I: pbuilder: network access will be disabled during build
I: Current time: Tue May 16 21:27:11 +14 2023
I: pbuilder-time-stamp: 1684222031
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 Sat Oct 8 04:31:55 2022 +14
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/30041/tmp/hooks/D01_modify_environment starting
debug: Running on ionos2-i386.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 May 16 21:27 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/30041/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/30041/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=7 '
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=0d2c5a3dcd0d4488aa356c72fc047610
LANG=C
LANGUAGE=de_CH:de
LC_ALL=C
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
MACHTYPE=i686-pc-linux-gnu
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnu
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=30041
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.omkZmCXZ/pbuilderrc_b9ua --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.omkZmCXZ/b2 --logfile b2/build.log --extrapackages usrmerge libvcflib_1.0.3+dfsg-2.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://78.137.99.97:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-23-686-pae #1 SMP Debian 5.10.179-1 (2023-05-12) i686 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 24 11:24 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 21 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 21 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 6 03:20 dash
-rwxr-xr-x 1 root root 137160 Sep 21 2022 date
-rwxr-xr-x 1 root root 100364 Sep 21 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 21 2022 df
-rwxr-xr-x 1 root root 162152 Sep 21 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 24 00:20 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep
-rwxr-xr-x 1 root root 34664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep
-rwxr-xr-x 1 root root 84272 Mar 24 00:20 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 22:38 fusermount
-rwxr-xr-x 1 root root 218680 Jan 25 04:43 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 20 03:33 hostname
-rwxr-xr-x 1 root root 75756 Sep 21 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 24 01:43 login
-rwxr-xr-x 1 root root 162152 Sep 21 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 24 00:20 lsblk
-rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 24 00:20 more
-rwsr-xr-x 1 root root 58912 Mar 24 00:20 mount
-rwxr-xr-x 1 root root 13856 Mar 24 00:20 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 21 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 6 09:55 sed
lrwxrwxrwx 1 root root 9 May 16 21:27 sh -> /bin/bash
-rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 21 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 24 00:20 su
-rwxr-xr-x 1 root root 38792 Sep 21 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 7 04:25 tar
-rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 21 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 21 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 22:38 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 24 00:20 umount
-rwxr-xr-x 1 root root 38760 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 24 00:20 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/30041/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 <pbuilder-maint@lists.alioth.debian.org>
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]
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Setting up libpkgconf3:i386 (1.8.1-1) ...
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Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libproc2-0:i386 (2:4.0.2-3) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
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-> Finished parsing the build-deps
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usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/30041/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
removed '/etc/unsupported-skip-usrmerge-conversion'
The system has been successfully converted.
I: user script /srv/workspace/pbuilder/30041/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/libvcflib-1.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-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 <tille@debian.org>
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
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-- 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:
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cd obj-i686-linux-gnu && make -j7 "INSTALL=install --strip-program=true" VERBOSE=1
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[ 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/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/var.cpp.o
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[ 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
/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
[ 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/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
[ 4%] Building C object CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 5%] Linking CXX shared library libvcflib.so
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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 -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend
/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/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
[ 6%] Building CXX object CMakeFiles/pVst.dir/src/pVst.cpp.o
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=
/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/pVst.dir/src/pVst.cpp.o -MF CMakeFiles/pVst.dir/src/pVst.cpp.o.d -o CMakeFiles/pVst.dir/src/pVst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/pVst.cpp
[ 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.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/wcFst.dir/build.make CMakeFiles/wcFst.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 8%] Building CXX object CMakeFiles/popStats.dir/src/popStats.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/popStats.dir/src/popStats.cpp.o -MF CMakeFiles/popStats.dir/src/popStats.cpp.o.d -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/popStats.cpp
[ 9%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/dumpContigsFromHeader.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 9%] 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
[ 10%] 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
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'
[ 10%] Built target dumpContigsFromHeader
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/iHS.dir/DependInfo.cmake --color=
[ 10%] Built target vcfecho
make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.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]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
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 -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.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'
[ 11%] Building CXX object CMakeFiles/iHS.dir/src/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/iHS.dir/src/iHS.cpp.o -MF CMakeFiles/iHS.dir/src/iHS.cpp.o.d -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/iHS.cpp
[ 11%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.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/segmentFst.dir/src/segmentFst.cpp.o -MF CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o.d -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/segmentFst.cpp
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 12%] Linking CXX executable segmentFst
/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.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/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 12%] Built target segmentFst
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/segmentIhs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
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'
[ 12%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.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/segmentIhs.dir/src/segmentIhs.cpp.o -MF CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o.d -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp
[ 13%] 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
[ 14%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 14%] Built target wcFst
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'
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=
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 15%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.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/genotypeSummary.dir/src/genotypeSummary.cpp.o -MF CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o.d -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 15%] Built target bFst
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/sequenceDiversity.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]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 15%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.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/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
[ 16%] 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'
[ 17%] Linking CXX executable popStats
/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1
[ 17%] Built target pVst
make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.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/pFst.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/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'
make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 17%] Building CXX object CMakeFiles/pFst.dir/src/pFst.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/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
[ 18%] Linking CXX executable segmentIhs
/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 18%] Built target popStats
make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.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/smoother.dir/DependInfo.cmake --color=
make[4]: Leaving 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'
[ 19%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 19%] Built target segmentIhs
make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.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/vcfld.dir/DependInfo.cmake --color=
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
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 20%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 20%] Linking CXX executable hapLrt
