general/STLUtilities.cpp... Generating code for file general/STLUtilities.h... Generating code for file general/String.cpp... Generating code for file general/StringAlias.cpp... Generating code for file general/StringAlias.h... Generating code for file general/StringArray.cpp... Generating code for file general/StringArray.h... Generating code for file general/StringBasics.cpp... Generating code for file general/StringBasics.h... Generating code for file general/StringHash.cpp... Generating code for file general/StringHash.h... Generating code for file general/StringMap.cpp... Generating code for file general/StringMap.h... Generating code for file general/Tabix.cpp... Generating code for file general/Tabix.h... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Generating code for file general/test/Chromosome_test.cpp... Generating code for file general/test/cigar/CigarRollerTest.cpp... Generating code for file general/test/cigar/CigarRollerTest.h... Generating code for file general/test/GenomeSequence_test.cpp... Generating code for file general/test/GreedyTupleAligner_test.cpp... Generating code for file general/test/gtest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.h... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Generating code for file general/test/packedVectorTest/PackedVectorTest.cpp... Generating code for file general/test/packedVectorTest/PackedVectorTest.h... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.h... Generating code for file general/test/reusableVector/ReusableVectorTest.cpp... Generating code for file general/test/reusableVector/ReusableVectorTest.h... Generating code for file general/test/STLUtilities_test.cpp... Generating code for file general/test/string/StringTest.cpp... Generating code for file general/test/string/StringTest.h... Generating code for file general/test/trimSequence/TrimSequence.cpp... Generating code for file general/test/TrimSequence_test.cpp... Generating code for file general/TrimSequence.h... Generating code for file general/UncompressedFileType.cpp... Generating code for file general/UncompressedFileType.h... Generating code for file general/UnitTest.h... Generating code for file glf/GlfException.cpp... Generating code for file glf/GlfException.h... Generating code for file glf/GlfFile.cpp... Generating code for file glf/GlfFile.h... Generating code for file glf/GlfHeader.cpp... Generating code for file glf/GlfHeader.h... Generating code for file glf/GlfRecord.cpp... Generating code for file glf/GlfRecord.h... Generating code for file glf/GlfRefSection.cpp... Generating code for file glf/GlfRefSection.h... Generating code for file glf/GlfStatus.cpp... Generating code for file glf/GlfStatus.h... Generating code for file glf/test/Validate.cpp... Generating code for file glf/test/Validate.h... Generating code for file samtools/bam.h... Generating code for file samtools/bgzf.c... Generating code for file samtools/bgzf.h... Generating code for file samtools/khash.h... Generating code for file samtools/knetfile.c... Generating code for file samtools/knetfile.h... Generating file documentation... Generating docs for file general/InputFile.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound __kstring_t... Generating docs for compound Alleles... Generating docs for compound AnalyzeClass... Generating docs for compound BamIndex... Generating docs for compound BamIndexFileTest... Generating docs for compound BamInterface... Generating docs for compound bamRecordStruct... Generating docs for compound BaseAsciiMap... Generating docs for compound BaseComposition... Generating docs for compound BaseCount... Generating docs for compound baseQualityConvertor... Generating docs for compound BaseUtilities... Generating docs for compound BasicHash... Generating docs for compound BGZF... Generating docs for compound CharBuffer... Generating docs for compound Chromosome... Generating docs for compound ChromosomeInfo... Generating docs for compound Chunk... Generating docs for compound Cigar... Generating docs for nested compound Cigar::CigarOperator... Generating docs for compound CigarHelper... Generating docs for compound CigarHelperTest... Generating docs for compound CigarRoller... Generating docs for compound CigarRollerTest... Generating docs for compound ColumnExtras... Generating docs for compound defaultPileup... Generating docs for compound