Thu May 9 11:43:48 UTC 2024 I: starting to build libstatgen/trixie/amd64 on jenkins on '2024-05-09 11:43' Thu May 9 11:43:48 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_2/6117/console.log Thu May 9 11:43:48 UTC 2024 I: Downloading source for trixie/libstatgen=1.0.15-7 --2024-05-09 11:43:48-- http://deb.debian.org/debian/pool/main/libs/libstatgen/libstatgen_1.0.15-7.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2297 (2.2K) [text/prs.lines.tag] Saving to: ‘libstatgen_1.0.15-7.dsc’ 0K .. 100% 287M=0s 2024-05-09 11:43:48 (287 MB/s) - ‘libstatgen_1.0.15-7.dsc’ saved [2297/2297] Thu May 9 11:43:48 UTC 2024 I: libstatgen_1.0.15-7.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libstatgen Binary: libstatgen1, libstatgen-dev, libstatgen-doc Architecture: any-amd64 all Version: 1.0.15-7 Maintainer: Debian Med Packaging Team Uploaders: Dylan Aïssi Homepage: https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/libstatgen Vcs-Git: https://salsa.debian.org/med-team/libstatgen.git Build-Depends: debhelper-compat (= 13), doxygen, libssl-dev, zlib1g-dev, d-shlibs Package-List: libstatgen-dev deb libdevel optional arch=any-amd64 libstatgen-doc deb doc optional arch=all libstatgen1 deb libs optional arch=any-amd64 Checksums-Sha1: ae8fc23f436aa9cb251fa997e96f79e49996c6d3 560782 libstatgen_1.0.15.orig.tar.gz ab511145885c7843e4708b1da6160654b32e9c84 21064 libstatgen_1.0.15-7.debian.tar.xz Checksums-Sha256: 075dcd891409c48d76c0c66186c0cc479bc3cd50bba093e7f318e1d1d19961ff 560782 libstatgen_1.0.15.orig.tar.gz f960ee08a99e6a14656f9c91fc9945a8ba1c405d330c91217b98ae35a459e531 21064 libstatgen_1.0.15-7.debian.tar.xz Files: e26eaeb3cdb938328c7b0b43b674a1c8 560782 libstatgen_1.0.15.orig.tar.gz 01846a78223e5493d7c71c37ad94ddd0 21064 libstatgen_1.0.15-7.debian.tar.xz Dgit: 89228ba886111ee941830bf958d3403104ee4640 debian archive/debian/1.0.15-7 https://git.dgit.debian.org/libstatgen -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmTnJqYUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdpoMw/9E7nn1moD2chZHD9BIlFPP3taeS0R iaSO1hnvwj+hyqZsqwd8Y9LsWvpDJtemB1zcFzq8KMOidN7L8chYs06TTFU0Sn8b Sz5y0ZefRWEXc/xl2pGZ9zalrXAkIfP/hc4aOZzko8FAnuWzfZLYQXIk76dVVo90 4eyROZTaCR9gugLCCh+49KhRBH27KoPZSb3FtBECWxbSfEGK51rzKlU/3ytUKDvs 0typwwYuo6bhau85e6W48RGhLcum2t4E8Od6KO/blJROyX9y1H6ZwQ76MiMP+Him Qp3mGa4C8U0zh+mKr6Xui7lvbcMvyd3K2toPnORAvhLkar7Jj+1SmH7fZ3O9JgsO zW+naJvJgF3CfeGdX1cLHi529bbH4wM/qDnNS737pCHk9O5wgMmpOoAKrTyRIDPp buGXJfdKnb6kB73U8NJesK9RXcu/tVHTV0rAxC/Mx10SfrhP4D1LmqgfUR/DLvNv 3Drhwa5SP/UK+XYI6+TxWHwNsGJy2/51SxtfyIOokge7xB0BJJTZ8ocs1b3amGeU UpTkkFYpga7v02YTkXY6k2P5Xfw5KVtTWfgcw6qQEr3UFdbPQW9pCGxptc4P7JDw AhIhPQkUuNp9T+2uJxNTg+0tuN7Eos/788Fu1btQOk+Sx6HHQhd602w8iHubOC7i /RwAICZxf+wFYso= =yQ4W -----END PGP SIGNATURE----- Thu May 9 11:43:48 UTC 2024 I: Checking whether the package is not for us Thu May 9 11:43:48 UTC 2024 I: Starting 1st build on remote node ionos5-amd64.debian.net. Thu May 9 11:43:48 UTC 2024 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Thu May 9 11:47:21 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 11 06:06:51 -12 2025 I: pbuilder-time-stamp: 1749665211 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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_1.0.15-7.dsc] I: copying [./libstatgen_1.0.15.orig.tar.gz] I: copying [./libstatgen_1.0.15-7.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Aug 24 09:45:10 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libstatgen_1.0.15-7.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_1.0.15-7.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/3759246/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=42 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='46017a69b5604cf2b8357234b9dcb6bb' 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='3759246' 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.xIoFdxpx/pbuilderrc_UlCg --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xIoFdxpx/b1 --logfile b1/build.log libstatgen_1.0.15-7.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://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 10 17:46 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3759246/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 ... 19699 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-cpp16t64{a} libclang1-16t64{a} libdebhelper-perl{a} libedit2{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libfmt9{a} libicu72{a} libllvm16t64{a} libmagic-mgc{a} libmagic1t64{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, 41 newly installed, 0 to remove and 0 not upgraded. Need to get 76.5 MB of archives. After unpacking 357 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 d-shlibs all 0.106 [10.9 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 24 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20230828-1+b1 [93.5 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libllvm16t64 amd64 1:16.0.6-26 [23.1 MB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libclang-cpp16t64 amd64 1:16.0.6-26 [11.5 MB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libclang1-16t64 amd64 1:16.0.6-26 [6591 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 doxygen amd64 1.9.8+ds-2+b1 [4913 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libssl-dev amd64 3.2.1-3 [2699 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Fetched 76.5 MB in 5s (16.6 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 ... 19699 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../15-d-shlibs_0.106_all.deb ... Unpacking d-shlibs (0.106) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../23-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../25-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-14+b1_amd64.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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_1.0.15-7_source.changes dpkg-buildpackage: info: source package libstatgen dpkg-buildpackage: info: source version 1.0.15-7 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier 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/reproducible-path/libstatgen-1.0.15' make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15/samtools' make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15/general' make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15/bam' make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15/fastq' make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15/glf' make[2]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15/vcf' rm -f libStatGen.a rm -f libStatGen_debug.a rm -f libStatGen_profile.a make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.15' 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/reproducible-path/libstatgen-1.0.15' dh_auto_build make -j1 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/libstatgen-1.0.15' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/knetfile.o -c knetfile.c ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.15/samtools' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from MemoryMapArray.h:43, from GenomeSequence.h:27, from Chromosome.h:4, from Chromosome.cpp:2: MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': GenomeSequence.h:99:31: required from here MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from MemoryMapArray.h:43, from GenomeSequence.h:27, from GenomeSequence.cpp:25: MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': GenomeSequence.h:99:31: required from here MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_1Bit, Packed1BitElementCount2Bytes, MemoryMapArrayHeader>': GenomeSequence.cpp:1217:5: required from here MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_1Bit, Packed1BitElementCount2Bytes, MemoryMapArrayHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_1Bit, Packed1BitElementCount2Bytes, MemoryMapArrayHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15/general' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamFile.h:24, from SamFile.