Tue May 7 18:43:44 UTC 2024 I: starting to build libvcflib/trixie/amd64 on jenkins on '2024-05-07 18:43' Tue May 7 18:43:44 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_9/5281/console.log Tue May 7 18:43:44 UTC 2024 I: Downloading source for trixie/libvcflib=1.0.9+dfsg1-3 --2024-05-07 18:43:44-- http://deb.debian.org/debian/pool/main/libv/libvcflib/libvcflib_1.0.9%2bdfsg1-3.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2652 (2.6K) [text/prs.lines.tag] Saving to: ‘libvcflib_1.0.9+dfsg1-3.dsc’ 0K .. 100% 359M=0s 2024-05-07 18:43:44 (359 MB/s) - ‘libvcflib_1.0.9+dfsg1-3.dsc’ saved [2652/2652] Tue May 7 18:43:44 UTC 2024 I: libvcflib_1.0.9+dfsg1-3.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libvcflib Binary: libvcflib2, libvcflib-dev, libvcflib-tools Architecture: any-amd64 arm64 loong64 mips64el ppc64el s390x ia64 ppc64 riscv64 sparc64 alpha Version: 1.0.9+dfsg1-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/vcflib/vcflib Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/libvcflib Vcs-Git: https://salsa.debian.org/med-team/libvcflib.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, markdown , libtabixpp-dev, libbz2-dev, libdisorder-dev, libhts-dev, libsmithwaterman-dev, libssw-dev, libfastahack-dev, libwfa2-dev, pkg-config, libgtest-dev , python3-dev, python3-pybind11 Package-List: libvcflib-dev deb libdevel optional arch=any-amd64,arm64,loong64,mips64el,ppc64el,s390x,ia64,ppc64,riscv64,sparc64,alpha libvcflib-tools deb science optional arch=any-amd64,arm64,mips64el,ppc64el,s390x,ia64,ppc64,riscv64,sparc64,alpha libvcflib2 deb libs optional arch=any-amd64,arm64,loong64,mips64el,ppc64el,s390x,ia64,ppc64,riscv64,sparc64,alpha Checksums-Sha1: a0f15b1c0caa573f3a37f9b97cc70eb1cfa97636 9044176 libvcflib_1.0.9+dfsg1.orig.tar.xz 24708201b032e6b20a4ea93209a0eae3c0801dae 74256 libvcflib_1.0.9+dfsg1-3.debian.tar.xz Checksums-Sha256: 3d0f48f9157a9f9b896143b6789f52f12898cb8e1438a4ad50d4ef27477f300f 9044176 libvcflib_1.0.9+dfsg1.orig.tar.xz 6bfa8f11e3054e5e67a929769884daba8581e1ffbd5954a3aa2301b4254f4a71 74256 libvcflib_1.0.9+dfsg1-3.debian.tar.xz Files: 3a90b784ea60b24902d932b29af4a7dc 9044176 libvcflib_1.0.9+dfsg1.orig.tar.xz aaddd80b0f025304f3ed08c618c11ae0 74256 libvcflib_1.0.9+dfsg1-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmVsdokRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFTYQ/+OJxGZVUP7yI9XS+YECjUn+nYLTZYftuh S5yrRWeWzy9XvrxKzK/t2kE5WuMwO449fG9REi98/awCEVgUYTbJI6DK90qBnHdn 70vNJzSVuXDOaSxiyXlSe2yW9ps+Rs/iydALYa/8Ef0ppKR3tdEIQFcx39e0i+nm 53/wiX4vDOc1mdq1k7H25AATL+dCQ6m5g0o9ENd4pAk2Upo5U/b75143rIdb7s53 /2UEv+ElD/zGQWO2rJyZwMOmwROKpwFNUmh52vRsWy9rxYaWB0IlyBt9kqCH7ips 6nHT2X5/hEyaaLG0+BT5bF+9wBIlCtqLSf1epK4Sn1KqJJUridkbZXz03ADwQNSu KDjPMdDrY4aH1hoA6wFAuFGgSE64HpSSN+lzvljZYpsbSzyK9Q69sAWMdpWurF4d HIk2k2vTID4Kv3khRffDTtzLQgKlSbS/pI00blRi5N+oNCi3ZrIXjmQ2ahOF0eDO jof3aLlLOItpQxtEMZjqObshfF/tj68z38mb16+SzCOqdCKu0ZA7UCUOQa639ZwY jXQNbXrAyfpAQAP25K/xVXse5RAG6dIHz9v8Utd1OPqZCCch/mYF8/113XAU1sQ2 CX+7BtsoI8aVRzWu81ftV7G48/9rkRf6qkLtfGAGYntOFtXh5uBJpG+VZMZZ6dSz B39/9pvr/O0= =TxCU -----END PGP SIGNATURE----- Tue May 7 18:43:44 UTC 2024 I: Checking whether the package is not for us Tue May 7 18:43:44 UTC 2024 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue May 7 18:43:44 UTC 2024 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue May 7 18:47:57 UTC 2024 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 7 06:43:46 -12 2024 I: pbuilder-time-stamp: 1715107426 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libvcflib_1.0.9+dfsg1-3.dsc] I: copying [./libvcflib_1.0.9+dfsg1.orig.tar.xz] I: copying [./libvcflib_1.0.9+dfsg1-3.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Dec 3 12:37:29 2023 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_1.0.9+dfsg1-3.dsc: no acceptable signature found dpkg-source: info: extracting libvcflib in libvcflib-1.0.9+dfsg1 dpkg-source: info: unpacking libvcflib_1.0.9+dfsg1.orig.tar.xz dpkg-source: info: unpacking libvcflib_1.0.9+dfsg1-3.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 wfa2_linking I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3547587/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='8f375e2b7e54407598ce3a5ff2fbca05' 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='3547587' 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.PrSozQgn/pbuilderrc_o01M --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/b1 --logfile b1/build.log libvcflib_1.0.9+dfsg1-3.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 5 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3547587/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libhts-dev, libsmithwaterman-dev, libssw-dev, libfastahack-dev, libwfa2-dev, pkg-config, libgtest-dev, python3-dev, python3-pybind11 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19698 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 libhts-dev; however: Package libhts-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 libwfa2-dev; however: Package libwfa2-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 python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-pybind11; however: Package python3-pybind11 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} libarchive13t64{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libgtest-dev{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libpython3.11t64{a} libreadline8t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1t64{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libwfa2-0{a} libwfa2-dev{a} libxml2{a} m4{a} man-db{a} markdown{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} pybind11-dev{a} python3{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pybind11{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libeigen3-dev libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix python3-numpy wget 0 packages upgraded, 108 newly installed, 0 to remove and 0 not upgraded. Need to get 55.8 MB of archives. After unpacking 219 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-3 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 22 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40-8 [92.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.2-2 [346 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1~rc2-1 [22.6 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 39 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.7.1-3 [441 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-1.1 [147 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.29.2-2 [2167 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.29.2-2 [10.7 MB] Get: 54 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 61 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 googletest all 1.14.0-1 [512 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libbz2-dev amd64 1.0.8-5.1 [31.3 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.7.1-3 [432 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libcurl4-gnutls-dev amd64 8.7.1-3 [537 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libdeflate-dev amd64 1.20-1 [54.5 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B] Get: 74 http://deb.debian.org/debian trixie/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b1 [4860 B] Get: 75 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.2-1 [155 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libfastahack0 amd64 1.0.0+dfsg-11+b1 [27.6 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libfastahack-dev amd64 1.0.0+dfsg-11+b1 [275 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libgtest-dev amd64 1.14.0-1+b1 [250 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 liblzma-dev amd64 5.6.1+really5.4.5-1 [293 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 libhts-dev amd64 1.19+ds-1.1+b1 [1667 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libpython3.11t64 amd64 3.11.9-1 [1960 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libpython3.11-dev amd64 3.11.9-1 [4513 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.11.8-1 [9560 B] Get: 91 http://deb.debian.org/debian trixie/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libssw0 amd64 1.1-14+b1 [21.2 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libssw-dev amd64 1.1-14+b1 [24.0 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 libtabixpp0t64 amd64 1.1.2-2.1 [10.1 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libtabixpp-dev amd64 1.1.2-2.1 [9652 B] Get: 97 http://deb.debian.org/debian trixie/main amd64 libwfa2-0 amd64 2.3.3-4 [60.5 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libwfa2-dev amd64 2.3.3-4 [79.4 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 markdown all 1.0.1-12 [17.7 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 pybind11-dev all 2.11.1-2 [191 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 python3.11-dev amd64 3.11.9-1 [501 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 python3-lib2to3 all 3.12.3-1 [77.6 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 python3-distutils all 3.12.3-1 [131 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.11.8-1 [26.1 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 python3-pybind11 all 2.11.1-2 [201 kB] Fetched 55.8 MB in 1s (49.