DoubleParameter... Generating docs for compound emptyGenericHeader... Generating docs for compound EqualsTest... Generating docs for compound ErrorHandler... Generating docs for compound Family... Generating docs for compound FastQFile... Generating docs for compound FastQStatus... Generating docs for compound FileType... Generating docs for compound FilterTest... Generating docs for compound FortranFormat... Generating docs for compound GenericSamInterface... Generating docs for compound GenomeSequence... Generating docs for compound genomeSequenceMmapHeader... Generating docs for compound GenotypeList... Generating docs for compound glfEntry... Generating docs for compound GlfException... Generating docs for compound GlfFile... Generating docs for compound GlfFileReader... Generating docs for compound GlfFileWriter... Generating docs for compound glfHandler... Generating docs for compound GlfHeader... Generating docs for compound glfIndel... Generating docs for compound GlfRecord... Generating docs for compound GlfRefSection... Generating docs for compound GlfStatus... Generating docs for compound GlobalTestEnvironment... Generating docs for compound GreedyTupleAligner... Generating docs for compound GzipHeader... Generating docs for compound HiddenDouble... Generating docs for compound HiddenInteger... Generating docs for compound HiddenString... Generating docs for compound HiddenSwitch... Generating docs for compound IFILE_Test... Generating docs for compound IndexBase... Generating docs for nested compound IndexBase::Bin... Generating docs for nested compound IndexBase::Reference... Generating docs for compound InputFile... Generating docs for compound IntArray... Generating docs for compound IntHash... Generating docs for compound IntParameter... Generating docs for compound knetFile_s... Generating docs for compound ListParameter... Generating docs for compound LongCounter... Generating docs for compound LongHash... Generating docs for compound LongParamContainer... Generating docs for compound LongParameterList... Generating docs for compound LongParameters... Generating docs for compound MarkerInfo... Generating docs for compound Matrix... Generating docs for compound MD5_CTX... Generating docs for compound MemoryMap... Generating docs for compound MemoryMapArray... Generating docs for compound MemoryMapArrayHeader... Generating docs for compound MemoryMapArrayTest... Generating docs for compound MemoryMapGenericHeader... Generating docs for compound MiniDeflate... Generating docs for compound MockGenomeSequence... Generating docs for compound modify... Generating docs for compound modifyVar... Generating docs for compound NonOverlapRegionPos... Generating docs for compound NonOverlapRegions... Generating docs for compound NonOverlapRegionsTest... Generating docs for compound OptionList... Generating docs for compound PackedArrayTest... Generating docs for compound PackedRead... Generating docs for compound PackedSequenceData... Generating docs for compound PackedVector... Generating docs for compound Parameter... Generating docs for compound ParameterList... Generating docs for compound Pedigree... Generating docs for compound PedigreeDescription... Generating docs for compound PedigreeGlobals... Generating docs for compound PedigreeKey... Generating docs for compound Person... Generating docs for compound PhoneHome... Generating docs for compound Pileup... Generating docs for compound PileupElement... Generating docs for compound PileupElementBaseQual... Generating docs for compound PileupHelper... Generating docs for compound PosList... Generating docs for compound QuickIndex... Generating docs for compound Random... Generating docs for compound ReferenceSequenceTest... Generating docs for compound ReusableVector... Generating docs for compound ReusableVectorTest... Generating docs for compound ReusableVectorTestDataType... Generating docs for compound RunningStat... Generating docs for compound SamCoordOutput... Generating docs for compound SamCoordOutputTest... Generating docs for compound SamFile... Generating docs for compound SamFileHeader... Generating docs for compound SamFileReader... Generating docs for compound SamFileWriter... Generating docs for compound SamFilter... Generating docs for compound SamFlag... Generating docs for compound SamHeaderHD... Generating docs for compound SamHeaderPG... Generating