/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.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/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 20%] Built target hapLrt
make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.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/plotHaps.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 21%] 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/vcfld.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 21%] Linking CXX executable smoother
/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.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/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
[ 21%] 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/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
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'
[ 21%] Built target smoother
make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend
[ 21%] Built target iHS
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 -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'
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'
[ 22%] 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
[ 22%] 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
[ 22%] Linking CXX executable genotypeSummary
/usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.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/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'
[ 22%] Built target genotypeSummary
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=
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make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 23%] 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
[ 24%] Linking CXX executable pFst
/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 24%] Built target pFst
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'
[ 24%] 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
[ 24%] 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'
[ 24%] Built target permuteGPAT++
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'
[ 25%] 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
[ 26%] 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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 26%] Built target sequenceDiversity
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=
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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'
[ 27%] 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
[ 28%] Linking CXX executable normalize-iHS
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make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 28%] 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=
[ 28%] Linking CXX executable plotHaps
/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1
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'
/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
[ 29%] 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
[ 29%] 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'
[ 29%] Built target plotHaps
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'
[ 30%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 30%] Built target permuteSmooth
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=
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'
[ 31%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfhetcount.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 32%] Linking CXX executable vcfld
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 32%] Built target vcfld
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=
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'
[ 33%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcffilter.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 34%] Linking CXX executable abba-baba
/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 34%] Built target abba-baba
make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.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/vcfgenotypes.dir/DependInfo.cmake --color=
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
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 34%] 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
[ 34%] Linking CXX executable vcfaltcount
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 34%] Built target vcfaltcount
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=
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'
[ 35%] 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
[ 35%] 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'
[ 35%] Built target vcfhetcount
make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.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/vcfcommonsamples.dir/DependInfo.cmake --color=
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'
[ 36%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 36%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 36%] Built target vcfhethomratio
make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.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/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'
[ 36%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 37%] 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
[ 38%] Linking CXX executable vcfcommonsamples
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.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/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
[ 39%] 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
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'
[ 39%] Built target vcfcommonsamples
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=
[ 39%] Built target vcf2tsv
make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.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/vcfsamplenames.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'
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]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 40%] 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
[ 41%] 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
[ 42%] 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'
[ 42%] Built target meltEHH
make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.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/vcfgenotypecompare.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'
[ 42%] 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[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 42%] Built target vcfgenotypes
make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.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=
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
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 42%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 43%] Linking CXX executable vcffilter
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.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/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
[ 44%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 44%] Built target vcfremovesamples
make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.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/vcfclassify.dir/DependInfo.cmake --color=
[ 44%] Built target vcffilter
make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
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'
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]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 45%] 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
make[4]: Leaving 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'
[ 46%] 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
[ 47%] 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'
[ 47%] Built target vcfsamplenames
make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.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/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color=
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'
[ 47%] 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
[ 47%] 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'
[ 47%] Built target vcfkeepsamples
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'
[ 48%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfrandom.cpp:13:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 49%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 49%] Built target vcffixup
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=
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'
[ 49%] 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
[ 49%] Linking CXX executable vcfclassify
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.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/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 49%] Built target vcfclassify
make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.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/vcfstats.dir/DependInfo.cmake --color=
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'
[ 49%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 49%] Linking CXX executable vcfrandom
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.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/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
[ 50%] 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'
[ 51%] Linking CXX executable vcfremoveaberrantgenotypes
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1
[ 51%] Built target vcfrandom
make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.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/vcfflatten.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/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'
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'
[ 51%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 51%] Built target vcfannotategenotypes
make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.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/vcfprimers.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'
[ 51%] Built target vcfremoveaberrantgenotypes
make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build
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'
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=
[ 52%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.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/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
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'
[ 52%] 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
[ 52%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 52%] Built target vcfsamplediff