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from GenericSamInterface.h:24, from GenericSamInterface.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from GenericSamInterface.h:24, from SamInterface.h:21, from SamInterface.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from GenericSamInterface.h:24, from BamInterface.h:21, from BamInterface.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamRecord.cpp:24: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamFile.h:24, from SamValidation.h:21, from SamValidation.cpp:20: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamStatistics.h:22, from SamStatistics.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamQuerySeqWithRefHelper.h:23, from SamQuerySeqWithRefHelper.cpp:20: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamFilter.h:21, from SamFilter.cpp:21: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from PileupElement.h:21, from PileupElement.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from PileupElement.h:21, from PileupElementBaseQual.h:22, from PileupElementBaseQual.cpp:20: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamTags.h:23, from SamTags.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from CigarHelper.h:21, from CigarHelper.cpp:20: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamRecordPool.h:22, from SamRecordPool.cpp:19: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamFile.h:24, from SamCoordOutput.h:21, from SamCoordOutput.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ g++ -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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\"" In file included from ../include/MemoryMapArray.h:43, from ../include/GenomeSequence.h:27, from SamRecord.h:23, from SamRecordHelper.h:21, from SamRecordHelper.cpp:18: ../include/MemoryMapArray.h: In instantiation of 'class MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>': ../include/GenomeSequence.h:99:31: required from here ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/MemoryMapArray.h:250:9: note: by 'MemoryMapArray, PackedAssign_4Bit, Packed4BitElementCount2Bytes, genomeSequenceMmapHeader>::create' 250 | int create(indexT elementCount, int optionalHeaderCount = 0) | ^~~~~~ ../include/MemoryMap.h:207:18: warning: 'virtual bool MemoryMap::create(size_t)' was hidden [-Woverloaded-virtual=] 207 | virtual bool create(size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ../include/MemoryMap.h:198:18: warning: 'virtual bool MemoryMap::create(const char*, size_t)' was hidden [-Woverloaded-virtual=] 198 | virtual bool create(const char * file, size_t size); | ^~~~~~ ../include/GenomeSequence.h:169:10: note: by 'bool GenomeSequence::create(bool)' 169 | bool create(bool isColor = false); | ^~~~~~ ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o ar: `u' modifier ignored since `D' is the default (see `U') make[3]: Leaving directory '/build/reproducible-path/libstatgen-1.0.15/bam' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15/fastq' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15/glf' make[3]: Entering directory '/build/reproducible-path/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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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/reproducible-path/libstatgen-1.0.15/vcf' make[2]: Leaving directory '/build/reproducible-path/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: Tag 'DOT_FONTNAME' at line 1373 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 'DOT_FONTSIZE' at line 1378 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 'DOT_TRANSPARENT' at line 1502 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: 1.9.8 Notice: Output directory 'dox' does not exist. I have created it for you. Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for files to exclude Searching for files in directory /build/reproducible-path/libstatgen-1.0.15/include Searching for files in directory /build/reproducible-path/libstatgen-1.0.15/copyrights Searching for files in directory /build/reproducible-path/libstatgen-1.0.15/dox Searching for files in directory /build/reproducible-path/libstatgen-1.0.15/dox/html Searching for files in directory /build/reproducible-path/libstatgen-1.0.15/dox/man Searching INPUT for files to process... 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Preprocessing /build/reproducible-path/libstatgen-1.0.15/fastq/FastQFile.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/fastq/FastQFile.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/fastq/FastQStatus.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/fastq/FastQStatus.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/fastq/FastQStatus.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/fastq/FastQStatus.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/fastq/test/FastQFileTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/fastq/test/FastQFileTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/BaseAsciiMap.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BaseAsciiMap.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/BaseAsciiMap.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BaseAsciiMap.h... 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Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BasicHash.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileType.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileType.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileType.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileType.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileTypeRecovery.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileTypeRecovery.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileTypeRecovery.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/BgzfFileTypeRecovery.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/CharBuffer.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/CharBuffer.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/CharBuffer.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/CharBuffer.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Chromosome.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Chromosome.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Chromosome.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Chromosome.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Cigar.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Cigar.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Cigar.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Cigar.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/CigarRoller.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/CigarRoller.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/CigarRoller.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/CigarRoller.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Constant.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Constant.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/CSG_MD5.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/CSG_MD5.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Error.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Error.