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 19698 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 20014 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2024a-3_all.deb ... Unpacking tzdata (2024a-3) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../8-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 21006 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-4_amd64.deb ... Unpacking procps (2:4.0.4-4) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.40-8_amd64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../18-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../19-libxml2_2.9.14+dfsg-1.3+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../20-libarchive13t64_3.7.2-2_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.2-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.1~rc2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1~rc2-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.20.1-6+b1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.20.1-6+b1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.20.1-6+b1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../28-libsasl2-modules-db_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../29-libsasl2-2_2.1.28+dfsg1-6_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../30-libldap-2.5-0_2.5.17+dfsg-1_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.17+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../31-libnghttp2-14_1.61.0-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.61.0-1+b1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../32-libpsl5t64_0.21.2-1.1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../33-librtmp1_2.4+20151223.gitfa8646d.1-2+b4_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../34-libssh2-1t64_1.11.0-4.1+b2_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../35-libcurl4t64_8.7.1-3_amd64.deb ... Unpacking libcurl4t64:amd64 (8.7.1-3) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../36-libjsoncpp25_1.9.5-6+b2_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-6+b2) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../37-librhash0_1.4.3-3+b1_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3+b1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../38-libuv1t64_1.48.0-1.1_amd64.deb ... Unpacking libuv1t64:amd64 (1.48.0-1.1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../39-cmake-data_3.29.2-2_all.deb ... Unpacking cmake-data (3.29.2-2) ... Selecting previously unselected package cmake. Preparing to unpack .../40-cmake_3.29.2-2_amd64.deb ... Unpacking cmake (3.29.2-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../41-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../42-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../43-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../44-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../45-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../46-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../47-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../48-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../49-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../50-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../51-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../52-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../53-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package googletest. Preparing to unpack .../54-googletest_1.14.0-1_all.deb ... Unpacking googletest (1.14.0-1) ... Selecting previously unselected package libbz2-dev:amd64. Preparing to unpack .../55-libbz2-dev_1.0.8-5.1_amd64.deb ... Unpacking libbz2-dev:amd64 (1.0.8-5.1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../56-libcurl3t64-gnutls_8.7.1-3_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.7.1-3) ... Selecting previously unselected package libcurl4-gnutls-dev:amd64. Preparing to unpack .../57-libcurl4-gnutls-dev_8.7.1-3_amd64.deb ... Unpacking libcurl4-gnutls-dev:amd64 (8.7.1-3) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../58-libdeflate0_1.20-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.20-1) ... Selecting previously unselected package libdeflate-dev:amd64. Preparing to unpack .../59-libdeflate-dev_1.20-1_amd64.deb ... Unpacking libdeflate-dev:amd64 (1.20-1) ... Selecting previously unselected package libdisorder0:amd64. Preparing to unpack .../60-libdisorder0_0.0.2+git20130809.8062ee1-4+b1_amd64.deb ... Unpacking libdisorder0:amd64 (0.0.2+git20130809.8062ee1-4+b1) ... Selecting previously unselected package libdisorder-dev:amd64. Preparing to unpack .../61-libdisorder-dev_0.0.2+git20130809.8062ee1-4+b1_amd64.deb ... Unpacking libdisorder-dev:amd64 (0.0.2+git20130809.8062ee1-4+b1) ... Selecting previously unselected package libexpat1-dev:amd64. Preparing to unpack .../62-libexpat1-dev_2.6.2-1_amd64.deb ... Unpacking libexpat1-dev:amd64 (2.6.2-1) ... Selecting previously unselected package libfastahack0:amd64. Preparing to unpack .../63-libfastahack0_1.0.0+dfsg-11+b1_amd64.deb ... Unpacking libfastahack0:amd64 (1.0.0+dfsg-11+b1) ... Selecting previously unselected package libfastahack-dev:amd64. Preparing to unpack .../64-libfastahack-dev_1.0.0+dfsg-11+b1_amd64.deb ... Unpacking libfastahack-dev:amd64 (1.0.0+dfsg-11+b1) ... Selecting previously unselected package libgtest-dev:amd64. Preparing to unpack .../65-libgtest-dev_1.14.0-1+b1_amd64.deb ... Unpacking libgtest-dev:amd64 (1.14.0-1+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/ && 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_1.0.9+dfsg1-3_source.changes dpkg-buildpackage: info: source package libvcflib dpkg-buildpackage: info: source version 1.0.9+dfsg1-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem cmake debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_auto_clean || true make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_autoreconf_clean -O--buildsystem=cmake debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_clean find . -name "*.o" -delete rm -f README.html build/ rm -rf contrib/filevercmp contrib/multichoose contrib/intervaltree make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' 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/reproducible-path/libvcflib-1.0.9+dfsg1' cp -a debian/ext/* contrib/ dh_auto_configure -- -DOPENMP=ON -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON -DZIG=OFF -DWFA_GITMODULE=OFF -DHTSLIB_FOUND=ON -DTABIX_FOUND=ON cd obj-x86_64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb 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/x86_64-linux-gnu -DOPENMP=ON -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON -DZIG=OFF -DWFA_GITMODULE=OFF -DHTSLIB_FOUND=ON -DTABIX_FOUND=ON .. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- 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") CMake Warning (dev) at /usr/lib/cmake/pybind11/FindPythonLibsNew.cmake:98 (find_package): Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules are removed. Run "cmake --help-policy CMP0148" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): /usr/lib/cmake/pybind11/pybind11Tools.cmake:50 (find_package) /usr/lib/cmake/pybind11/pybind11Common.cmake:188 (include) /usr/lib/cmake/pybind11/pybind11Config.cmake:250 (include) CMakeLists.txt:19 (find_package) This warning is for project developers. Use -Wno-dev to suppress it. -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.9", minimum required is "3.6") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.11.so -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- Found pybind11: /usr/include (found version "2.11.1") -- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.8") -- Looking for BZ2_bzCompressInit -- Looking for BZ2_bzCompressInit - found -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_auto_decoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_easy_encoder in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so -- Looking for lzma_lzma_preset in /usr/lib/x86_64-linux-gnu/liblzma.so - found -- Found LibLZMA: /usr/lib/x86_64-linux-gnu/liblzma.so (found version "5.4.5") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3") -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.7.1") -- -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Checking for module 'htslib' -- Found htslib, version 1.19 -- 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 -- WFA using include /usr/include/wfa2lib Pandoc needs to be installed to generate the man pages -- Configuring done (9.1s) -- Generating done (0.9s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_auto_build cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libvcflib-1.0.9+dfsg1 -B/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: 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CMakeFiles/vcflib.dir/contrib/filevercmp/filevercmp.c.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp/filevercmp.c /usr/bin/cc -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -fPIC -MD -MT CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o -MF CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o.d -o CMakeFiles/vcflib.dir/contrib/c-progress-bar/progress.c.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c: In function 'print_timedelta': /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:79:28: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); | ~~~^ ~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:79:34: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); | ~~~^ ~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:79:40: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 5 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 79 | fprintf(stderr,"%lluh %llum %llus ", hours, minutes, seconds); | ~~~^ ~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:82:28: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 82 | fprintf(stderr,"%llum %02llus ", minutes, seconds); | ~~~^ ~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:82:36: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 82 | fprintf(stderr,"%llum %02llus ", minutes, seconds); | ~~~~~^ ~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %02lu /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:85:28: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 85 | fprintf(stderr,"%llu.%llus ", seconds, mseconds); | ~~~^ ~~~~~~~ | | | | | uint64_t {aka long unsigned int} | long long unsigned int | %lu /build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar/progress.c:85:33: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 4 has type 'uint64_t' {aka 'long unsigned int'} [-Wformat=] 85 | fprintf(stderr,"%llu.%llus ", seconds, mseconds); | ~~~^ ~~~~~~~~ | | | | long long unsigned int uint64_t {aka long unsigned int} | %lu In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf-c-api.cpp:9: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf-wfa.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/legacy.cpp:12: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 9%] Linking CXX shared library 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CMakeFiles/bFst.dir/src/bFst.cpp.o [ 14%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o [ 14%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o [ 14%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend [ 14%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o [ 14%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/bFst.