I: pbuilder: network access will be disabled during build I: Current time: Mon Jun 17 01:47:29 -12 2024 I: pbuilder-time-stamp: 1718632049 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [libvcflib_1.0.3+dfsg-2.dsc] I: copying [./libvcflib_1.0.3+dfsg.orig.tar.xz] I: copying [./libvcflib_1.0.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Oct 7 02:31:55 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libvcflib_1.0.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting libvcflib in libvcflib-1.0.3+dfsg dpkg-source: info: unpacking libvcflib_1.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking libvcflib_1.0.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_fsom dpkg-source: info: applying use_debian_packaged_smithwaterman.patch dpkg-source: info: applying use_debian_packaged_fastahack.patch dpkg-source: info: applying use_debian_packaged_libssw.patch dpkg-source: info: applying shared_lib.patch dpkg-source: info: applying pkg-config.patch dpkg-source: info: applying tabix_linking dpkg-source: info: applying tests I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/126865/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='2e8cc37324be400d9d7f979392efd475' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' 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='126865' 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.omkZmCXZ/pbuilderrc_GDJe --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.omkZmCXZ/b1 --logfile b1/build.log libvcflib_1.0.3+dfsg-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://85.184.249.68:3128' I: uname -a Linux ionos16-i386 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 22 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 9 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 22 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 22 2023 more -rwsr-xr-x 1 root root 58912 Mar 22 2023 mount -rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 22 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 22 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 22 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/126865/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: i386 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), cmake, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libsmithwaterman-dev, libssw-dev, libfastahack-dev, pkg-config, libgtest-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19604 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on markdown; however: Package markdown is not installed. pbuilder-satisfydepends-dummy depends on libtabixpp-dev; however: Package libtabixpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libdisorder-dev; however: Package libdisorder-dev is not installed. pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however: Package libsmithwaterman-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libfastahack-dev; however: Package libfastahack-dev is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on libgtest-dev; however: Package libgtest-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} googletest{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbrotli1{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgtest-dev{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} markdown{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 39.3 MB of archives. After unpacking 141 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 11 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-9 [420 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 googletest all 1.12.1-0.2 [506 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 libbz2-dev i386 1.0.8-5+b1 [31.5 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-9 [527 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 libdisorder0 i386 0.0.2+git20130809.8062ee1-4+b1 [4880 B] Get: 56 http://deb.debian.org/debian bookworm/main i386 libdisorder-dev i386 0.0.2+git20130809.8062ee1-4+b1 [4900 B] Get: 57 http://deb.debian.org/debian bookworm/main i386 libfastahack0 i386 1.0.0+dfsg-10 [28.4 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libfastahack-dev i386 1.0.0+dfsg-10 [30.0 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libgtest-dev i386 1.12.1-0.2 [254 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-12+b1 [38.7 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-12+b1 [43.4 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 libssw0 i386 1.1-13 [27.1 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libssw-dev i386 1.1-13 [30.2 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 libtabixpp0 i386 1.1.2-1 [10.0 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 libtabixpp-dev i386 1.1.2-1 [9588 B] Get: 72 http://deb.debian.org/debian bookworm/main i386 markdown all 1.0.1-12 [17.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Fetched 39.3 MB in 1s (26.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19604 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_i386.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../04-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../07-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... 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Setting up libelf1:i386 (0.188-2.1) ... Setting up libssw0:i386 (1.1-13) ... Setting up libxml2:i386 (2.9.14+dfsg-1.2) ... Setting up markdown (1.0.1-12) ... Setting up libbz2-dev:i386 (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libgtest-dev:i386 (1.12.1-0.2) ... Setting up libssw-dev:i386 (1.1-13) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:i386 (3.6.2-1) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up pkgconf:i386 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up pkg-config:i386 (1.8.1-1) ... Setting up libsmithwaterman-dev:i386 (0.0+git20160702.2610e25-12+b1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/libvcflib-1.0.3+dfsg/ && 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 > ../libvcflib_1.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --buildsystem cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_auto_clean || true make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' dh_autoreconf_clean -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_clean find . -name "*.o" -delete rm -f README.html make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' debian/rules binary dh binary --buildsystem cmake dh_update_autotools_config -O--buildsystem=cmake dh_autoreconf -O--buildsystem=cmake debian/rules override_dh_auto_configure make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_auto_configure -- -DOPENMP=ON -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DOPENMP=ON -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Found BZip2: /usr/lib/i386-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for lzma_auto_decoder in /usr/lib/i386-linux-gnu/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/i386-linux-gnu/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/i386-linux-gnu/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/i386-linux-gnu/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/i386-linux-gnu/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/i386-linux-gnu/liblzma.so - found -- Found LibLZMA: /usr/lib/i386-linux-gnu/liblzma.so (found version "5.4.1") -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.13") -- -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.16 -- Checking for module 'tabixpp' -- Package 'tabixpp', required by 'virtual:world', not found -- Checking for module 'libsmithwaterman' -- Found libsmithwaterman, version 0.0 -- Checking for module 'libfastahack' -- Found libfastahack, version 0.0 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Pandoc needs to be installed to generate the man pages -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_auto_build cd obj-i686-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/libvcflib-1.0.3+dfsg -B/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcflib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 0%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/Variant.cpp [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/var.cpp [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF CMakeFiles/vcflib.dir/src/rnglib.cpp.o.d -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/rnglib.cpp [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pdflib.cpp [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o [ 3%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/cdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/cdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/cdflib.cpp [ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/split.cpp /usr/bin/cc -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -MF CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o.d -o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -c /build/libvcflib-1.0.3+dfsg/filevercmp/filevercmp.c In file included from /build/libvcflib-1.0.3+dfsg/src/Variant.