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Error.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Error.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/ErrorHandler.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/ErrorHandler.cpp... 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Parsing file /build/reproducible-path/libstatgen-1.0.15/general/GenotypeLists.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/glfHandler.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/glfHandler.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/glfHandler.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/glfHandler.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/GreedyTupleAligner.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/GreedyTupleAligner.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/GzipFileType.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/GzipFileType.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/GzipFileType.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/GzipFileType.h... 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Parsing file /build/reproducible-path/libstatgen-1.0.15/general/MathMatrix.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/MathMatrix.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/MathMatrix.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/MathVector.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/MathVector.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/MathVector.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/MathVector.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/MemoryAllocators.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/MemoryAllocators.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/MemoryAllocators.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/MemoryAllocators.h... 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Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Parameters.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Parameters.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Parameters.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Pedigree.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Pedigree.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Pedigree.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Pedigree.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreeAlleleFreq.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeAlleleFreq.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreeAlleleFreq.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeAlleleFreq.h... 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Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeGlobals.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreeGlobals.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeGlobals.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreeLoader.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeLoader.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreePerson.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreePerson.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreePerson.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreePerson.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreeTrim.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeTrim.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PedigreeTwin.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PedigreeTwin.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Performance.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Performance.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PhoneHome.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PhoneHome.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/PhoneHome.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/PhoneHome.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/QuickIndex.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/QuickIndex.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/QuickIndex.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/QuickIndex.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Random.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Random.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Random.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Random.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/ReferenceSequence.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/ReferenceSequence.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/ReferenceSequence.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/ReferenceSequence.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/ReusableVector.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/ReusableVector.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/SimpleStats.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/SimpleStats.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/SmithWaterman.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/SmithWaterman.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/SmithWaterman.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/SmithWaterman.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Sort.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Sort.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Sort.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Sort.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StatGenStatus.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StatGenStatus.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StatGenStatus.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StatGenStatus.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/STLUtilities.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/STLUtilities.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/STLUtilities.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/STLUtilities.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/String.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/String.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringAlias.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringAlias.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringAlias.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringAlias.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringArray.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringArray.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringArray.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringArray.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringBasics.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringBasics.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringBasics.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringBasics.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringHash.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringHash.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringHash.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringHash.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringMap.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringMap.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/StringMap.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/StringMap.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Tabix.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Tabix.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/Tabix.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/Tabix.