make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.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/vcfcleancomplex.dir/DependInfo.cmake --color=
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'
[ 53%] 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/vcfflatten.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfprimers.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfnumalt.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfcleancomplex.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 54%] Linking CXX executable vcfparsealts
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.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/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 54%] Built target vcfparsealts
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'
[ 54%] 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
[ 55%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 55%] Built target vcfgenotypecompare
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'
[ 56%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 56%] Linking CXX executable vcfprimers
/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'
[ 56%] Built target vcfprimers
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'
[ 57%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 58%] 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/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'
[ 58%] Built target vcfnumalt
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'
[ 58%] 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
[ 58%] Linking CXX executable vcfcleancomplex
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.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
[ 59%] Linking CXX executable vcfflatten
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 59%] Built target vcfcleancomplex
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=
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'
[ 59%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 59%] Built target vcfflatten
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'
[ 60%] 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/vcfoverlay.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfaddinfo.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfkeepinfo.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 61%] Linking CXX executable vcfstats
/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 61%] Built target vcfstats
make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.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]: 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'
[ 62%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 63%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 63%] Built target vcfaddinfo
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/vcfafpath.dir/DependInfo.cmake --color=
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'
[ 63%] 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
[ 63%] 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'
[ 63%] Built target vcfkeepinfo
make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.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/vcfcountalleles.dir/DependInfo.cmake --color=
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'
[ 63%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 63%] Linking CXX executable vcfkeepgeno
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 63%] Built target vcfkeepgeno
make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.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/vcflength.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
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'
[ 63%] 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/vcfcountalleles.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 64%] Linking CXX executable vcfoverlay
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.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/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]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 64%] Built target vcfoverlay
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]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 65%] Linking CXX executable vcfcountalleles
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1
[ 65%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.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/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
/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 65%] Built target vcfcountalleles
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'
[ 66%] 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
[ 66%] 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
[ 67%] 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/vcfdistance.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 67%] Built target vcfannotate
make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.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/vcfentropy.dir/DependInfo.cmake --color=
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'
[ 68%] 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'
[ 68%] Built target vcfafpath
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'
[ 69%] 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
[ 70%] Linking CXX executable vcflength
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 70%] Built target vcflength
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'
[ 71%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfentropy.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 72%] Linking CXX executable vcfintersect
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.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/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'
[ 72%] Linking CXX executable vcfallelicprimitives
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1
[ 72%] Built target vcfintersect
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=
/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
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'
[ 72%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 72%] Built target vcfallelicprimitives
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'
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'
[ 72%] 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
[ 73%] Linking CXX executable vcfdistance
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 73%] Built target vcfdistance
make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.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/vcfuniq.dir/DependInfo.cmake --color=
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'
[ 74%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 75%] Linking CXX executable vcfrandomsample
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 75%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 75%] Built target vcfrandomsample
make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend
[ 75%] Linking CXX executable vcfglxgt
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.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/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/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'
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'
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 76%] 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
[ 76%] Built target vcfentropy
make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.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/vcfremap.dir/DependInfo.cmake --color=
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'
[ 76%] 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]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 76%] Built target vcfglxgt
make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.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/vcf2fasta.dir/DependInfo.cmake --color=
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
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 77%] 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
[ 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 78%] Built target vcfcheck
make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.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/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'
[ 78%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfremap.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcf2fasta.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 78%] Linking CXX executable vcfuniq
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 78%] Built target vcfuniq
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 -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 78%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfbreakmulti.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 78%] 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'
[ 78%] Built target vcfuniqalleles
make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.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/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'
[ 78%] 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
[ 79%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 79%] Built target vcfsitesummarize
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=
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'
[ 80%] 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
[ 81%] 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'
[ 81%] Built target vcfstreamsort
make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.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=
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 81%] 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
[ 82%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 82%] Built target vcfremap
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/vcfgenosummarize.dir/DependInfo.cmake --color=
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'
[ 83%] 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
[ 83%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 83%] Built target vcf2fasta
make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.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/vcfgenosamplenames.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'
[ 84%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.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/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
[ 85%] Linking CXX executable vcfbreakmulti