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 5%] Linking CXX shared library libvcflib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvcflib.so.1 -o libvcflib.so.1 CMakeFiles/vcflib.dir/src/Variant.cpp.o CMakeFiles/vcflib.dir/src/rnglib.cpp.o CMakeFiles/vcflib.dir/src/var.cpp.o CMakeFiles/vcflib.dir/src/pdflib.cpp.o CMakeFiles/vcflib.dir/src/cdflib.cpp.o CMakeFiles/vcflib.dir/src/split.cpp.o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -lssw -ltabixpp -lsmithwaterman -ldisorder -lfastahack /usr/bin/cmake -E cmake_symlink_library libvcflib.so.1 libvcflib.so.1 libvcflib.so make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 5%] Built target vcflib make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/bFst.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/pVst.dir/DependInfo.cmake --color= make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/popStats.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/wcFst.dir/DependInfo.cmake --color= make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/iHS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build [ 6%] Building CXX object 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'/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= [ 7%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp [ 7%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 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-I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/bFst.dir/src/bFst.cpp.o -MF CMakeFiles/bFst.dir/src/bFst.cpp.o.d -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/bFst.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT 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-I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/wcFst.cpp /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat 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/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build [ 11%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -MF CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o.d -o CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 11%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pFst.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 12%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/smoother.cpp [ 13%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp [ 14%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -MF CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o.d -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/pFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfld.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/popStats.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/wcFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 15%] Linking CXX executable dumpContigsFromHeader /usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 16%] Linking CXX executable segmentIhs /usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 16%] Built target dumpContigsFromHeader make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 16%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp [ 17%] Linking CXX executable segmentFst /usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 17%] Built target segmentIhs make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 18%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 18%] Built target segmentFst make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color= [ 18%] Linking CXX executable smoother /usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 19%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 19%] Built target smoother make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 19%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -MF CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o.d -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp [ 19%] Linking CXX executable vcfecho /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 19%] Built target vcfecho make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 20%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] Linking CXX executable permuteGPAT++ /usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 20%] Built target permuteGPAT++ make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 21%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] Linking CXX executable normalize-iHS /usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 22%] Built target normalize-iHS make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 23%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -MF CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o.d -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp [ 23%] Linking CXX executable permuteSmooth /usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 23%] Built target permuteSmooth make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 24%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp [ 25%] Linking CXX executable bFst /usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 26%] Linking CXX executable pVst /usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 26%] Built target bFst make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= [ 27%] Linking CXX executable wcFst /usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 28%] Linking CXX executable popStats /usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1 [ 29%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 29%] Built target pVst make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color= [ 30%] Linking CXX executable pFst In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 30%] Built target wcFst make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend [ 31%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= [ 31%] Linking CXX executable hapLrt /usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 31%] Built target popStats make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= [ 31%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -MF CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o.d -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 32%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -MF CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o.d -o CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 32%] Built target pFst make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 32%] Linking CXX executable genotypeSummary /usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -o genotypeSummary -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 32%] Built target hapLrt make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend [ 33%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -MF CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o.d -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 33%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -MF CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o.d -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 33%] Built target genotypeSummary make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 34%] Linking CXX executable abba-baba /usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 [ 35%] Linking CXX executable vcfld /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 [ 36%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 36%] Linking CXX executable iHS /usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 36%] Linking CXX executable vcfaltcount /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 [ 36%] Linking CXX executable plotHaps /usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 37%] Linking CXX executable sequenceDiversity /usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 37%] Built target abba-baba make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= [ 37%] Built target iHS make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 37%] Built target vcfld make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend [ 38%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -MF CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o.d -o CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp [ 38%] Built target plotHaps make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= [ 38%] Built target vcfaltcount make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build [ 38%] Built target sequenceDiversity make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 38%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -MF CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o.d -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 38%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -MF CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o.d -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp [ 39%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -MF CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o.d -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp [ 40%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 40%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcffixup.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 40%] Linking CXX executable vcfhetcount /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 40%] Built target vcfhetcount make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 41%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp [ 42%] Linking CXX executable vcfremovesamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 43%] Linking CXX executable meltEHH /usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 43%] Linking CXX executable vcfhethomratio /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 44%] Linking CXX executable vcfsamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 44%] Built target meltEHH make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= [ 44%] Built target vcfremovesamples make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 44%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp [ 44%] Built target vcfsamplenames make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= [ 44%] Built target vcfhethomratio make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend [ 44%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstats.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 44%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -MF CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o.d -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 46%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o [ 46%] Linking CXX executable vcfcommonsamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 46%] Linking CXX executable vcfkeepsamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 46%] Built target vcfcommonsamples make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 46%] Built target vcfkeepsamples make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= [ 46%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 47%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:13: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 48%] Linking CXX executable vcfgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 48%] Built target vcfgenotypes make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 48%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -MF CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o.d -o CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp [ 48%] Linking CXX executable vcfclassify /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfstats.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 49%] Linking CXX executable vcf2tsv /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 49%] Built target vcfclassify make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 50%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -MF CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o.d -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 50%] Built target vcf2tsv make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 51%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp [ 51%] Linking CXX executable vcfsamplediff /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] Linking CXX executable vcfremoveaberrantgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 52%] Built target vcfsamplediff make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 52%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 52%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= In file included from /build/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 52%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] Linking CXX executable vcffixup /usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] Built target vcffixup make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 54%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Linking CXX executable vcfparsealts /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 [ 55%] Linking CXX executable vcfprimers /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 55%] Built target vcfprimers make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend [ 55%] Built target vcfparsealts make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 56%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp [ 56%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 56%] Linking CXX executable vcfcleancomplex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1 [ 57%] Linking CXX executable vcfnumalt /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 57%] Built target vcfcleancomplex make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend [ 58%] Linking CXX executable vcffilter /usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 58%] Built target vcfnumalt make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake --color= [ 58%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp [ 58%] Linking CXX executable vcfrandom /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 58%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcflength.dir/src/vcflength.cpp.o -MF CMakeFiles/vcflength.dir/src/vcflength.cpp.o.d -o CMakeFiles/vcflength.dir/src/vcflength.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcflength.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 58%] Built target vcffilter make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 58%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o [ 58%] Built target vcfrandom /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -MF CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o.d -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 59%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcflength.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] Linking CXX executable vcfaddinfo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 60%] Built target vcfaddinfo make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend [ 61%] Linking CXX executable vcfflatten /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 62%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 62%] Built target vcfflatten make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 63%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -MF CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o.d -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp [ 64%] Linking CXX executable vcfgenotypecompare /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 64%] Linking CXX executable vcfkeepinfo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 64%] Built target vcfgenotypecompare make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 65%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp [ 65%] Built target vcfkeepinfo make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 65%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Linking CXX executable vcfkeepgeno /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 [ 66%] Linking CXX executable vcfcountalleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 66%] Built target vcfkeepgeno make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 66%] Built target vcfcountalleles make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= [ 66%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 67%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp [ 68%] Linking CXX executable vcfafpath /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] Linking CXX executable vcflength /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 70%] Linking CXX executable vcfdistance [ 70%] Built target vcfafpath /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 71%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -MF CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o.d -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 71%] Built target vcflength make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= [ 71%] Built target vcfdistance make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build [ 71%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -MF CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o.d -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 72%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp [ 73%] Linking CXX executable vcfannotategenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 74%] Linking CXX executable vcfoverlay /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 [ 74%] Built target vcfannotategenotypes make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend In file included from /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 75%] Linking CXX executable vcfrandomsample /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 75%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 75%] Built target vcfoverlay make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 75%] Built target vcfrandomsample make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend [ 75%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -MF CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o.d -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 75%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -MF CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o.d -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp [ 76%] Linking CXX executable vcfstats In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremap.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 76%] Built target vcfstats make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color= In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 77%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -MF CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o.d -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] Linking CXX executable vcfentropy /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 78%] Linking CXX executable vcfcheck /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 78%] Built target vcfcheck make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend [ 78%] Built target vcfentropy make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 78%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -MF CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o.d -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcat.cpp [ 79%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -MF CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o.d -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Linking CXX executable vcfuniq /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 [ 79%] Linking CXX executable vcfglxgt /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 79%] Built target vcfuniq make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= [ 79%] Built target vcfglxgt make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcat.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 80%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -MF CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o.d -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 81%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -MF CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o.d -o CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp [ 81%] Linking CXX executable vcfannotate /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Built target vcfannotate make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 81%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -MF CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o.d -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp [ 81%] Linking CXX executable vcfuniqalleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 81%] Built target vcfuniqalleles make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 82%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -MF CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o.d -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Linking CXX executable vcfsitesummarize /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 83%] Built target vcfsitesummarize make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build In file included from /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 84%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -MF CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o.d -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 84%] Linking CXX executable vcfevenregions /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 84%] Linking CXX executable vcfallelicprimitives /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 85%] Linking CXX executable vcfcat /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 85%] Built target vcfevenregions make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 86%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp [ 87%] Linking CXX executable vcfintersect /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 87%] Built target vcfcat make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend [ 87%] Built target vcfallelicprimitives make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build [ 88%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 89%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -MF CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o.d -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 89%] Built target vcfintersect make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 90%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 90%] Linking CXX executable vcfgenosamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 90%] Built target vcfgenosamplenames make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 90%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -MF CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o.d -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 91%] Linking CXX executable vcfbreakmulti /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 92%] Linking CXX executable vcfremap /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] Linking CXX executable vcf2fasta /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 92%] Built target vcfbreakmulti make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 92%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -MF CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o.d -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp [ 92%] Built target vcfremap make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' cd /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= [ 92%] Built target vcf2fasta make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 92%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -MF CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o.d -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp [ 93%] Linking CXX executable vcfgenosummarize /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 93%] Built target vcfgenosummarize In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Linking CXX executable vcfcreatemulti /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 94%] Built target vcfcreatemulti [ 95%] Linking CXX executable vcfindex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 95%] Built target vcfindex [ 95%] Linking CXX executable vcfgeno2alleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 96%] Linking CXX executable vcfstreamsort /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 96%] Built target vcfgeno2alleles make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 96%] Built target vcfstreamsort [ 96%] Linking CXX executable vcfqual2info /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 96%] Built target vcfqual2info [ 96%] Linking CXX executable vcfroc /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 96%] Built target vcfroc [ 97%] Linking CXX executable vcfinfo2qual /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 97%] Linking CXX executable vcfsample2info /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 97%] Built target vcfinfo2qual make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 97%] Built target vcfsample2info [ 98%] Linking CXX executable vcfglbound /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [ 98%] Linking CXX executable vcf2dag /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 98%] Built target vcfglbound make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 98%] Built target vcf2dag [ 99%] Linking CXX executable vcfinfosummarize /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [ 99%] Built target vcfinfosummarize [ 99%] Linking CXX executable vcfcombine /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp [100%] Linking CXX executable vcfleftalign /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [100%] Built target vcfcombine /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [100%] Built target vcfleftalign [100%] Linking CXX executable vcfgeno2haplo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' [100%] Built target vcfgeno2haplo make[3]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' markdown README.md > README.html make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' export LD_LIBRARY_PATH=/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu/:$LD_LIBRARY_PATH && cd test && /usr/bin/make make[2]: Entering directory '/build/libvcflib-1.0.3+dfsg/test' g++ -Wall -std=c++0x -I../src -I../googletest/googletest/include/ -I../fastahack -I../smithwaterman/ -I../multichoose/ -I../filevercmp/ -I../googletest/googletest/make/ tests/mainTest.cpp -o tests/main -lvcflib -lgtest_main -lgtest -L../obj-i686-linux-gnu/ -L../googletest/googletest/make/ -lm -ltabixpp -lhts -lpthread In file included from tests/variantTests.h:2, from tests/mainTest.cpp:4: ../src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/unique_ptr.h:37, from /usr/include/c++/12/memory:76, from /usr/include/gtest/gtest.h:54, from tests/mainTest.cpp:3: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ./tests/main [==========] Running 5 tests from 2 test suites. [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype [ OK ] Variant.correctGenotype (5636 ms) [----------] 1 test from Variant (5636 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open [ OK ] VariantCallFile.open (0 ms) [ RUN ] VariantCallFile.recordCountUncompressed [ OK ] VariantCallFile.recordCountUncompressed (0 ms) [ RUN ] VariantCallFile.recordCountCompressed [ OK ] VariantCallFile.recordCountCompressed (7 ms) [ RUN ] VariantCallFile.sampleNamesCompressed [ OK ] VariantCallFile.sampleNamesCompressed (3 ms) [----------] 4 tests from VariantCallFile (11 ms total) [----------] Global test environment tear-down [==========] 5 tests from 2 test suites ran. (5648 ms total) [ PASSED ] 5 tests. make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/test' make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-i686-linux-gnu && make -j16 install DESTDIR=/build/libvcflib-1.