docs for compound SamHeaderRecord... Generating docs for compound SamHeaderRG... Generating docs for compound SamHeaderSQ... Generating docs for compound SamHeaderTag... Generating docs for compound SamHelper... Generating docs for compound SamInterface... Generating docs for compound SamQuerySeqWithRef... Generating docs for compound SamQuerySeqWithRefIter... Generating docs for compound SamRecord... Generating docs for compound SamRecordHelper... Generating docs for compound SamRecordHelperTest... Generating docs for compound SamRecordPool... Generating docs for compound SamRecordPoolTest... Generating docs for compound SamReferenceInfo... Generating docs for compound SamSingleBaseMatchInfo... Generating docs for compound SamStatistics... Generating docs for compound SamTags... Generating docs for compound SamValidationError... Generating docs for compound SamValidationErrors... Generating docs for compound SamValidator... Generating docs for compound SetParameter... Generating docs for compound 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 concept documentation... 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/baseUtilitiesTest Generating dependency graph for directory general/test/cigar Generating dependency graph for directory general/test/dbsnp Generating dependency graph for directory bam/examples 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/memoryMapArrayTest Generating dependency graph for directory general/test/nonOverlapRegions Generating dependency graph for directory general/test/packedVectorTest Generating dependency graph for directory bam/examples/pileup Generating dependency graph for directory bam/examples/printRefPositions Generating dependency graph for directory general/test/referenceSequenceTest Generating dependency graph for directory general/test/reusableVector Generating dependency graph for directory general/test/string Generating dependency graph for directory bam/test Generating dependency graph for directory fastq/test Generating dependency graph for directory general/test Generating dependency graph for directory glf/test Generating dependency graph for directory general/test/trimSequence Generating index page... Generating page index... Generating module index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating filsh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found e index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 16 parallel threads... Running dot for graph 1/301 Running dot for graph 2/301 Running dot for graph 3/301 Running dot for graph 4/301 Running dot for graph 5/301 Running dot for graph 6/301 Running dot for graph 7/301 Running dot for graph 8/301 Running dot for graph 9/301 Running dot for graph 10/301 Running dot for graph 11/301 Running dot for graph 12/301 Running dot for graph 13/301 Running dot for graph 14/301 Running dot for graph 15/301 Running dot for graph 16/301 Running dot for graph 17/301 Running dot for graph 18/301 Running dot for graph 19/301 Running dot for graph 20/301 Running dot for graph 21/301 Running dot for graph 22/301 Running dot for graph 23/301 Running dot for graph 24/301 Running dot for graph 25/301 Running dot for graph 26/301 Running dot for graph 27/301 Running dot for graph 28/301 Running dot for graph 29/301 Running dot for graph 30/301 Running dot for graph 31/301 Running dot for graph 32/301 Running dot for graph 33/301 Running dot for graph 34/301 Running dot for graph 35/301 Running dot for graph 36/301 Running dot for graph 37/301 Running dot for graph 38/301 Running dot for graph 39/301 Running dot for graph 40/301 Running dot for graph 41/301 Running dot for graph 42/301 Running dot for graph 43/301 Running dot for graph 44/301 Running dot for graph 45/301 Running dot for graph 46/301 Running dot for graph 47/301 Running dot for graph 48/301 Running dot for graph 49/301 Running dot for graph 50/301 Running dot for graph 51/301 Running dot for graph 52/301 Running dot for graph 53/301 Running dot for graph 54/301 Running dot for graph 55/301 Running dot for graph 56/301 Running dot for graph 57/301 Running dot for graph 58/301 Running dot for graph 59/301 Running dot for graph 60/301 Running dot for graph 61/301 Running dot for graph 62/301 Running dot for graph 63/301 Running dot for graph 64/301 Running dot for graph 65/301 Running dot for graph 66/301 Running dot for