I: pbuilder: network access will be disabled during build I: Current time: Tue May 30 19:36:31 -12 2023 I: pbuilder-time-stamp: 1685518591 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libvcflib_1.0.3+dfsg-2.dsc] I: copying [./libvcflib_1.0.3+dfsg.orig.tar.xz] I: copying [./libvcflib_1.0.3+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Oct 7 02:31:55 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libvcflib_1.0.3+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting libvcflib in libvcflib-1.0.3+dfsg dpkg-source: info: unpacking libvcflib_1.0.3+dfsg.orig.tar.xz dpkg-source: info: unpacking libvcflib_1.0.3+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_fsom dpkg-source: info: applying use_debian_packaged_smithwaterman.patch dpkg-source: info: applying use_debian_packaged_fastahack.patch dpkg-source: info: applying use_debian_packaged_libssw.patch dpkg-source: info: applying shared_lib.patch dpkg-source: info: applying pkg-config.patch dpkg-source: info: applying tabix_linking dpkg-source: info: applying tests I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10593/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='28a74c57626b44cd967e80a1aae07a21' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='10593' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QwhaB0Cr/pbuilderrc_SEFn --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QwhaB0Cr/b1 --logfile b1/build.log libvcflib_1.0.3+dfsg-2.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux ff4a 5.10.0-23-armmp-lpae #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash -rwxr-xr-x 1 root root 133220 Sep 20 2022 date -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd -rwxr-xr-x 1 root root 68104 Sep 20 2022 df -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep -rwxr-xr-x 1 root root 67548 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch -rwxr-xr-x 1 root root 67548 Sep 20 2022 true -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew I: user script /srv/workspace/pbuilder/10593/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: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libsmithwaterman-dev, libssw-dev, libfastahack-dev, pkg-config, libgtest-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19324 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 32.1 MB of archives. After unpacking 118 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf libproc2-0 armhf 2:4.0.2-3 [54.2 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf procps armhf 2:4.0.2-3 [695 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libarchive13 armhf 3.6.2-1 [299 kB] Get: 21 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 23 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf libcurl4 armhf 7.88.1-9 [347 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf libexpat1 armhf 2.5.0-1 [79.9 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libjsoncpp25 armhf 1.9.5-4 [68.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf librhash0 armhf 1.4.3-3 [146 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libuv1 armhf 1.44.2-1 [126 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf cmake armhf 3.25.1-1 [4263 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf googletest all 1.12.1-0.2 [506 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libbz2-dev armhf 1.0.8-5+b1 [28.1 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB] Get: 53 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4+b1 [5220 B] Get: 56 http://deb.debian.org/debian bookworm/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4+b1 [4732 B] Get: 57 http://deb.debian.org/debian bookworm/main armhf libfastahack0 armhf 1.0.0+dfsg-10 [24.3 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libfastahack-dev armhf 1.0.0+dfsg-10 [27.9 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libgtest-dev armhf 1.12.1-0.2 [232 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12+b1 [33.0 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12+b1 [38.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libssw0 armhf 1.1-13 [21.2 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libssw-dev armhf 1.1-13 [24.3 kB] Get: 70 http://deb.debian.org/debian bookworm/main armhf libtabixpp0 armhf 1.1.2-1 [8696 B] Get: 71 http://deb.debian.org/debian bookworm/main armhf libtabixpp-dev armhf 1.1.2-1 [8532 B] Get: 72 http://deb.debian.org/debian bookworm/main armhf markdown all 1.0.1-12 [17.7 kB] Get: 73 http://deb.debian.org/debian bookworm/main armhf pkgconf-bin armhf 1.8.1-1 [28.5 kB] Get: 74 http://deb.debian.org/debian bookworm/main armhf pkgconf armhf 1.8.1-1 [25.9 kB] Get: 75 http://deb.debian.org/debian bookworm/main armhf pkg-config armhf 1.8.1-1 [13.7 kB] Fetched 32.1 MB in 4s (8749 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19324 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_armhf.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.44-3_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../04-libmagic1_1%3a5.44-3_armhf.deb ... Unpacking libmagic1:armhf (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.44-3_armhf.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-12_armhf.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.7-1_armhf.deb ... Unpacking libuchardet0:armhf (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.22.4-10_armhf.deb ... Unpacking groff-base (1.22.4-10) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/libvcflib-1.0.3+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libvcflib_1.0.3+dfsg-2_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.3+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf 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-arm-linux-gnueabihf && 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/arm-linux-gnueabihf -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/arm-linux-gnueabihf/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for lzma_auto_decoder in /usr/lib/arm-linux-gnueabihf/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/arm-linux-gnueabihf/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/arm-linux-gnueabihf/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/arm-linux-gnueabihf/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/arm-linux-gnueabihf/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/arm-linux-gnueabihf/liblzma.so - found -- Found LibLZMA: /usr/lib/arm-linux-gnueabihf/liblzma.so (found version "5.4.1") -- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.13") -- -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.16 -- Checking for module 'tabixpp' -- Package 'tabixpp', required by 'virtual:world', not found -- Checking for module 'libsmithwaterman' -- Found libsmithwaterman, version 0.0 -- Checking for module 'libfastahack' -- Found libfastahack, version 0.0 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") Pandoc needs to be installed to generate the man pages -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_auto_build cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libvcflib-1.0.3+dfsg -B/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o [ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/var.cpp /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/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 In file included from /build/libvcflib-1.0.3+dfsg/src/Variant.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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 In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/var.hpp:17, from /build/libvcflib-1.0.3+dfsg/src/var.cpp:20: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:286:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:287:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:288:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:293:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:296:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:300:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:303:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:304:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:305:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:306:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:307:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void genotype::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:308:26: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'virtual void pooled::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:185:18: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void pooled::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:187:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'virtual void pooled::loadPop(std::vector, std::vector > > >&, std::string, long int)' at /build/libvcflib-1.0.3+dfsg/src/var.cpp:188:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 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 [ 5%] Linking CXX shared library libvcflib.so /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libvcflib.so.1 -o libvcflib.so.1 CMakeFiles/vcflib.dir/src/Variant.cpp.o CMakeFiles/vcflib.dir/src/rnglib.cpp.o CMakeFiles/vcflib.dir/src/var.cpp.o CMakeFiles/vcflib.dir/src/pdflib.cpp.o CMakeFiles/vcflib.dir/src/cdflib.cpp.o CMakeFiles/vcflib.dir/src/split.cpp.o CMakeFiles/vcflib.dir/filevercmp/filevercmp.c.o -lssw -ltabixpp -lsmithwaterman -ldisorder -lfastahack /usr/bin/cmake -E cmake_symlink_library libvcflib.so.1 libvcflib.so.1 libvcflib.so make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 5%] Built target vcflib make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/depend cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfecho.dir/DependInfo.cmake --color= make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/dumpContigsFromHeader.