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/Chromosome_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/Chromosome_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/cigar/CigarRollerTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/dbsnp/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/dbsnp/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/GenomeSequence_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/GenomeSequence_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/GreedyTupleAligner_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/GreedyTupleAligner_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/gtest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/gtest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/inputFileTest/InputFileTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/packedVectorTest/PackedVectorTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/referenceSequenceTest/ReferenceSequenceTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/reusableVector/ReusableVectorTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/STLUtilities_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/STLUtilities_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/string/StringTest.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/string/StringTest.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/string/StringTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/string/StringTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/trimSequence/TrimSequence.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/trimSequence/TrimSequence.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/test/TrimSequence_test.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/test/TrimSequence_test.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/TrimSequence.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/TrimSequence.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/UncompressedFileType.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/UncompressedFileType.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/UncompressedFileType.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/UncompressedFileType.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/general/UnitTest.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/general/UnitTest.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfException.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfException.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfException.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfException.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfFile.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfFile.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfFile.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfFile.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfHeader.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfHeader.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfHeader.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfHeader.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfRecord.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfRecord.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfRecord.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfRecord.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfRefSection.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfRefSection.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfRefSection.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfRefSection.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfStatus.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfStatus.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/GlfStatus.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/GlfStatus.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/Main.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/Main.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/ReadFiles.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/ReadFiles.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/ReadFiles.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/ReadFiles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/Validate.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/Validate.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/Validate.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/Validate.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/WriteFiles.cpp... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/WriteFiles.cpp... Preprocessing /build/reproducible-path/libstatgen-1.0.15/glf/test/WriteFiles.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/glf/test/WriteFiles.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/samtools/bam.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/samtools/bam.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/samtools/bgzf.c... Parsing file /build/reproducible-path/libstatgen-1.0.15/samtools/bgzf.c... Preprocessing /build/reproducible-path/libstatgen-1.0.15/samtools/bgzf.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/samtools/bgzf.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/samtools/khash.h... Parsing file /build/reproducible-path/libstatgen-1.0.15/samtools/khash.h... Preprocessing /build/reproducible-path/libstatgen-1.0.15/samtools/knetfile.c... Parsing file /build/reproducible-path/libstatgen-1.0.15/samtools/knetfile.c... Preprocessing /build/reproducible-path/libstatgen-1.0.15/samtools/knetfile.h... Parsing file /build/reproducible-path/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... Associating documentation with modules... 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... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file bam/BamIndex.cpp... Generating code for file bam/BamIndex.h... Generating code for file bam/BamInterface.cpp... Generating code for file bam/BamInterface.h... Generating code for file bam/CigarHelper.cpp... Generating code for file bam/CigarHelper.h... Generating code for file bam/examples/pileup/Main.cpp... Generating code for file bam/examples/printRefPositions/Main.cpp... Generating code for file bam/test/Main.cpp... Generating code for file general/test/dbsnp/Main.cpp... Generating code for file glf/test/Main.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.cpp... Generating code for file bam/examples/printRefPositions/PrintRefPositions.h... Generating code for file bam/GenericSamInterface.cpp... Generating code for file bam/GenericSamInterface.h... Generating code for file bam/Pileup.h... Generating code for file bam/PileupElement.cpp... Generating code for file bam/PileupElement.h... Generating code for file bam/PileupElementBaseQual.cpp... Generating code for file bam/PileupElementBaseQual.h... Generating code for file bam/PosList.cpp... Generating code for file bam/PosList.h... Generating code for file bam/SamCoordOutput.cpp... Generating code for file bam/SamCoordOutput.h... Generating code for file bam/SamFile.cpp... Generating code for file bam/SamFile.h... Generating code for file bam/SamFileHeader.cpp... Generating code for file bam/SamFileHeader.h... Generating code for file bam/SamFilter.cpp... Generating code for file bam/SamFilter.h... Generating code for file bam/SamFlag.h... Generating code for file bam/SamHeaderHD.cpp... Generating code for file bam/SamHeaderHD.h... Generating code for file bam/SamHeaderPG.cpp... Generating code for file bam/SamHeaderPG.h... Generating code for file bam/SamHeaderRecord.cpp... Generating