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake "--color=" make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/permuteSmooth.dir/DependInfo.cmake "--color=" /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/segmentIhs.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/pFst.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/wcFst.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/genotypeSummary.cpp [ 15%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o [ 15%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o [ 16%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/sequenceDiversity.cpp [ 17%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o [ 17%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/iHS.cpp [ 17%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/plotHaps.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfld.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/abba-baba.cpp /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/smoother.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 18%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/permuteSmooth.cpp [ 18%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/normalize-iHS.cpp [ 19%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/permuteGPAT++.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/dumpContigsFromHeader.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfecho.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/hapLrt.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 19%] Linking CXX executable segmentFst /usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/popStats.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/genotypeSummary.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/iHS.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/abba-baba.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp: In function 'void calc(copyNcounts*)': /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pVst.cpp:191:24: warning: 'void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]' is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations] 191 | std::random_shuffle(d->total.begin(), d->total.end()); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/functional:67, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:24: /usr/include/c++/13/bits/stl_algo.h:4581:5: note: declared here 4581 | random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last) | ^~~~~~~~~~~~~~ [ 20%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pFst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/plotHaps.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 21%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/wcFst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 23%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 23%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfld.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/bFst.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 23%] Built target segmentFst make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 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CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 23%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/meltEHH.cpp [ 23%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 23%] Built target permuteGPAT++ make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfnullgenofields.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfnullgenofields.dir/build.make CMakeFiles/vcfnullgenofields.dir/build [ 23%] Built target dumpContigsFromHeader make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfaltcount.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 24%] Building CXX object CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -MD -MT CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -MF CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o.d -o CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnullgenofields.cpp [ 24%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaltcount.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/sequenceDiversity.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 24%] Built target segmentIhs make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend [ 24%] Built target vcfecho make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfhetcount.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 24%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhetcount.cpp [ 24%] Built target normalize-iHS make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend [ 24%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhethomratio.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu 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-fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffilter.cpp [ 26%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 27%] Linking CXX executable abba-baba /usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1 [ 28%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 28%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 29%] Linking CXX executable wcFst /usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 29%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 29%] Built target smoother make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2tsv.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 29%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2tsv.cpp [ 30%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 30%] Built target permuteSmooth make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/meltEHH.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 31%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o [ 32%] Linking CXX executable pFst /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypes.cpp /usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 32%] Linking CXX executable vcfld /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnullgenofields.cpp:12: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaltcount.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhethomratio.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffilter.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfhetcount.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 33%] Linking CXX executable sequenceDiversity /usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2tsv.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 33%] Linking CXX executable vcfnullgenofields /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnullgenofields.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfnullgenofields.dir/src/vcfnullgenofields.cpp.o -o vcfnullgenofields -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 33%] Built target popStats make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 34%] Linking CXX executable vcfhethomratio [ 35%] Linking CXX executable vcfaltcount /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1 /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1 [ 36%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotategenotypes.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 36%] Built target plotHaps make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 37%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcommonsamples.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 37%] Built target genotypeSummary make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 37%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremovesamples.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypes.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 37%] Built target abba-baba make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 38%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 38%] Built target wcFst make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake "--color=" [ 39%] Linking CXX executable vcfhetcount /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 40%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplenames.cpp [ 41%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 42%] Linking CXX executable vcffilter /usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 42%] Built target pFst make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 43%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypecompare.cpp [ 44%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 44%] Built target vcfaltcount make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcffixup.dir/DependInfo.cmake "--color=" [ 44%] Linking CXX executable vcfgenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotategenotypes.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 44%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffixup.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 44%] Built target bFst make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfclassify.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 45%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfclassify.cpp [ 45%] Built target hapLrt make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcommonsamples.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 46%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplediff.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepsamples.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 46%] Built target pVst make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend [ 46%] Built target vcfnullgenofields make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfrandom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 46%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp [ 46%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp [ 46%] Built target vcfhethomratio make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfparsealts.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 47%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfparsealts.cpp [ 47%] Built target iHS make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfstats.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 48%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstats.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremovesamples.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 48%] Built target vcfhetcount make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfflatten.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplenames.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 49%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfflatten.cpp [ 49%] Built target vcfld make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend [ 49%] Linking CXX executable vcfkeepsamples make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfprimers.dir/DependInfo.cmake "--color=" /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 50%] Linking CXX executable vcfcommonsamples /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1 [ 51%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfprimers.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenotypecompare.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 51%] Built target sequenceDiversity In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcffixup.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfnumalt.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfclassify.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 51%] Linking CXX executable vcfannotategenotypes /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1 [ 52%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnumalt.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 52%] Linking CXX executable vcfsamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1 [ 53%] Linking CXX executable vcfremovesamples /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 53%] Built target vcf2tsv make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremoveaberrantgenotypes.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsamplediff.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcleancomplex.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:13: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandom.cpp:10: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfparsealts.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Built target vcfgenotypes make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfintersect.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstats.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 54%] Built target vcfkeepsamples [ 54%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfintersect.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfannotate.dir/DependInfo.cmake "--color=" [ 54%] Built target vcfcommonsamples make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build [ 55%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotate.cpp [ 55%] Built target meltEHH make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/depend [ 55%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfwave.dir/DependInfo.cmake "--color=" /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfallelicprimitives.cpp [ 55%] Built target vcfsamplenames make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfoverlay.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 55%] Linking CXX executable vcfclassify make -f CMakeFiles/vcfwave.dir/build.make CMakeFiles/vcfwave.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1 [ 56%] Building CXX object CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto 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/usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 57%] Linking CXX executable vcffixup /usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1 [ 58%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfoverlay.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfprimers.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfflatten.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Linking CXX executable vcfremoveaberrantgenotypes [ 59%] Built target vcffilter /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1 make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 59%] Linking CXX executable vcfparsealts /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1 [ 60%] Linking CXX executable vcfrandom /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 60%] Linking CXX executable vcfgenotypecompare /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1 [ 60%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 61%] Linking CXX executable vcfprimers /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1 [ 61%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Built target vcfremovesamples make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfnumalt.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepinfo.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfintersect.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Built target vcfclassify make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfannotate.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcleancomplex.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfoverlay.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfallelicprimitives.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Linking CXX executable vcfstats /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1 [ 61%] Built target vcfparsealts /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfafpath.dir/DependInfo.cmake "--color=" In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfwave.cpp:19: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfwave.cpp:11: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o [ 61%] Linking CXX executable vcfnumalt /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1 /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfafpath.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfaddinfo.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepinfo.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Built target vcfremoveaberrantgenotypes make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcountalleles.cpp [ 61%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfkeepgeno.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 61%] Built target vcffixup make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcflength.dir/DependInfo.cmake "--color=" [ 61%] Built target vcfprimers make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfdistance.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 62%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcflength.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 63%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o [ 64%] Linking CXX executable vcfkeepinfo /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfdistance.cpp /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 64%] Built target vcfrandom make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake "--color=" [ 64%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 64%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandomsample.cpp [ 64%] Linking CXX executable vcfoverlay /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfafpath.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 65%] Linking CXX executable vcfwave /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfwave.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfwave.dir/src/vcfwave.cpp.o -o vcfwave -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 65%] Built target vcfsamplediff make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfentropy.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 65%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcountalleles.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Built target vcfnumalt make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfglxgt.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 66%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglxgt.cpp [ 66%] Built target vcfgenotypecompare make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfroc.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 66%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfroc.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcflength.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] Built target vcfannotategenotypes make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcheck.dir/DependInfo.cmake "--color=" [ 67%] Linking CXX executable vcfallelicprimitives make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfdistance.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 68%] Linking CXX executable vcfintersect [ 69%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1 /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcheck.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 70%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 70%] Built target vcfaddinfo make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 71%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.cpp [ 72%] Linking CXX executable vcfcountalleles make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 72%] Built target vcfcleancomplex make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend [ 72%] Linking CXX executable vcflength /usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfuniq.dir/DependInfo.cmake "--color=" /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build [ 72%] Built target vcfkeepinfo make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake "--color=" [ 73%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniq.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 74%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniqalleles.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfrandomsample.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 74%] Built target vcfkeepgeno make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfremap.dir/DependInfo.cmake "--color=" [ 75%] Linking CXX executable vcfdistance /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 75%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremap.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 75%] Built target vcfflatten make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2fasta.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 75%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2fasta.