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/libvcflib-1.0.3+dfsg -B/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfecho -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfecho" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/dumpContigsFromHeader -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/dumpContigsFromHeader" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bFst -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bFst" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pVst -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pVst" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/hapLrt -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/hapLrt" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/popStats -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/popStats" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/wcFst -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/wcFst" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/iHS -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/iHS" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentFst -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentFst" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentIhs -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentIhs" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/genotypeSummary -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/genotypeSummary" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/sequenceDiversity -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/sequenceDiversity" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pFst -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pFst" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/smoother -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/smoother" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfld -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfld" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/plotHaps -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/plotHaps" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/abba-baba -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/abba-baba" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteGPAT++ -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteGPAT++" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteSmooth -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteSmooth" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/normalize-iHS -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/normalize-iHS" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/meltEHH -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/meltEHH" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaltcount -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaltcount" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhetcount -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhetcount" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhethomratio -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhethomratio" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffilter -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffilter" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2tsv -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2tsv" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypes -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypes" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotategenotypes -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotategenotypes" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcommonsamples -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcommonsamples" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremovesamples -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremovesamples" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepsamples -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepsamples" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplenames -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplenames" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypecompare -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypecompare" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffixup -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffixup" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclassify -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclassify" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplediff -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplediff" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremoveaberrantgenotypes -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremoveaberrantgenotypes" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandom -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandom" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfparsealts -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfparsealts" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstats -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstats" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfflatten -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfflatten" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprimers -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprimers" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnumalt -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnumalt" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcleancomplex -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcleancomplex" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfintersect -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfintersect" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotate -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotate" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfallelicprimitives -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfallelicprimitives" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfoverlay -- Set runtime 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"/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcflength" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfdistance -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfdistance" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandomsample -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandomsample" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfentropy -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfentropy" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglxgt -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglxgt" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfroc -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfroc" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcheck -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcheck" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstreamsort -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstreamsort" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniq -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniq" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniqalleles -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniqalleles" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremap -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremap" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2fasta -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2fasta" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsitesummarize -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsitesummarize" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfbreakmulti -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfbreakmulti" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcreatemulti -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcreatemulti" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfevenregions -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfevenregions" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcat -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcat" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosummarize -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosummarize" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosamplenames -- Set 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path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2dag" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsample2info -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsample2info" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfqual2info -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfqual2info" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfo2qual -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfo2qual" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglbound -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglbound" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfosummarize -- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfosummarize" to "" -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bed2region -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bgziptabix -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2bed.py -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2sqlite.py -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfbiallelic -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclearid -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclearinfo -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcomplex -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffirstheader -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgtcompare.sh -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindelproximity -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindels -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfjoincalls -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfmultiallelic -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfmultiway -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfmultiwayscripts -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnobiallelicsnps -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnoindels -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnosnps -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnulldotslashdot -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplotaltdiscrepancy.r -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplotaltdiscrepancy.sh -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplotsitediscrepancy.r -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplottstv.sh -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprintaltdiscrepancy.r -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprintaltdiscrepancy.sh -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfqualfilter -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce_and_cut -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce_pipe -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce_uncompressed -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremovenonATGC -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsnps -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsort -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf_strip_extra_headers -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfvarstats -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libvcflib.so.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/lib/i386-linux-gnu/libvcflib.so -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/filevercmp.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/IntervalTree.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/catch.hpp -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/multichoose.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/multipermute.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/BedReader.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/Variant.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/cdflib.hpp -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/convert.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/gpatInfo.hpp -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/join.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/makeUnique.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/mt19937ar.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/pdflib.hpp -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/rnglib.hpp -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/split.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/var.hpp -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/vec128int.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/veclib_types.h -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcheck.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/iHS.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfintersect.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/meltEHH.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfclassify.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniq.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstats.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfafpath.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2dag.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfdistance.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandom.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfindex.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/abba-baba.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/popStats.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfentropy.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pFst.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentFst.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfprimers.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/smoother.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffixup.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/bFst.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteSmooth.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcombine.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfqual2info.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfroc.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/hapLrt.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/genotypeSummary.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentIhs.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/plotHaps.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcat.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflib.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflength.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfld.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pVst.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffilter.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfflatten.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/wcFst.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglbound.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotate.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremap.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfecho.1 make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_install find debian -name filevercmp.h -delete cp -a filevercmp/filevercmp.h debian/libvcflib-dev/usr/include/vcflib/ mkdir -p debian/libvcflib-dev/usr/include/intervaltree mv debian/libvcflib-dev/usr/include/vcflib/IntervalTree.h debian/libvcflib-dev/usr/include/intervaltree # install pkg-config file mkdir -p /build/libvcflib-1.0.3+dfsg/debian/libvcflib-dev/usr/lib/i386-linux-gnu/pkgconfig mv libvcflib.pc /build/libvcflib-1.0.3+dfsg/debian/libvcflib-dev/usr/lib/i386-linux-gnu/pkgconfig rm -rf debian/*/usr/lib/vcflib/bin/*.R for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libvcflib-dev/usr/lib/i386-linux-gnu/libvcflib.so: No such file or directory make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake debian/rules override_dh_link make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_link for rscript in debian/libvcflib-tools/usr/lib/vcflib/scripts/*.R ; do \ scriptname=$(basename $rscript) ; \ dh_link -p libvcflib-tools usr/lib/vcflib/scripts/$scriptname usr/lib/R/site-library/vcflib/$scriptname ; \ done make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_fixperms chmod -x debian/*/usr/lib/vcflib/scripts/*.R make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libvcflib1/usr/lib/i386-linux-gnu/libvcflib.so.1 was not linked against libdisorder.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_i386.deb'. dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.3+dfsg-2_i386.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.3+dfsg-2_i386.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.3+dfsg-2_i386.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.3+dfsg-2_i386.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.3+dfsg-2_i386.buildinfo dpkg-genchanges --build=binary -O../libvcflib_1.0.3+dfsg-2_i386.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/126865 and its subdirectories I: Current time: Mon Jun 17 01:50:08 -12 2024 I: pbuilder-time-stamp: 1718632208