code for file bam/SamHeaderRecord.h... Generating code for file bam/SamHeaderRG.cpp... Generating code for file bam/SamHeaderRG.h... Generating code for file bam/SamHeaderSQ.cpp... Generating code for file bam/SamHeaderSQ.h... Generating code for file bam/SamHeaderTag.cpp... Generating code for file bam/SamHeaderTag.h... Generating code for file bam/SamHelper.h... Generating code for file bam/SamInterface.cpp... Generating code for file bam/SamInterface.h... Generating code for file bam/SamQuerySeqWithRefHelper.cpp... Generating code for file bam/SamQuerySeqWithRefHelper.h... Generating code for file bam/SamRecord.cpp... Generating code for file bam/SamRecord.h... Generating code for file bam/SamRecordHelper.cpp... Generating code for file bam/SamRecordHelper.h... Generating code for file bam/SamRecordPool.cpp... Generating code for file bam/SamRecordPool.h... Generating code for file bam/SamReferenceInfo.cpp... Generating code for file bam/SamReferenceInfo.h... Generating code for file bam/SamStatistics.cpp... Generating code for file bam/SamStatistics.h... Generating code for file bam/SamStatus.h... Generating code for file bam/SamTags.cpp... Generating code for file bam/SamTags.h... Generating code for file bam/SamValidation.cpp... Generating code for file bam/SamValidation.h... Generating code for file bam/test/BamIndexTest.cpp... Generating code for file bam/test/BamIndexTest.h... Generating code for file bam/test/Modify.cpp... Generating code for file bam/test/Modify.h... Generating code for file bam/test/ModifyVar.cpp... Generating code for file bam/test/ModifyVar.h... Generating code for file bam/test/ReadFiles.cpp... Generating code for file glf/test/ReadFiles.cpp... Generating code for file bam/test/ReadFiles.h... Generating code for file glf/test/ReadFiles.h... Generating code for file bam/test/SamFileTest.cpp... Generating code for file bam/test/SamFileTest.h... Generating code for file bam/test/ShiftIndels.cpp... Generating code for file bam/test/ShiftIndels.h... Generating code for file bam/test/TestCigarHelper.cpp... Generating code for file bam/test/TestCigarHelper.h... Generating code for file bam/test/TestEquals.cpp... Generating code for file bam/test/TestEquals.h... Generating code for file bam/test/TestFilter.cpp... Generating code for file bam/test/TestFilter.h... Generating code for file bam/test/TestPileup.cpp... Generating code for file bam/test/TestPileup.h... Generating code for file bam/test/TestPosList.cpp... Generating code for file bam/test/TestPosList.h... Generating code for file bam/test/TestSamCoordOutput.cpp... Generating code for file bam/test/TestSamCoordOutput.h... Generating code for file bam/test/TestSamRecordHelper.cpp... Generating code for file bam/test/TestSamRecordHelper.h... Generating code for file bam/test/TestSamRecordPool.cpp... Generating code for file bam/test/TestSamRecordPool.h... Generating code for file bam/test/TestValidate.cpp... Generating code for file bam/test/TestValidate.h... Generating code for file bam/test/ValidationTest.cpp... Generating code for file bam/test/ValidationTest.h... Generating code for file bam/test/WriteFiles.cpp... Generating code for file glf/test/WriteFiles.cpp... Generating code for file bam/test/WriteFiles.h... Generating code for file glf/test/WriteFiles.h... Generating code for file fastq/BaseComposition.cpp... Generating code for file fastq/BaseComposition.h... Generating code for file fastq/BaseCount.cpp... Generating code for file fastq/BaseCount.h... Generating code for file fastq/FastQFile.cpp... Generating code for file fastq/FastQFile.h... Generating code for file fastq/FastQStatus.cpp... Generating code for file fastq/FastQStatus.h... Generating code for file fastq/test/FastQFileTest.cpp... Generating code for file general/BaseAsciiMap.cpp... Generating code for file general/BaseAsciiMap.h... Generating code for file general/BaseQualityHelper.cpp... Generating code for file general/BaseQualityHelper.h... Generating code for file general/BaseUtilities.cpp... Generating code for file general/BaseUtilities.h... Generating code for file general/BasicHash.cpp... Generating code for file general/BasicHash.h... Generating code for file general/BgzfFileType.cpp... Generating code for file general/BgzfFileType.h... Generating code for file general/BgzfFileTypeRecovery.cpp... Generating code for file general/BgzfFileTypeRecovery.h... Generating code for file general/CharBuffer.cpp... Generating code for file general/CharBuffer.h... Generating code for file general/Chromosome.cpp... Generating code for file general/Chromosome.h... Generating code for file general/Cigar.cpp... Generating code for file general/Cigar.h... Generating code for file general/CigarRoller.cpp... Generating code for file general/CigarRoller.h... Generating code for file general/Constant.h... Generating code for file general/CSG_MD5.h... Generating code for file general/Error.cpp... Generating code for file general/Error.h... Generating code for file general/ErrorHandler.cpp... Generating code for file general/ErrorHandler.h... Generating code for file general/FileType.cpp... Generating code for file general/FileType.h... Generating code for file general/FortranFormat.cpp... Generating code for file general/FortranFormat.h... Generating code for file general/Generic.cpp... Generating code for file general/Generic.h... Generating code for file general/GenomeSequence.cpp... Generating code for file general/GenomeSequence.h... Generating code for file general/GenomeSequenceHelpers.h... Generating code for file general/GenotypeLists.cpp... Generating code for file general/GenotypeLists.h... Generating code for file general/glfHandler.cpp... Generating code for file general/glfHandler.h... Generating code for file general/GreedyTupleAligner.h... Generating code for file general/GzipFileType.cpp... Generating code for file general/GzipFileType.h... Generating code for file general/GzipHeader.cpp... Generating code for file general/GzipHeader.h... Generating code for file general/Hash.cpp... Generating code for file general/Hash.h... Generating code for file general/IndexBase.cpp... Generating code for file general/IndexBase.h... Generating code for file general/InplaceMerge.cpp... Generating code for file general/InplaceMerge.h... Generating code for file general/Input.cpp... Generating code for file general/Input.h... Generating code for file general/InputFile.cpp... Generating code for file general/InputFile.h... Generating code for file general/IntArray.cpp... Generating code for file general/IntArray.h... Generating code for file general/IntHash.cpp... Generating code for file general/IntHash.h... Generating code for file general/LongHash.h... Generating code for file general/LongInt.h... Generating code for file general/LongLongCounter.cpp... Generating code for file general/LongLongCounter.h... Generating code for file general/MapFunction.cpp... Generating code for file general/MapFunction.h... Generating code for file general/MathConstant.h... Generating code for file general/MathMatrix.cpp... Generating code for file general/MathMatrix.h... Generating code for file general/MathVector.cpp... Generating code for file general/MathVector.h... Generating code for file general/MemoryAllocators.cpp... Generating code for file general/MemoryAllocators.h... Generating code for file general/MemoryInfo.cpp... Generating code for file general/MemoryInfo.h... Generating code for file general/MemoryMap.cpp... Generating code for file general/MemoryMap.h... Generating code for file general/MemoryMapArray.cpp... Generating