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfroc.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglxgt.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 75%] Built target vcfcountalleles make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 76%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsitesummarize.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfentropy.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 76%] Built target vcfoverlay make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 77%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfbreakmulti.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 77%] Built target vcfafpath make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfevenregions.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 78%] Linking CXX executable vcfrandomsample /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1 [ 78%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfevenregions.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcheck.cpp:11: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniq.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 78%] Built target vcfdistance make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcat.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 79%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcat.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 79%] Built target vcfannotate make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake "--color=" [ 80%] Linking CXX executable vcfentropy /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfstreamsort.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosummarize.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfuniqalleles.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 82%] Linking CXX executable vcfcheck In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2fasta.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 82%] Built target vcfstats make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake "--color=" [ 82%] Built target vcflength make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build [ 82%] Linking CXX executable vcfuniq In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsitesummarize.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfremap.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1 make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 83%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosamplenames.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 84%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgeno2haplo.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfbreakmulti.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfevenregions.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 84%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 84%] Built target vcfrandomsample make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfleftalign.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 85%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfleftalign.cpp [ 85%] Linking CXX executable vcfsitesummarize /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcat.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 85%] Linking CXX executable vcfstreamsort /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 85%] Built target vcfcheck make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcombine.dir/DependInfo.cmake "--color=" [ 85%] Built target vcfuniq make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 86%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcombine.cpp make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 87%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgeno2alleles.cpp [ 87%] Built target vcfglxgt make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfindex.dir/DependInfo.cmake "--color=" [ 88%] Linking CXX executable vcf2fasta In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosummarize.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 88%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfindex.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgeno2haplo.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 89%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 90%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 90%] Linking CXX executable vcfbreakmulti /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgenosamplenames.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Linking CXX executable vcfroc /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1 [ 91%] Built target vcfwave make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcf2dag.dir/DependInfo.cmake "--color=" [ 91%] Built target vcfuniqalleles make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfsample2info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Linking CXX executable vcfcat /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1 [ 91%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2dag.cpp [ 91%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsample2info.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Built target vcfentropy make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfqual2info.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfqual2info.cpp [ 91%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Built target vcfintersect make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Built target vcfsitesummarize [ 91%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfinfo2qual.cpp make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfglbound.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 91%] Linking CXX executable vcfgenosamplenames /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1 [ 92%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglbound.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfgeno2alleles.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target vcfevenregions make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 92%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfinfosummarize.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfleftalign.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfindex.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target vcfallelicprimitives make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 92%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIE -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/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcreatemulti.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcombine.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 92%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 92%] Built target vcfcat make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/depend make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1 /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles/pyvcflib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make -f CMakeFiles/pyvcflib.dir/build.make CMakeFiles/pyvcflib.dir/build make[4]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 93%] Building CXX object CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o /usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -Dpyvcflib_EXPORTS -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/include -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/intervaltree -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/multichoose -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/filevercmp -I/build/reproducible-path/libvcflib-1.0.9+dfsg1/contrib/c-progress-bar -I/usr/include/wfa2lib -isystem /usr/include/python3.11 -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=gnu++17 -flto=auto -fno-fat-lto-objects -fPIC -fvisibility=hidden -MD -MT CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -MF CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o.d -o CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -c /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pythonffi.cpp In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcf2dag.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfsample2info.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfqual2info.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 94%] Linking CXX executable vcfleftalign /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 94%] Built target vcfbreakmulti In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfglbound.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 94%] Built target vcfgenosamplenames [ 94%] Linking CXX executable vcfgeno2haplo /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 94%] Built target vcfstreamsort In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfinfosummarize.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 95%] Linking CXX executable vcfqual2info /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1 [ 95%] Built target vcf2fasta In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfinfo2qual.