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/bFst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfecho.dir/build.make CMakeFiles/vcfecho.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/dumpContigsFromHeader.dir/build.make CMakeFiles/dumpContigsFromHeader.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 6%] Building CXX object CMakeFiles/vcfecho.dir/src/vcfecho.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/vcfecho.dir/src/vcfecho.cpp.o -MF CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o.d -o CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/bFst.dir/build.make CMakeFiles/bFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 6%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-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/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp [ 6%] Building CXX object CMakeFiles/bFst.dir/src/bFst.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/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 In file included from /build/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfecho.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 7%] 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-arm-linux-gnueabihf' [ 7%] Built target dumpContigsFromHeader make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pVst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/pVst.dir/build.make CMakeFiles/pVst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 7%] Building CXX object CMakeFiles/pVst.dir/src/pVst.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/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%] Linking CXX executable vcfecho /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 7%] Built target vcfecho make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/hapLrt.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 8%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void phardy(std::vector&, double, double)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:179:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void phardy(std::vector&, double, double)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:180:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void phardy(std::vector&, double, double)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:181:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadPop(std::vector, std::vector > > >&, pop&)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:73:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadPop(std::vector, std::vector > > >&, pop&)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:74:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadPop(std::vector, std::vector > > >&, pop&)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:75:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/bFst.cpp:583:22: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void calc(copyNcounts*)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:203:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void calc(copyNcounts*)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:206:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 9%] 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-arm-linux-gnueabihf' [ 9%] Built target bFst make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 10%] 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 In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadDat(copyNcounts*, std::string&, std::vector, std::vector > > >&, std::vector, std::vector > > >&)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:265:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadDat(copyNcounts*, std::string&, std::vector, std::vector > > >&, std::vector, std::vector > > >&)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:266:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadDat(copyNcounts*, std::string&, std::vector, std::vector > > >&, std::vector, std::vector > > >&)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:274:28: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void loadDat(copyNcounts*, std::string&, std::vector, std::vector > > >&, std::vector, std::vector > > >&)' at /build/libvcflib-1.0.3+dfsg/src/pVst.cpp:275:23: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/popStats.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:609:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 11%] 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-arm-linux-gnueabihf' [ 11%] Built target pVst make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/wcFst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 12%] 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/wcFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 12%] 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-arm-linux-gnueabihf' [ 12%] Built target hapLrt make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/iHS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 13%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] Linking CXX executable popStats /usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.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/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-arm-linux-gnueabihf' [ 14%] Built target popStats make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentFst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 14%] 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 /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, from /build/libvcflib-1.0.3+dfsg/src/segmentFst.cpp:59: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/segmentFst.cpp:294:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 15%] 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 In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool gDist(int, int, double*)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:106:40: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool gDist(int, int, double*)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:106:69: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] 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-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 15%] 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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void loadGeneticMap(int, int)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:151:25: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 16%] Linking CXX executable wcFst /usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 16%] Built target wcFst In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 17%] 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 In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, from /build/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp:59: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp:291:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/iHS.cpp:648:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target segmentIhs make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 18%] 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 [ 18%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 18%] Built target iHS make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pFst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 18%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/pFst.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 18%] 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-arm-linux-gnueabihf' [ 18%] Built target genotypeSummary make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/smoother.