code for file general/MemoryMapArray.h... Generating code for file general/MiniDeflate.cpp... Generating code for file general/MiniDeflate.h... Generating code for file general/NonOverlapRegions.cpp... Generating code for file general/NonOverlapRegions.h... Generating code for file general/PackedVector.h... Generating code for file general/Parameters.cpp... Generating code for file general/Parameters.h... Generating code for file general/Pedigree.cpp... Generating code for file general/Pedigree.h... Generating code for file general/PedigreeAlleleFreq.cpp... Generating code for file general/PedigreeAlleleFreq.h... Generating code for file general/PedigreeAlleles.h... Generating code for file general/PedigreeDescription.cpp... Generating code for file general/PedigreeDescription.h... Generating code for file general/PedigreeFamily.cpp... Generating code for file general/PedigreeFamily.h... Generating code for file general/PedigreeGlobals.cpp... Generating code for file general/PedigreeGlobals.h... Generating code for file general/PedigreeLoader.cpp... Generating code for file general/PedigreePerson.cpp... Generating code for file general/PedigreePerson.h... Generating code for file general/PedigreeTrim.cpp... Generating code for file general/PedigreeTwin.cpp... Generating code for file general/Performance.h... Generating code for file general/PhoneHome.cpp... Generating code for file general/PhoneHome.h... Generating code for file general/QuickIndex.cpp... Generating code for file general/QuickIndex.h... Generating code for file general/Random.cpp... Generating code for file general/Random.h... Generating code for file general/ReferenceSequence.cpp... Generating code for file general/ReferenceSequence.h... Generating code for file general/ReusableVector.h... Generating code for file general/SimpleStats.h... Generating code for file general/SmithWaterman.cpp... Generating code for file general/SmithWaterman.h... Generating code for file general/Sort.cpp... Generating code for file general/Sort.h... Generating code for file general/StatGenStatus.cpp... Generating code for file general/StatGenStatus.h... Generating code for file general/STLUtilities.cpp... Generating code for file general/STLUtilities.h... Generating code for file general/String.cpp... Generating code for file general/StringAlias.cpp... Generating code for file general/StringAlias.h... Generating code for file general/StringArray.cpp... Generating code for file general/StringArray.h... Generating code for file general/StringBasics.cpp... Generating code for file general/StringBasics.h... Generating code for file general/StringHash.cpp... Generating code for file general/StringHash.h... Generating code for file general/StringMap.cpp... Generating code for file general/StringMap.h... Generating code for file general/Tabix.cpp... Generating code for file general/Tabix.h... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.cpp... Generating code for file general/test/baseUtilitiesTest/BaseUtilitiesTest.h... Generating code for file general/test/Chromosome_test.cpp... Generating code for file general/test/cigar/CigarRollerTest.cpp... Generating code for file general/test/cigar/CigarRollerTest.h... Generating code for file general/test/GenomeSequence_test.cpp... Generating code for file general/test/GreedyTupleAligner_test.cpp... Generating code for file general/test/gtest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.cpp... Generating code for file general/test/inputFileTest/InputFileTest.h... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.cpp... Generating code for file general/test/memoryMapArrayTest/MemoryMapArrayTest.h... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.cpp... Generating code for file general/test/nonOverlapRegions/NonOverlapRegionsTest.h... Generating code for file general/test/packedVectorTest/PackedVectorTest.cpp... Generating code for file general/test/packedVectorTest/PackedVectorTest.h... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.cpp... Generating code for file general/test/referenceSequenceTest/ReferenceSequenceTest.h... Generating code for file general/test/reusableVector/ReusableVectorTest.cpp... Generating code for file general/test/reusableVector/ReusableVectorTest.h... Generating code for file general/test/STLUtilities_test.cpp... Generating code for file general/test/string/StringTest.cpp... Generating code for file general/test/string/StringTest.h... Generating code for file general/test/trimSequence/TrimSequence.cpp... Generating code for file general/test/TrimSequence_test.cpp... Generating code for file general/TrimSequence.h... Generating code for file general/UncompressedFileType.cpp... Generating code for file general/UncompressedFileType.h... Generating code for file general/UnitTest.h... Generating code for file glf/GlfException.cpp... Generating code for file glf/GlfException.h... Generating code for file glf/GlfFile.cpp... Generating code for file glf/GlfFile.h... Generating code for file glf/GlfHeader.cpp... Generating code for file glf/GlfHeader.h... Generating code for file glf/GlfRecord.cpp... Generating code for file glf/GlfRecord.h... Generating code for file glf/GlfRefSection.cpp... Generating code for file glf/GlfRefSection.h... Generating code for file glf/GlfStatus.cpp... Generating code for file glf/GlfStatus.h... Generating code for file glf/test/Validate.cpp... Generating code for file glf/test/Validate.h... Generating code for file samtools/bam.h... Generating code for file samtools/bgzf.c... Generating code for file samtools/bgzf.h... Generating code for file samtools/khash.h... Generating code for file samtools/knetfile.c... Generating code for file samtools/knetfile.h... Generating file documentation... Generating docs for file general/InputFile.h... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound __kstring_t... Generating docs for compound Alleles... Generating docs for compound AnalyzeClass... Generating docs for compound BamIndex... Generating docs for compound BamIndexFileTest... Generating docs for compound BamInterface... Generating docs for compound bamRecordStruct... Generating docs for compound BaseAsciiMap... Generating docs for compound BaseComposition... Generating docs for compound BaseCount... Generating docs for compound baseQualityConvertor... Generating docs for compound BaseUtilities... Generating docs for compound BasicHash... Generating docs for compound BGZF... Generating docs for compound CharBuffer... Generating docs for compound Chromosome... Generating docs for compound ChromosomeInfo... Generating docs for compound Chunk... Generating docs for compound Cigar... Generating docs for nested compound Cigar::CigarOperator... Generating docs for compound CigarHelper... Generating docs for compound CigarHelperTest... Generating docs for compound CigarRoller... Generating docs for compound CigarRollerTest... Generating docs for compound ColumnExtras... Generating docs for compound defaultPileup... Generating docs for compound DoubleParameter... Generating docs for compound emptyGenericHeader... Generating docs for compound EqualsTest... Generating docs for compound ErrorHandler... Generating docs for compound Family... Generating docs for compound FastQFile... Generating docs for compound FastQStatus... Generating docs for compound FileType... Generating docs for compound FilterTest... Generating docs for compound FortranFormat... Generating docs for compound GenericSamInterface... Generating docs for compound GenomeSequence... Generating docs for compound genomeSequenceMmapHeader... Generating