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target vcfgenosummarize make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 95%] Built target vcfremap [ 95%] Built target vcfgeno2alleles In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/vcfcreatemulti.cpp:10: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Linking CXX executable vcf2dag /usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 97%] Linking CXX executable vcfcombine /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1 [ 97%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 [ 98%] 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/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 99%] Linking CXX executable vcfinfo2qual [ 99%] Built target vcfindex /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 In file included from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/pythonffi.cpp:5: /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:650:28: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 650 | struct stringcasecmp : binary_function { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/reproducible-path/libvcflib-1.0.9+dfsg1/src/Variant.h:651:42: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 651 | struct charcasecmp : public std::binary_function { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [ 99%] Built target vcfqual2info [100%] Linking CXX executable vcfcreatemulti /usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so libvcflib.so.2 /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfinfo2qual make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfleftalign [100%] Built target vcfsample2info make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfglbound make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfroc make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcf2dag make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfinfosummarize make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfcombine make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfcreatemulti make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target vcfgeno2haplo [100%] Linking CXX shared module pyvcflib.cpython-311-x86_64-linux-gnu.so /usr/bin/cmake -E cmake_link_script CMakeFiles/pyvcflib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libvcflib-1.0.9+dfsg1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -flto=auto -fno-fat-lto-objects -Wl,-z,relro -Wl,-z,now -shared -o pyvcflib.cpython-311-x86_64-linux-gnu.so CMakeFiles/pyvcflib.dir/src/pythonffi.cpp.o -Wl,-rpath,"\$ORIGIN:" libvcflib.so.2 -lhts /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so /usr/lib/x86_64-linux-gnu/libbz2.so /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/x86_64-linux-gnu/libwfa2.so /usr/lib/x86_64-linux-gnu/libsmithwaterman.so /usr/lib/x86_64-linux-gnu/libdisorder.so /usr/lib/x86_64-linux-gnu/libfastahack.so -ltabixpp -lwfa2 /usr/bin/strip /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/pyvcflib.cpython-311-x86_64-linux-gnu.so make[4]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' [100%] Built target pyvcflib make[3]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' markdown README.md > README.html make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' cp obj-x86_64-linux-gnu/CTestTestfile.cmake test/ ln -sf obj-x86_64-linux-gnu/ build cd test && ctest . Test project /build/reproducible-path/libvcflib-1.0.9+dfsg1/test Start 1: realign 1/9 Test #1: realign .......................... Passed 0.17 sec Start 2: pyvcflib 2/9 Test #2: pyvcflib ......................... Passed 0.13 sec Start 3: vcflib-api 3/9 Test #3: vcflib-api ....................... Passed 0.12 sec Start 4: vcf2tsv 4/9 Test #4: vcf2tsv .......................... Passed 0.18 sec Start 5: vcfallelicprimitives 5/9 Test #5: vcfallelicprimitives ............. Passed 1.70 sec Start 6: vcfwave 6/9 Test #6: vcfwave .......................... Passed 0.78 sec Start 7: vcffilter 7/9 Test #7: vcffilter ........................ Passed 0.27 sec Start 8: vcfnulldotslashdot 8/9 Test #8: vcfnulldotslashdot ............... Passed 0.19 sec Start 9: doc/vcfintersect 9/9 Test #9: doc/vcfintersect ................. Passed 0.11 sec 100% tests passed, 0 tests failed out of 9 Total Test time (real) = 3.67 sec cd .. && rm -f build make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install -O--buildsystem=cmake cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/libvcflib-1.0.9\+dfsg1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libvcflib-1.0.9+dfsg1 -B/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfecho -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfecho" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/dumpContigsFromHeader -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/dumpContigsFromHeader" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/bFst -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/bFst" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/pVst -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/pVst" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/hapLrt -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/hapLrt" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/popStats -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/popStats" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/wcFst -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/wcFst" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/iHS -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/iHS" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/segmentFst -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/segmentFst" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/segmentIhs -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/segmentIhs" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/genotypeSummary -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/genotypeSummary" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/sequenceDiversity -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/sequenceDiversity" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/pFst -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/pFst" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/smoother -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/smoother" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfld -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfld" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/plotHaps -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/plotHaps" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/abba-baba -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/abba-baba" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/permuteGPAT++ -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/permuteGPAT++" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/permuteSmooth -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/permuteSmooth" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/normalize-iHS -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/normalize-iHS" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/meltEHH -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/meltEHH" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnullgenofields -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnullgenofields" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfaltcount -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfaltcount" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfhetcount -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfhetcount" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfhethomratio -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfhethomratio" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcffilter -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcffilter" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2tsv -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2tsv" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenotypes -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenotypes" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfannotategenotypes -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfannotategenotypes" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcommonsamples -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcommonsamples" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremovesamples -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremovesamples" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfkeepsamples -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfkeepsamples" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsamplenames -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsamplenames" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenotypecompare -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenotypecompare" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcffixup -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcffixup" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfclassify -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfclassify" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsamplediff -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsamplediff" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremoveaberrantgenotypes -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremoveaberrantgenotypes" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfrandom -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfrandom" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfparsealts -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfparsealts" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfstats -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfstats" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfflatten -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfflatten" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfprimers -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfprimers" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnumalt -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnumalt" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcleancomplex -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcleancomplex" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfintersect -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfintersect" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfannotate -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfannotate" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfallelicprimitives -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfallelicprimitives" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfwave -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfwave" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfoverlay -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfoverlay" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfaddinfo -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfaddinfo" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfkeepinfo -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfkeepinfo" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfkeepgeno -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfkeepgeno" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfafpath -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfafpath" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcountalleles -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcountalleles" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcflength -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcflength" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfdistance -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfdistance" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfrandomsample -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfrandomsample" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfentropy -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfentropy" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfglxgt -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfglxgt" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfroc -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfroc" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcheck -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcheck" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfstreamsort -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfstreamsort" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfuniq -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfuniq" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfuniqalleles -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfuniqalleles" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremap -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremap" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2fasta -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2fasta" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsitesummarize -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsitesummarize" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfbreakmulti -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfbreakmulti" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfevenregions -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfevenregions" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcat -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcat" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenosummarize -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenosummarize" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenosamplenames -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgenosamplenames" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgeno2haplo -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgeno2haplo" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfleftalign -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfleftalign" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcombine -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcombine" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgeno2alleles -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgeno2alleles" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfindex -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfindex" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2dag -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2dag" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsample2info -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsample2info" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfqual2info -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfqual2info" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfinfo2qual -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfinfo2qual" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfglbound -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfglbound" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfinfosummarize -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfinfosummarize" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcreatemulti -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcreatemulti" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/bed2region -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/bgziptabix -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2bed.py -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf2sqlite.py -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfbiallelic -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfclearid -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfclearinfo -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfcomplex -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcffirstheader -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfgtcompare.sh -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfindelproximity -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfindels -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfjoincalls -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfmultiallelic -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfmultiway -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfmultiwayscripts -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnobiallelicsnps -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnoindels -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnosnps -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfnulldotslashdot -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfplotaltdiscrepancy.r -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfplotaltdiscrepancy.sh -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfplotsitediscrepancy.r -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfplottstv.sh -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfprintaltdiscrepancy.r -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfprintaltdiscrepancy.sh -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfqualfilter -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfregionreduce -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfregionreduce_and_cut -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfregionreduce_pipe -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfregionreduce_uncompressed -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfremovenonATGC -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsnps -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfsort -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcf_strip_extra_headers -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/bin/vcfvarstats -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/lib/x86_64-linux-gnu/pyvcflib.cpython-311-x86_64-linux-gnu.so -- Set non-toolchain portion of runtime path of "/build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/lib/x86_64-linux-gnu/pyvcflib.cpython-311-x86_64-linux-gnu.so" to "" -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/lib/x86_64-linux-gnu/libvcflib.so.2 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/lib/x86_64-linux-gnu/libvcflib.so -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/filevercmp.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/IntervalTree.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/catch.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/multichoose.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/multipermute.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/BedReader.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/LeftAlign.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/Variant.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/allele.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/cdflib.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/cigar.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/convert.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/gpatInfo.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/join.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/makeUnique.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/mt19937ar.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/murmur3.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/pdflib.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/rkmh.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/rnglib.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/split.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/var.hpp -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/vcf-c-api.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/include/vcf-wfa.h -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgeno2haplo.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcountalleles.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfinfo2qual.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfentropy.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfparsealts.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfannotategenotypes.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepinfo.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/permuteGPAT++.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsample2info.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfleftalign.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflength.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfuniq.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfstreamsort.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnumalt.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfstats.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsamplenames.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfuniqalleles.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfbreakmulti.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgeno2alleles.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/iHS.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfld.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfrandomsample.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcleancomplex.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfhetcount.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfflatten.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/segmentIhs.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfqual2info.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcombine.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/smoother.