graph 67/301 Running dot for graph 68/301 Running dot for graph 69/301 Running dot for graph 70/301 Running dot for graph 71/301 Running dot for graph 72/301 Running dot for graph 73/301 Running dot for graph 74/301 Running dot for graph 75/301 Running dot for graph 76/301 Running dot for graph 77/301 Running dot for graph 78/301 Running dot for graph 79/301 Running dot for graph 80/301 Running dot for graph 81/301 Running dot for graph 82/301 Running dot for graph 83/301 Running dot for graph 84/301 Running dot for graph 85/301 Running dot for graph 86/301 Running dot for graph 87/301 Running dot for graph 88/301 Running dot for graph 89/301 Running dot for graph 90/301 Running dot for graph 91/301 Running dot for graph 92/301 Running dot for graph 93/301 Running dot for graph 94/301 Running dot for graph 95/301 Running dot for graph 96/301 Running dot for graph 97/301 Running dot for graph 98/301 Running dot for graph 99/301 Running dot for graph 100/301 Running dot for graph 101/301 Running dot for graph 102/301 Running dot for graph 103/301 Running dot for graph 104/301 Running dot for graph 105/301 Running dot for graph 106/301 Running dot for graph 107/301 Running dot for graph 108/301 Running dot for graph 109/301 Running dot for graph 110/301 Running dot for graph 111/301 Running dot for graph 112/301 Running dot for graph 113/301 Running dot for graph 114/301 Running dot for graph 115/301 Running dot for graph 116/301 Running dot for graph 117/301 Running dot for graph 118/301 Running dot for graph 119/301 Running dot for graph 120/301 Running dot for graph 121/301 Running dot for graph 122/301 Running dot for graph 123/301 Running dot for graph 124/301 Running dot for graph 125/301 Running dot for graph 126/301 Running dot for graph 127/301 Running dot for graph 128/301 Running dot for graph 129/301 Running dot for graph 130/301 Running dot for graph 131/301 Running dot for graph 132/301 Running dot for graph 133/301 Rsh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found unning dot for graph 134/301 Running dot for graph 135/301 Running dot for graph 136/301 Running dot for graph 137/301 Running dot for graph 138/301 Running dot for graph 139/301 Running dot for graph 140/301 Running dot for graph 141/301 Running dot for graph 142/301 Running dot for graph 143/301 Running dot for graph 144/301 Running dot for graph 145/301 Running dot for graph 146/301 Running dot for graph 147/301 Running dot for graph 148/301 Running dot for graph 149/301 Running dot for graph 150/301 Running dot for graph 151/301 Running dot for graph 152/301 Running dot for graph 153/301 Running dot for graph 154/301 Running dot for graph 155/301 Running dot for graph 156/301 Running dot for graph 157/301 Running dot for graph 158/301 Running dot for graph 159/301 Running dot for graph 160/301 Running dot for graph 161/301 Running dot for graph 162/301 Running dot for graph 163/301 Running dot for graph 164/301 Running dot for graph 165/301 Running dot for graph 166/301 Running dot for graph 167/301 Running dot for graph 168/301 Running dot for graph 169/301 Running dot for graph 170/301 Running dot for graph 171/301 Running dot for graph 172/301 Running dot for graph 173/301 Running dot for graph 174/301 Running dot for graph 175/301 Running dot for graph 176/301 Running dot for graph 177/301 Running dot for graph 178/301 Running dot for graph 179/301 Running dot for graph 180/301 Running dot for graph 181/301 Running dot for graph 182/301 Running dot for graph 183/301 Running dot for graph 184/301 Running dot for graph 185/301 Running dot for graph 186/301 Running dot for graph 187/301 Running dot for graph 188/301 Running dot for graph 189/301 Running dot for graph 190/301 Running dot for graph 191/301 Running dot for graph 192/301 Running dot for graph 193/301 Running dot for graph 194/301 Running dot for graph 195/301 Running dot for graph 196/301 Running dot for graph 197/301 Running dot for graph 198/301 Running dot for graph 199/301 Running dot for graph 200/301 Running dot for graph 201/301 Running dot for graph 202/301 Running dot for graph 203/301 Running dot for graph 204/301 Running dot for graph 205/301 Running dot for graph 206/301 Running dot for graph 207/301 Running dot for graph 208/301 Running dot for graph 209/301 Running dot for graph 210/301 Running dot for graph 211/301 Running dot for graph 212/301 Running