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 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 [ 20%] 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 [ 21%] Linking CXX executable pFst /usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 21%] Built target sequenceDiversity /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfld.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 22%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 22%] Built target pFst make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/plotHaps.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 23%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 23%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 23%] Built target smoother make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/abba-baba.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 23%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/abba-baba.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:375:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 23%] Linking CXX executable plotHaps /usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 23%] Built target plotHaps make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 24%] 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 [ 25%] Linking CXX executable abba-baba /usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.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/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-arm-linux-gnueabihf' [ 25%] Built target abba-baba make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 26%] 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 In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, from /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:49: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:184:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 27%] 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 [ 27%] 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-arm-linux-gnueabihf' [ 27%] Built target vcfld make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 27%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 27%] 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-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 28%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, from /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:49: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'bool getContiguousWindow(std::vector&, std::vector&, int, int*)' at /build/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:249:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/libvcflib-1.0.3+dfsg/src/split.h:15, from /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:59: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void normalize(std::vector&, int*)' at /build/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:229:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 29%] Linking CXX executable normalize-iHS /usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 29%] Built target normalize-iHS make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend [ 29%] Linking CXX executable permuteSmooth /usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1 make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/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]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 30%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 30%] Built target permuteSmooth make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 31%] 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 In file included from /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool gDist(int, int, double*)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:105:40: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'bool gDist(int, int, double*)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:105:69: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void loadGeneticMap(int, int)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:150:25: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:636:20: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 31%] 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-arm-linux-gnueabihf' [ 31%] Built target vcfaltcount make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 32%] 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 [ 32%] 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-arm-linux-gnueabihf' [ 32%] Built target vcfhetcount make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 33%] 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/vcfhethomratio.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 34%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcffilter.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 34%] Built target meltEHH make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] 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/vcf2tsv.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 35%] 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-arm-linux-gnueabihf' [ 35%] Built target vcfhethomratio make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 35%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 36%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 36%] Built target vcf2tsv make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 37%] 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 [ 38%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 38%] Built target vcffilter make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 39%] 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/vcfannotategenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 40%] 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-arm-linux-gnueabihf' [ 40%] Built target vcfgenotypes make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 40%] 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/vcfcommonsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 41%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 41%] 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-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 42%] 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 [ 43%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 43%] Built target vcfremovesamples make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 44%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >, std::__cxx11::basic_string, std::allocator > >&&>, std::tuple<>}; _Key = std::pair, std::__cxx11::basic_string >; _Val = std::pair, std::__cxx11::basic_string >, vcflib::Variant>; _KeyOfValue = std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] 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 [ 45%] 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 In file included from /usr/include/c++/12/map:61: /usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair, std::__cxx11::basic_string >; _Tp = vcflib::Variant; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]': /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 45%] Built target vcfkeepsamples make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color= [ 45%] Built target vcfsamplenames make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffixup.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 45%] 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 [ 45%] 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/vcffixup.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:202:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:201:28: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair, std::__cxx11::basic_string >; _Tp = vcflib::Variant; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:215:62: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair, std::__cxx11::basic_string >; _Tp = vcflib::Variant; _Compare = std::less, std::__cxx11::basic_string > >; _Alloc = std::allocator, std::__cxx11::basic_string >, vcflib::Variant> >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:218:62: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::__cxx11::basic_string >, std::pair, std::__cxx11::basic_string >, vcflib::Variant>, std::_Select1st, std::__cxx11::basic_string >, vcflib::Variant> >, std::less, std::__cxx11::basic_string > >, std::allocator, std::__cxx11::basic_string >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 46%] 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 [ 47%] 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-arm-linux-gnueabihf' [ 47%] Built target vcffixup make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 48%] 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-arm-linux-gnueabihf' [ 48%] Built target vcfannotategenotypes make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 49%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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-arm-linux-gnueabihf' [ 49%] Built target vcfclassify make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 49%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] 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 [ 50%] 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-arm-linux-gnueabihf' [ 50%] Built target vcfgenotypecompare make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 51%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 51%] Built target vcfsamplediff make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 51%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:13: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:10: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] Linking CXX executable vcfremoveaberrantgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstats.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 52%] 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 [ 53%] 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-arm-linux-gnueabihf' [ 53%] Built target vcfparsealts make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 53%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 53%] Built target vcfrandom make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] 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-arm-linux-gnueabihf' [ 54%] Built target vcfprimers make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 54%] 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 [ 55%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 55%] Built target vcfflatten make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 56%] 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/vcfnumalt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] 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-arm-linux-gnueabihf' [ 57%] Built target vcfstats make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 57%] 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 [ 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-arm-linux-gnueabihf' [ 58%] Built target vcfnumalt make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 59%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 59%] Built target vcfcleancomplex make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 60%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = vcflib::VariantAllele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:61: /usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = vcflib::VariantAllele; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long unsigned int; _Tp = vcflib::Variant; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 60%] Linking CXX executable vcfannotate /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 60%] Built target vcfannotate make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 60%] 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 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = vcflib::VariantAllele; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:207:46: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long unsigned int; _Tp = vcflib::Variant; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:306:46: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 61%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 61%] Built target vcfintersect make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 61%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Linking CXX executable vcfallelicprimitives /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 61%] Built target vcfallelicprimitives make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 62%] 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 [ 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-arm-linux-gnueabihf' [ 63%] Built target vcfaddinfo make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 64%] 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/vcfkeepinfo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] 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-arm-linux-gnueabihf' [ 65%] Built target vcfoverlay make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] 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 [ 65%] 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-arm-linux-gnueabihf' [ 65%] 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-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Linking CXX executable vcfkeepgeno /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1 /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-arm-linux-gnueabihf' [ 65%] 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-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 65%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcflength.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:78:26: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 66%] Linking CXX executable vcfcountalleles /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/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-arm-linux-gnueabihf' [ 66%] Built target vcfcountalleles make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 66%] 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 [ 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 67%] Built target vcfafpath make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 68%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 69%] Built target vcflength make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 70%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 71%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 71%] Built target vcfdistance make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 72%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 72%] 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 [ 73%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 73%] Built target vcfentropy make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfroc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Built target vcfrandomsample make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Linking CXX executable vcfglxgt /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/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-arm-linux-gnueabihf' [ 74%] Built target vcfglxgt make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 74%] 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 [ 75%] 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-arm-linux-gnueabihf' [ 75%] Built target vcfcheck make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 76%] 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/map:60, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:15: /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 /usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long double; _Val = std::pair >; _KeyOfValue = std::_Select1st > >; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 In file included from /usr/include/c++/12/map:61: /usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]': /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ [ 76%] 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-arm-linux-gnueabihf' [ 76%] Built target vcfuniq make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 77%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:257:33: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:278:52: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:305:50: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:306:63: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:314:50: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:316:63: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 512 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector; _Compare = std::less; _Alloc = std::allocator > >]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:384:88: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree >, std::_Select1st > >, std::less, std::allocator > > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp:117:71: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 77%] 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-arm-linux-gnueabihf' [ 77%] Built target vcfuniqalleles make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 77%] 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 [ 77%] 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/vcfremap.