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.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/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
[ 85%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 85%] Built target vcfbreakmulti
make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend
[ 85%] Built target vcfroc
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/vcfgeno2haplo.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/vcfleftalign.dir/DependInfo.cmake --color=
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
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/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 86%] 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
[ 86%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 86%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfleftalign.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 86%] Built target vcfevenregions
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'
[ 87%] 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
[ 88%] 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'
[ 89%] Linking CXX executable vcfcreatemulti
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1
[ 89%] Built target vcfcat
make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend
/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
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
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 90%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 90%] Built target vcfcreatemulti
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'
[ 91%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfgeno2alleles.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfindex.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 91%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 91%] Built target vcfgenosamplenames
make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.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]: 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'
[ 92%] 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
[ 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 93%] Built target vcfgenosummarize
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/vcfsample2info.dir/DependInfo.cmake --color=
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
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 94%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfsample2info.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 94%] 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
[ 95%] Linking CXX executable vcfindex
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1
[ 95%] Built target vcfgeno2alleles
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=
/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'
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'
[ 96%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 96%] Built target vcfindex
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'
[ 96%] 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/vcfqual2info.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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/vcfinfo2qual.cpp:10:
/build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 96%] 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'
[ 96%] Built target vcf2dag
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=
[ 97%] 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'
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'
[ 97%] 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
/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
[ 97%] Linking CXX executable vcfsample2info
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.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/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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 97%] Built target vcfleftalign
make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend
[ 97%] Linking CXX executable vcfcombine
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=
/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
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/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build
make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 97%] Built target vcfsample2info
[ 97%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 97%] Built target vcfcombine
[ 97%] 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
[ 98%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 98%] Built target vcfqual2info
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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'
[ 98%] Built target vcfinfo2qual
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 98%] 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'
[ 98%] Built target vcfgeno2haplo
[ 99%] 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
make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-i686-linux-gnu'
[ 99%] Built target vcfglbound
[100%] 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'
[100%] Built target vcfinfosummarize
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/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 (5596 ms)
[----------] 1 test from Variant (5596 ms total)
[----------] 4 tests from VariantCallFile
[ RUN ] VariantCallFile.open
[ OK ] VariantCallFile.open (1 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 (12 ms total)
[----------] Global test environment tear-down
[==========] 5 tests from 2 test suites ran. (5609 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 -j7 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 path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfoverlay" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaddinfo
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaddinfo" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepinfo
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepinfo" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepgeno
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepgeno" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfafpath
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfafpath" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcountalleles
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcountalleles" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcflength
-- Set runtime path of "/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 runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosamplenames" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2haplo
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2haplo" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfleftalign
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfleftalign" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcombine
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcombine" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2alleles
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2alleles" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindex
-- Set runtime path of "/build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindex" to ""
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2dag
-- Set runtime 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/vcfgeno2haplo.1
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfecho.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/vcfcleancomplex.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/vcfstats.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/vcfroc.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/vcfclassify.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/permuteSmooth.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/vcfcat.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/vcfrandomsample.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/vcfcountalleles.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/vcfflatten.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/vcfhetcount.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/vcfprimers.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/vcfaltcount.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/vcfremap.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/vcfindex.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/vcfgenosamplenames.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/hapLrt.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/vcf2tsv.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/vcflib.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/vcfgenotypes.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/vcf2dag.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/segmentIhs.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/vcfcommonsamples.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/vcfglbound.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/abba-baba.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/pFst.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/vcfsamplediff.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/vcfgeno2alleles.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/vcfgenosummarize.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/vcffilter.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/vcflength.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/normalize-iHS.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/vcfleftalign.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/vcfentropy.1
-- 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/vcfqual2info.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/vcfaddinfo.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/vcfintersect.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/vcfcreatemulti.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/vcfhethomratio.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/vcfcombine.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/vcfannotategenotypes.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/vcfuniq.1
-- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfdistance.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-dev' in '../libvcflib-dev_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-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: user script /srv/workspace/pbuilder/30041/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/30041/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/30041 and its subdirectories
I: Current time: Tue May 16 21:31:25 +14 2023
I: pbuilder-time-stamp: 1684222285