docs for compound GenotypeList... Generating docs for compound glfEntry... Generating docs for compound GlfException... Generating docs for compound GlfFile... Generating docs for compound GlfFileReader... Generating docs for compound GlfFileWriter... Generating docs for compound glfHandler... Generating docs for compound GlfHeader... Generating docs for compound glfIndel... Generating docs for compound GlfRecord... Generating docs for compound GlfRefSection... Generating docs for compound GlfStatus... Generating docs for compound GlobalTestEnvironment... Generating docs for compound GreedyTupleAligner... Generating docs for compound GzipHeader... Generating docs for compound HiddenDouble... Generating docs for compound HiddenInteger... Generating docs for compound HiddenString... Generating docs for compound HiddenSwitch... Generating docs for compound IFILE_Test... Generating docs for compound IndexBase... Generating docs for nested compound IndexBase::Bin... Generating docs for nested compound IndexBase::Reference... Generating docs for compound InputFile... Generating docs for compound IntArray... Generating docs for compound IntHash... Generating docs for compound IntParameter... Generating docs for compound knetFile_s... Generating docs for compound ListParameter... Generating docs for compound LongCounter... Generating docs for compound LongHash... Generating docs for compound LongParamContainer... Generating docs for compound LongParameterList... Generating docs for compound LongParameters... Generating docs for compound MarkerInfo... Generating docs for compound Matrix... Generating docs for compound MD5_CTX... Generating docs for compound MemoryMap... Generating docs for compound MemoryMapArray... Generating docs for compound MemoryMapArrayHeader... Generating docs for compound MemoryMapArrayTest... Generating docs for compound MemoryMapGenericHeader... Generating docs for compound MiniDeflate... Generating docs for compound MockGenomeSequence... Generating docs for compound modify... Generating docs for compound modifyVar... Generating docs for compound NonOverlapRegionPos... Generating docs for compound NonOverlapRegions... Generating docs for compound NonOverlapRegionsTest... Generating docs for compound OptionList... Generating docs for compound PackedArrayTest... Generating docs for compound PackedRead... Generating docs for compound PackedSequenceData... Generating docs for compound PackedVector... Generating docs for compound Parameter... Generating docs for compound ParameterList... Generating docs for compound Pedigree... Generating docs for compound PedigreeDescription... Generating docs for compound PedigreeGlobals... Generating docs for compound PedigreeKey... Generating docs for compound Person... Generating docs for compound PhoneHome... Generating docs for compound Pileup... Generating docs for compound PileupElement... Generating docs for compound PileupElementBaseQual... Generating docs for compound PileupHelper... Generating docs for compound PosList... Generating docs for compound QuickIndex... Generating docs for compound Random... Generating docs for compound ReferenceSequenceTest... Generating docs for compound ReusableVector... Generating docs for compound ReusableVectorTest... Generating docs for compound ReusableVectorTestDataType... Generating docs for compound RunningStat... Generating docs for compound SamCoordOutput... Generating docs for compound SamCoordOutputTest... Generating docs for compound SamFile... Generating docs for compound SamFileHeader... Generating docs for compound SamFileReader... Generating docs for compound SamFileWriter... Generating docs for compound SamFilter... Generating docs for compound SamFlag... Generating docs for compound SamHeaderHD... Generating docs for compound SamHeaderPG... Generating docs for compound SamHeaderRecord... Generating docs for compound SamHeaderRG... Generating docs for compound SamHeaderSQ... Generating docs for compound SamHeaderTag... Generating docs for compound SamHelper... Generating docs for compound SamInterface... Generating docs for compound SamQuerySeqWithRef... Generating docs for compound SamQuerySeqWithRefIter... Generating docs for compound SamRecord... Generating docs for compound SamRecordHelper... Generating docs for compound SamRecordHelperTest... Generating docs for compound SamRecordPool... Generating docs for compound SamRecordPoolTest... Generating docs for compound SamReferenceInfo... Generating docs for compound SamSingleBaseMatchInfo... Generating docs for compound SamStatistics... Generating docs for compound SamTags... Generating docs for compound SamValidationError... Generating docs for compound Samsh: 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: dot: 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 ValidationErrors... 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 module documentation... Generating namespace documentation... 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 topic index... Generating module index... Generating module member 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 file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running dot... Generating dot graphs using 43 parallel threads... 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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 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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 type lookup cache used 20326/65536 hits=184977 misses=20874 symbol lookup cache used 17817/65536 hits=234471 misses=17817 finished... make[1]: Leaving directory '/build/reproducible-path/libstatgen-1.0.15' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libstatgen-1.0.15' echo "Build time test is not run here." Build time test is not run here. make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below dpkg-gensymbols: warning: debian/libstatgen1/DEBIAN/symbols doesn't match completely debian/libstatgen1.symbols --- debian/libstatgen1.symbols (libstatgen1_1.0.15-7_amd64) +++ dpkg-gensymbolsSMNVS8 2025-06-11 18:10:10.498169961 +0000 @@ -1642,21 +1642,22 @@ (optional)_ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_SaIS5_ENSt8__detail9_IdentityESt8equal_toIS5_ESt4hashIS5_ENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb1ELb1ELb1EEEED2Ev@Base 1.0.15 _ZNSt12_Destroy_auxILb0EE9__destroyIP6StringEEvT_S4_@Base 1.0.14 _ZNSt12_Destroy_auxILb0EE9__destroyIPN9IndexBase9ReferenceEEEvT_S5_@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIN5Cigar13CigarOperatorESaIS1_EED1Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIN5Cigar13CigarOperatorESaIS1_EED2Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIP15SamHeaderRecordSaIS1_EED1Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIP15SamHeaderRecordSaIS1_EED2Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIcSaIcEED1Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIcSaIcEED2Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIfSaIfEED1Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIfSaIfEED2Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIiSaIiEED1Ev@Base 1.0.14 - (optional)_ZNSt12_Vector_baseIiSaIiEED2Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIN5Cigar13CigarOperatorESaIS1_EED1Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIN5Cigar13CigarOperatorESaIS1_EED2Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIP15SamHeaderRecordSaIS1_EED1Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIP15SamHeaderRecordSaIS1_EED2Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIcSaIcEED1Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIcSaIcEED2Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIfSaIfEED1Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIfSaIfEED2Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIiSaIiEED1Ev@Base 