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 77%] Built target vcfroc make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 78%] 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 [ 79%] 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-arm-linux-gnueabihf' [ 79%] Built target vcfstreamsort make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 79%] 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/vcf2fasta.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Linking CXX executable vcfsitesummarize /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] Built target vcfsitesummarize make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 80%] 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 [ 81%] 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-arm-linux-gnueabihf' [ 81%] Built target vcfremap make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 81%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Linking CXX executable vcf2fasta /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 81%] Built target vcf2fasta make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 82%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -MF CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o.d -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:100:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ [ 83%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 83%] Built target vcfbreakmulti make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 83%] 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 In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcat.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 83%] Built target vcfevenregions make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 84%] 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 [ 85%] Linking CXX executable vcfcreatemulti /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 85%] Built target vcfcreatemulti make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 86%] 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 [ 87%] 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-arm-linux-gnueabihf' [ 87%] Built target vcfcat make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 88%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 89%] 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-arm-linux-gnueabihf' [ 89%] Built target vcfgenosummarize make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 89%] 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 [ 89%] 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-arm-linux-gnueabihf' [ 89%] Built target vcfgenosamplenames make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 90%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -MF CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o.d -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'double entropy(const std::string&)' at /build/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:140:24: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: /usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator]': /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 90%] 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-arm-linux-gnueabihf' [ 90%] Built target vcfgeno2haplo make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 91%] 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 [ 92%] Linking CXX executable vcfleftalign /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.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/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 92%] Built target vcfleftalign make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] 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 [ 93%] Linking CXX executable vcfcombine /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 93%] Built target vcfcombine make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 94%] 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfindex.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 94%] Built target vcfgeno2alleles make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 95%] 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 [ 96%] Linking CXX executable vcfindex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 96%] Built target vcfindex make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/build/libvcflib-1.0.3+dfsg/include -I/build/libvcflib-1.0.3+dfsg/intervaltree -I/build/libvcflib-1.0.3+dfsg/multichoose -I/build/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp In file included from /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/queue:62, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:23: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ [ 97%] 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-arm-linux-gnueabihf' [ 97%] Built target vcf2dag make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] 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 /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:194:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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 make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 97%] Built target vcfqual2info make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 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 [ 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-arm-linux-gnueabihf' [ 97%] Built target vcfsample2info make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' cd /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /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-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' [ 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 In file included from /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:10: /build/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:13: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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-arm-linux-gnueabihf' [ 98%] Built target vcfinfo2qual In file included from /usr/include/c++/12/queue:62, from /build/libvcflib-1.0.3+dfsg/src/Variant.h:23: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:137:34: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'int main(int, char**)' at /build/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:204:31: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [ 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-arm-linux-gnueabihf' [ 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-arm-linux-gnueabihf' [100%] Built target vcfinfosummarize make[3]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0 make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' 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-arm-linux-gnueabihf/:$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-arm-linux-gnueabihf/ -L../googletest/googletest/make/ -lm -ltabixpp -lhts -lpthread In file included from tests/variantTests.h:2, from tests/mainTest.cpp:4: ../src/Variant.h:651:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/unique_ptr.h:37, from /usr/include/c++/12/memory:76, from /usr/include/gtest/gtest.h:54, from tests/mainTest.cpp:3: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ../src/Variant.h:652:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 652 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ ./tests/main [==========] Running 5 tests from 2 test suites. [----------] Global test environment set-up. [----------] 1 test from Variant [ RUN ] Variant.correctGenotype [ OK ] Variant.correctGenotype (19341 ms) [----------] 1 test from Variant (19341 ms total) [----------] 4 tests from VariantCallFile [ RUN ] VariantCallFile.open [ OK ] VariantCallFile.open (4 ms) [ RUN ] VariantCallFile.recordCountUncompressed [ OK ] VariantCallFile.recordCountUncompressed (1 ms) [ RUN ] VariantCallFile.recordCountCompressed [ OK ] VariantCallFile.recordCountCompressed (43 ms) [ RUN ] VariantCallFile.sampleNamesCompressed [ OK ] VariantCallFile.sampleNamesCompressed (19 ms) [----------] 4 tests from VariantCallFile (69 ms total) [----------] Global test environment tear-down [==========] 5 tests from 2 test suites ran. (19411 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-arm-linux-gnueabihf && make -j3 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-arm-linux-gnueabihf' /usr/bin/cmake -S/build/libvcflib-1.0.3+dfsg -B/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' 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/arm-linux-gnueabihf/libvcflib.so.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/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/plotHaps.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/vcfcreatemulti.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/vcfuniq.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/pVst.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/vcfgeno2alleles.