dot for graph 213/301 Running dot for graph 214/301 Running dot for graph 215/301 Running dot for graph 216/301 Running dot for graph 217/301 Running dot for graph 218/301 Running dot for graph 219/301 Running dot for graph 220/301 Running dot for graph 221/301 Running dot for graph 222/301 Running dot for graph 223/301 Running dot for graph 224/301 Running dot for graph 225/301 Running dot for graph 226/301 Running dot for graph 227/301 Running dot for graph 228/301 Running dot for graph 229/301 Running dot for graph 230/301 Running dot for graph 231/301 Running dot for graph 232/301 Running dot for graph 233/301 Running dot for graph 234/301 Running dot for graph 235/301 Running dot for graph 236/301 Running dot for graph 237/301 Running dot for graph 238/301 Running dot for graph 239/301 Running dot for graph 240/301 Running dot for graph 241/301 Running dot for graph 242/301 Running dot for graph 243/301 Running dot for graph 244/301 Running dot for graph 245/301 Running dot for graph 246/301 Running dot for graph 247/301 Running dot for graph 248/301 Running dot for graph 249/301 Running dot for graph 250/301 Running dot for graph 251/301 Running dot for graph 252/301 Running dot for graph 253/301 Running dot for graph 254/301 Running dot for graph 255/301 Running dot for graph 256/301 Running dot for graph 257/301 Running dot for graph 258/301 Running dot for graph 259/301 Running dot for graph 260/301 Running dot for graph 261/301 Running dot for graph 262/301 Running dot for graph 263/301 Running dot for graph 264/301 Running dot for graph 265/301 Running dot for graph 266/301 Running dot for graph 267/301 Running dot for graph 268/301 Running dot for graph 269/301 Running dot for gsh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: sh: 1: dot: not found dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found sh: 1: dot: not found raph 270/301 Running dot for graph 271/301 Running dot for graph 272/301 Running dot for graph 273/301 Running dot for graph 274/301 Running dot for graph 275/301 Running dot for graph 276/301 Running dot for graph 277/301 Running dot for graph 278/301 Running dot for graph 279/301 Running dot for graph 280/301 Running dot for graph 281/301 Running dot for graph 282/301 Running dot for graph 283/301 Running dot for graph 284/301 Running dot for graph 285/301 Running dot for graph 286/301 Running dot for graph 287/301 Running dot for graph 288/301 Running dot for graph 289/301 Running dot for graph 290/301 Running dot for graph 291/301 Running dot for graph 292/301 Running dot for graph 293/301 Running dot for graph 294/301 Running dot for graph 295/301 Running dot for graph 296/301 Running dot for graph 297/301 Running dot for graph 298/301 Running dot for graph 299/301 Running dot for graph 300/301 Running dot for graph 301/301 Patching output file 1/113 Patching output file 2/113 Patching output file 3/113 Patching output file 4/113 Patching output file 5/113 Patching output file 6/113 Patching output file 7/113 Patching output file 8/113 Patching output file 9/113 Patching output file 10/113 Patching output file 11/113 Patching output file 12/113 Patching output file 13/113 Patching output file 14/113 Patching output file 15/113 Patching output file 16/113 Patching output file 17/113 Patching output file 18/113 Patching output file 19/113 Patching output file 20/113 Patching output file 21/113 Patching output file 22/113 Patching output file 23/113 Patching output file 24/113 Patching output file 25/113 Patching output file 26/113 Patching output file 27/113 Patching output file 28/113 Patching output file 29/113 Patching output file 30/113 Patching output file 31/113 Patching output file 32/113 Patching output file 33/113 Patching output file 34/113 Patching output file 35/113 Patching output file 36/113 Patching output file 37/113 Patching output file 38/113 Patching output file 39/113 Patching output file 40/113 Patching output file 41/113 Patching output file 42/113 Patching output file 43/113 Patching output file 44/113 Patching output file 45/113 Patching output file 46/113 Patching output file 47/113 Patching output file 48/113 Patching output file 49/113 Patching output file 50/113 Patching output file 51/113 Patching output file 52/113 Patching output file 53/113 Patching output file 54/113 Patching output file 55/113 Patching output file 56/113 Patching