1.0.14 +#MISSING: 1.0.15-7# (optional)_ZNSt12_Vector_baseIiSaIiEED2Ev@Base 1.0.14 (optional)_ZNSt6vectorIN5Cigar13CigarOperatorESaIS1_EED1Ev@Base 1.0.15 (optional)_ZNSt6vectorIN5Cigar13CigarOperatorESaIS1_EED2Ev@Base 1.0.15 _ZNSt6vectorIP12SamHeaderTagSaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base 1.0.14 (optional)_ZNSt6vectorIP15SamHeaderRecordSaIS1_EED1Ev@Base 1.0.15 (optional)_ZNSt6vectorIP15SamHeaderRecordSaIS1_EED2Ev@Base 1.0.15 + _ZNSt6vectorIbSaIbEE13_M_insert_auxESt13_Bit_iteratorb@Base 1.0.15-7 _ZNSt6vectorIcSaIcEE17_M_realloc_insertIJcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_@Base 1.0.14 (optional)_ZNSt6vectorIcSaIcEED1Ev@Base 1.0.15 (optional)_ZNSt6vectorIcSaIcEED2Ev@Base 1.0.15 @@ -1673,12 +1674,12 @@ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_@Base 1.0.15 _ZNSt7__cxx119to_stringEx@Base 1.0.15 _ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE22_M_emplace_hint_uniqueIJS0_ImS2_EEEESt17_Rb_tree_iteratorIS3_ESt23_Rb_tree_const_iteratorIS3_EDpOT_@Base 1.0.15 - (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE24_M_get_insert_unique_posERS1_@Base 1.0.15 - (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERS1_@Base 1.0.15 +#MISSING: 1.0.15-7# (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE24_M_get_insert_unique_posERS1_@Base 1.0.15 +#MISSING: 1.0.15-7# (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERS1_@Base 1.0.15 _ZSt16__do_uninit_copyIPK6StringPS0_ET0_T_S5_S4_@Base 1.0.15 _ZSt18__do_uninit_fill_nIPSt6vectorIbSaIbEEmS2_ET_S4_T0_RKT1_@Base 1.0.15 _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_@Base 1.0.15 - (optional)_ZZNSt8__detail18__to_chars_10_implIyEEvPcjT_E8__digits@Base 1.0.15 +#MISSING: 1.0.15-7# (optional)_ZZNSt8__detail18__to_chars_10_implIyEEvPcjT_E8__digits@Base 1.0.15 bQualityConvertor@Base 1.0.14 (c++)"baseQualityConvertor::baseQualityConvertor()@Base" 1.0.14 (c++)"baseQualityConvertor::toDouble(unsigned char)@Base" 1.0.14 dh_shlibdeps -a -O--no-parallel 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 crc32 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 gzrewind 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 inflateInit2_ used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzseek64 used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol deflateEnd used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries dpkg-shlibdeps: warning: symbol inflateEnd used by debian/libstatgen1/usr/lib/x86_64-linux-gnu/libStatGen.so.1 found in none of the libraries 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: 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 'libstatgen1-dbgsym' in '../libstatgen1-dbgsym_1.0.15-7_amd64.deb'. dpkg-deb: building package 'libstatgen1' in '../libstatgen1_1.0.15-7_amd64.deb'. dpkg-deb: building package 'libstatgen-dev' in '../libstatgen-dev_1.0.15-7_amd64.deb'. dpkg-deb: building package 'libstatgen-doc' in '../libstatgen-doc_1.0.15-7_all.deb'. dpkg-genbuildinfo --build=binary -O../libstatgen_1.0.15-7_amd64.buildinfo dpkg-genchanges --build=binary -O../libstatgen_1.0.15-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/3759246 and its subdirectories I: Current time: Wed Jun 11 06:10:20 -12 2025 I: pbuilder-time-stamp: 1749665420 Thu May 9 11:47:23 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net. Thu May 9 11:47:23 UTC 2024 I: Preparing to do remote build '2' on ionos1-amd64.debian.net. Thu May 9 11:55:36 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. Thu May 9 11:55:37 UTC 2024 I: libstatgen_1.0.15-7_amd64.changes: Format: 1.8 Date: Thu, 24 Aug 2023 11:34:46 +0200 Source: libstatgen Binary: libstatgen-dev libstatgen-doc libstatgen1 libstatgen1-dbgsym Architecture: amd64 all Version: 1.0.15-7 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libstatgen-dev - development files for the libStatGen libstatgen-doc - documentation files for the libStatGen libstatgen1 - processing and analyzing next generation sequencing and genotypin Closes: 1042116 Changes: libstatgen (1.0.15-7) unstable; urgency=medium . * Team upload. * d/*.symbols*: update to fix build failure with gcc 13. Several symbols having disappeared or having been introduced by the move to gcc 13 are most likely compiler leaked and shouldn't interfere with consumers of the library. They are marked as (optional). Closes: #1042116 * d/clean: remove leftover doxygen files. * d/control: declare compliance to standards version 4.6.2. Checksums-Sha1: 5c6bbb5b366820898bfa51ee8cfe74352a601769 121784 libstatgen-dev_1.0.15-7_amd64.deb 795788c5386d5a3f9e13eae8fe0fedd5beac51ff 1464996 libstatgen-doc_1.0.15-7_all.deb 7a209557fec47858e76d650de111ccef7d5b7cc8 2691960 libstatgen1-dbgsym_1.0.15-7_amd64.deb 966de7bed36c8a6d82f39e1e3fe618507375f143 320796 libstatgen1_1.0.15-7_amd64.deb a225dd8cbf102b34c0263b984c822c0bc04ba7d2 6560 libstatgen_1.0.15-7_amd64.buildinfo Checksums-Sha256: 71c6c35bc7652b9e688b1c167692e9a884624fe826512f6d36825c24d845f14a 121784 libstatgen-dev_1.0.15-7_amd64.deb 9ae93cb3da2cb47596f9610b9d473757655abe4841be1a4b4fe5f2837c73a811 1464996 libstatgen-doc_1.0.15-7_all.deb 6cb704bd2e5bf32013fc904a506d44884bb9d9355e0e7885126617d6bf455943 2691960 libstatgen1-dbgsym_1.0.15-7_amd64.deb 179fce33a08d501edf179d55066e987736cfd12d7b7a8f99eed2fd5d1df67979 320796 libstatgen1_1.0.15-7_amd64.deb f00725efbeff7acd9bc18480f8b5be049fe014a74ee967c3e6b2dd5c9b65081f 6560 libstatgen_1.0.15-7_amd64.buildinfo Files: e1e4e700c4a5ef05f25640adab0d7f58 121784 libdevel optional libstatgen-dev_1.0.15-7_amd64.deb 61ae2d92a8ac34a5bc55abc9c2592df1 1464996 doc optional libstatgen-doc_1.0.15-7_all.deb 6566605921b80e7c8e77e82fedddcfaf 2691960 debug optional libstatgen1-dbgsym_1.0.15-7_amd64.deb b470a6d9c019bd96cb6fdb2efc5ea53c 320796 libs optional libstatgen1_1.0.15-7_amd64.deb 41ba6a26aaba3ce74eb02e6f358a3a28 6560 science optional libstatgen_1.0.15-7_amd64.buildinfo Thu May 9 11:55:38 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_2-6117.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xIoFdxpx/libstatgen_1.0.15-7.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xIoFdxpx/libstatgen_1.0.15-7.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xIoFdxpx/libstatgen_1.0.15-7.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xIoFdxpx/b1/libstatgen_1.0.15-7_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xIoFdxpx/b2/libstatgen_1.0.15-7_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.440s) 0.439s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.068s) 0.068s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 813ms CPU time consumed: 809ms Thu May 9 11:55:39 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Thu May 9 11:55:39 UTC 2024 I: libstatgen from trixie built successfully and reproducibly on amd64. Thu May 9 11:55:40 UTC 2024 I: Submitting .buildinfo files to external archives: Thu May 9 11:55:40 UTC 2024 I: Submitting 8.0K b1/libstatgen_1.0.15-7_amd64.buildinfo.asc Thu May 9 11:55:41 UTC 2024 I: Submitting 8.0K b2/libstatgen_1.0.15-7_amd64.buildinfo.asc Thu May 9 11:55:42 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu May 9 11:55:42 UTC 2024 I: Done submitting .buildinfo files. Thu May 9 11:55:42 UTC 2024 I: Removing signed libstatgen_1.0.15-7_amd64.buildinfo.asc files: removed './b1/libstatgen_1.0.15-7_amd64.buildinfo.asc' removed './b2/libstatgen_1.0.15-7_amd64.buildinfo.asc'