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/vcfafpath.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/vcfecho.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/wcFst.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/vcffixup.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/dumpContigsFromHeader.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhetcount.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/vcfld.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/vcfinfo2qual.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/vcfkeepinfo.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/vcfsample2info.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/bFst.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/vcfqual2info.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/vcfremovesamples.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/vcfgenosummarize.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/vcf2dag.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/vcfcombine.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/vcfannotate.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/vcfglbound.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/vcfaddinfo.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/vcfrandomsample.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/vcflib.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/vcfremap.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/vcfoverlay.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/vcfdistance.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/vcfcat.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/segmentIhs.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/vcfroc.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/permuteGPAT++.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/popStats.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/vcfgenosamplenames.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/vcffilter.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/vcfrandom.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/vcfuniqalleles.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/vcfsamplenames.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.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/vcfnulldotslashdot.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/vcf2tsv.1 -- Installing: /build/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1 make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf' 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/arm-linux-gnueabihf/pkgconfig mv libvcflib.pc /build/libvcflib-1.0.3+dfsg/debian/libvcflib-dev/usr/lib/arm-linux-gnueabihf/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?' ${pl} ; \ done grep: debian/libvcflib-dev/usr/lib/arm-linux-gnueabihf/libvcflib.so: No such file or directory make[1]: Leaving directory '/build/libvcflib-1.0.3+dfsg' dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake debian/rules override_dh_link make[1]: Entering directory '/build/libvcflib-1.0.3+dfsg' dh_link for rscript in debian/libvcflib-tools/usr/lib/vcflib/scripts/*.R ; do \ scriptname=$(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: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libvcflib1/usr/lib/arm-linux-gnueabihf/libvcflib.so.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libvcflib1/usr/lib/arm-linux-gnueabihf/libvcflib.so.1 was not linked against libdisorder.so.0 (it uses none of the library's symbols) dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfecho contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfnumalt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/segmentFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfoverlay contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfevenregions contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/permuteGPAT++ contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/hapLrt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/permuteSmooth contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/popStats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplenames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstreamsort contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/genotypeSummary contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/normalize-iHS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfintersect contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfhethomratio contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsitesummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2dag contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcffixup contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcommonsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/smoother contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremovesamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2alleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepgeno contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosamplenames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfld contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcheck contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypecompare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/sequenceDiversity contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfdistance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandomsample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfindex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaltcount contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2haplo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfentropy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfqual2info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotategenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcreatemulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/dumpContigsFromHeader contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/meltEHH contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/pFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcountalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2tsv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcleancomplex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfflatten contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcflength contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/segmentIhs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfclassify contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcffilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfparsealts contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfafpath contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcombine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/abba-baba contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/pVst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfbreakmulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplediff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfroc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfinfosummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/wcFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/iHS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcf2tsv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/plotHaps contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcffilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglxgt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremoveaberrantgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcffixup contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaddinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfinfo2qual contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfprimers contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfhetcount contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsample2info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfkeepinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/bFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglbound contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin 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 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.3+dfsg-2_armhf.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.3+dfsg-2_armhf.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.3+dfsg-2_armhf.buildinfo dpkg-genchanges --build=binary -O../libvcflib_1.0.3+dfsg-2_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/10593 and its subdirectories I: Current time: Tue May 30 20:01:02 -12 2023 I: pbuilder-time-stamp: 1685520062