output file 57/113 Patching output file 58/113 Patching output file 59/113 Patching output file 60/113 Patching output file 61/113 Patching output file 62/113 Patching output file 63/113 Patching output file 64/113 Patching output file 65/113 Patching output file 66/113 Patching output file 67/113 Patching output file 68/113 Patching output file 69/113 Patching output file 70/113 Patching output file 71/113 Patching output file 72/113 Patching output file 73/113 Patching output file 74/113 Patching output file 75/113 Patching output file 76/113 Patching output file 77/113 Patching output file 78/113 Patching output file 79/113 Patching output file 80/113 Patching output file 81/113 Patching output file 82/113 Patching output file 83/113 Patching output file 84/113 Patching output file 85/113 Patching output file 86/113 Patching output file 87/113 Patching output file 88/113 Patching output file 89/113 Patching output file 90/113 Patching output file 91/113 Patching output file 92/113 Patching output file 93/113 Patching output file 94/113 Patching output file 95/113 Patching output file 96/113 Patching output file 97/113 Patching output file 98/113 Patching output file 99/113 Patching output file 100/113 Patching output file 101/113 Patching output file 102/113 Patching output file 103/113 Patching output file 104/113 Patching output file 105/113 Patching output file 106/113 Patching output file 107/113 Patching output file 108/113 Patching output file 109/113 Patching output file 110/113 Patching output file 111/113 Patching output file 112/113 Patching output file 113/113 lookup cache used 11613/65536 hits=120630 misses=12179 finished... make[1]: Leaving directory '/build/libstatgen-1.0.15' debian/rules override_dh_auto_test make[1]: Entering directory '/build/libstatgen-1.0.15' echo "Build time test is not run here." Build time test is not run here. make[1]: Leaving directory '/build/libstatgen-1.0.15' create-stamp debian/debhelper-build-stamp dh_testroot -O--no-parallel dh_prep -O--no-parallel debian/rules override_dh_auto_install make[1]: Entering directory '/build/libstatgen-1.0.15' mkdir -p debian/libstatgen-dev/usr/include/libStatGen/ cp -L include/* debian/libstatgen-dev/usr/include/libStatGen/ ln -s libStatGen.so.1 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/libstatgen1/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-1.0.15/libStatGen.so.1 debian/libstatgen1/usr/lib/x86_64-linux-gnu PKGDEV=libstatgen-dev PKGSHL=libstatgen1 mv: cannot stat './libStatGen.la': No such file or directory make[1]: Leaving directory '/build/libstatgen-1.0.15' dh_installdocs -O--no-parallel dh_installchangelogs -O--no-parallel dh_installsystemduser -O--no-parallel dh_perl -O--no-parallel dh_link -O--no-parallel dh_strip_nondeterminism -O--no-parallel dh_compress -O--no-parallel dh_fixperms -O--no-parallel dh_missing -O--no-parallel dh_dwz -a -O--no-parallel dh_strip -a -O--no-parallel dh_makeshlibs -a -O--no-parallel dh_shlibdeps -a -O--no-parallel dpkg-shlibdeps: warning: symbol gzclose used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzrewind used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateInit2_ used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gztell64 used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzdopen used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzwrite used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateInit2_ used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzeof used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflate used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v to see them all) dh_installdeb -O--no-parallel dh_gencontrol -O--no-parallel dh_md5sums -O--no-parallel dh_builddeb -O--no-parallel dpkg-deb: building package 'libstatgen-dev' in '../libstatgen-dev_1.0.15-6_amd64.deb'. dpkg-deb: building package 'libstatgen1' in '../libstatgen1_1.0.15-6_amd64.deb'. dpkg-deb: building package 'libstatgen1-dbgsym' in '../libstatgen1-dbgsym_1.0.15-6_amd64.deb'. dpkg-deb: building package 'libstatgen-doc' in '../libstatgen-doc_1.0.15-6_all.deb'. dpkg-genbuildinfo --build=binary -O../libstatgen_1.0.15-6_amd64.buildinfo dpkg-genchanges --build=binary -O../libstatgen_1.0.15-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/1026975 and its subdirectories I: Current time: Tue Apr 18 06:49:08 -12 2023 I: pbuilder-time-stamp: 1681843748