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfecho.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfannotate.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pFst.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfrandom.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pyvcflib.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/abba-baba.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2tsv.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/pVst.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/permuteSmooth.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/normalize-iHS.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/genotypeSummary.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcat.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/popStats.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflib-api.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepgeno.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfhethomratio.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcffixup.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnullgenofields.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfinfosummarize.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenotypecompare.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenosummarize.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfaddinfo.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/meltEHH.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2dag.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfclassify.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/dumpContigsFromHeader.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcreatemulti.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfdistance.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremap.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/wcFst.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsamplediff.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfaltcount.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/bFst.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfglbound.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfintersect.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfroc.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenosamplenames.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/sequenceDiversity.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfkeepsamples.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfsitesummarize.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcffilter.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfevenregions.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfoverlay.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfafpath.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcf2fasta.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfremovesamples.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcommonsamples.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfindex.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcflib.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfnulldotslashdot.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/hapLrt.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfcheck.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfgenotypes.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfglxgt.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/plotHaps.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfprimers.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfallelicprimitives.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/segmentFst.1 -- Installing: /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/tmp/usr/man/man1/vcfwave.1 make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1/obj-x86_64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_install find debian/lib* -name filevercmp.h -delete cp -a debian/ext/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 # Remove un-needed py so, install in separate binary package when needed find debian/ -name 'pyvcflib.cpython*.so' -delete # install pkg-config file mkdir -p /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/libvcflib-dev/usr/lib/x86_64-linux-gnu/pkgconfig mv libvcflib.pc /build/reproducible-path/libvcflib-1.0.9+dfsg1/debian/libvcflib-dev/usr/lib/x86_64-linux-gnu/pkgconfig rm -rf debian/*/usr/lib/vcflib/bin/*.R for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/libvcflib-dev/usr/lib/x86_64-linux-gnu/libvcflib.so: No such file or directory make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_installdocs -O--buildsystem=cmake dh_installchangelogs -O--buildsystem=cmake dh_installman -O--buildsystem=cmake dh_installsystemduser -O--buildsystem=cmake dh_lintian -O--buildsystem=cmake dh_perl -O--buildsystem=cmake debian/rules override_dh_link make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_link for rscript in debian/libvcflib-tools/usr/lib/vcflib/scripts/*.R ; do \ scriptname=$(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/reproducible-path/libvcflib-1.0.9+dfsg1' dh_strip_nondeterminism -O--buildsystem=cmake dh_compress -O--buildsystem=cmake debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_fixperms chmod -x debian/*/usr/lib/vcflib/scripts/*.R make[1]: Leaving directory '/build/reproducible-path/libvcflib-1.0.9+dfsg1' dh_missing -O--buildsystem=cmake dh_dwz -a -O--buildsystem=cmake dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libvcflib2/usr/lib/x86_64-linux-gnu/libvcflib.so.2 was not linked against libdisorder.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake dpkg-deb: building package 'libvcflib2' in '../libvcflib2_1.0.9+dfsg1-3_amd64.deb'. dpkg-deb: building package 'libvcflib2-dbgsym' in '../libvcflib2-dbgsym_1.0.9+dfsg1-3_amd64.deb'. dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.9+dfsg1-3_amd64.deb'. dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.9+dfsg1-3_amd64.deb'. dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.9+dfsg1-3_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libvcflib_1.0.9+dfsg1-3_amd64.buildinfo dpkg-genchanges --build=binary -O../libvcflib_1.0.9+dfsg1-3_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3547587 and its subdirectories I: Current time: Tue May 7 06:47:56 -12 2024 I: pbuilder-time-stamp: 1715107676 Tue May 7 18:47:58 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos5-amd64.debian.net. Tue May 7 18:47:58 UTC 2024 I: Preparing to do remote build '2' on ionos5-amd64.debian.net. Tue May 7 18:50:20 UTC 2024 I: Deleting $TMPDIR on ionos5-amd64.debian.net. Tue May 7 18:50:21 UTC 2024 I: libvcflib_1.0.9+dfsg1-3_amd64.changes: Format: 1.8 Date: Sun, 03 Dec 2023 13:29:41 +0100 Source: libvcflib Binary: libvcflib-dev libvcflib-tools libvcflib-tools-dbgsym libvcflib2 libvcflib2-dbgsym Architecture: amd64 Version: 1.0.9+dfsg1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libvcflib-dev - C++ library for parsing and manipulating VCF files (development) libvcflib-tools - C++ library for parsing and manipulating VCF files (tools) libvcflib2 - C++ library for parsing and manipulating VCF files Closes: 1057253 Changes: libvcflib (1.0.9+dfsg1-3) unstable; urgency=medium . * add support for loong64 arch Closes: #1057253 Checksums-Sha1: 4eb771bd695c054e95128c35ccb4f0114f2f50ad 77572 libvcflib-dev_1.0.9+dfsg1-3_amd64.deb 200db355a67fcaee318e8beb7c02e6a2485f94c4 11286860 libvcflib-tools-dbgsym_1.0.9+dfsg1-3_amd64.deb ec82387cbc0883c059e40fdd9b9728973a62c760 650528 libvcflib-tools_1.0.9+dfsg1-3_amd64.deb 017239ac04437b2bd92cc4e04f9e08f8744b76b2 2055444 libvcflib2-dbgsym_1.0.9+dfsg1-3_amd64.deb 3e61beb22df5234e3e45e470909a996050e7894e 187956 libvcflib2_1.0.9+dfsg1-3_amd64.deb 0c7f84f596626eefa52b71e8c3bc54791081605e 8806 libvcflib_1.0.9+dfsg1-3_amd64.buildinfo Checksums-Sha256: e1abd3387a81268c9dfa0a80f3ae943f8b637ad79a3d40629ac7fb5e27fddaf8 77572 libvcflib-dev_1.0.9+dfsg1-3_amd64.deb 2775de2b1fae41901dfe5e0725613c2e40b1a651d00453a751451c794b73d37a 11286860 libvcflib-tools-dbgsym_1.0.9+dfsg1-3_amd64.deb 831932787e9dd5ff47b0493bb3a29cecdc5cba7abb248022834ecf090b4cc658 650528 libvcflib-tools_1.0.9+dfsg1-3_amd64.deb 4d32f912206a6933c818ae52db93d0a3c9ac92f79e1935fcb03d927131598475 2055444 libvcflib2-dbgsym_1.0.9+dfsg1-3_amd64.deb cd1e0acba96fc39fa2680bf618b81fc497f0c1ef434af876aa7b2b861b8aa5f3 187956 libvcflib2_1.0.9+dfsg1-3_amd64.deb a72a609ba2ab1bddc412763bd2e8b8ffba7023c2117d78f3e9e68bc5bdc7aabf 8806 libvcflib_1.0.9+dfsg1-3_amd64.buildinfo Files: 14ce4b5205e2e7f30a7a9704be699e82 77572 libdevel optional libvcflib-dev_1.0.9+dfsg1-3_amd64.deb 57e827ab68c6880ccf6d2d2eeb08bb5a 11286860 debug optional libvcflib-tools-dbgsym_1.0.9+dfsg1-3_amd64.deb ed68d27fdce47212ed15a284b84c45d1 650528 science optional libvcflib-tools_1.0.9+dfsg1-3_amd64.deb 252cbc0a724dcec40c5522fdc8ff0439 2055444 debug optional libvcflib2-dbgsym_1.0.9+dfsg1-3_amd64.deb 55603e226eba4fc15384f34dd288a1b3 187956 libs optional libvcflib2_1.0.9+dfsg1-3_amd64.deb 51ed1c9ce22e98a15d3f427674d44380 8806 science optional libvcflib_1.0.9+dfsg1-3_amd64.buildinfo Tue May 7 18:50:23 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_9-5281.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/libvcflib_1.0.9+dfsg1-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/libvcflib_1.0.9+dfsg1-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/libvcflib_1.0.9+dfsg1-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/b1/libvcflib_1.0.9+dfsg1-3_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.PrSozQgn/b2/libvcflib_1.0.9+dfsg1-3_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.553s) 0.553s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.175s) 0.175s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 979ms CPU time consumed: 972ms Tue May 7 18:50:24 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Tue May 7 18:50:24 UTC 2024 I: libvcflib from trixie built successfully and reproducibly on amd64. Tue May 7 18:50:26 UTC 2024 I: Submitting .buildinfo files to external archives: Tue May 7 18:50:26 UTC 2024 I: Submitting 12K b1/libvcflib_1.0.9+dfsg1-3_amd64.buildinfo.asc Tue May 7 18:50:27 UTC 2024 I: Submitting 12K b2/libvcflib_1.0.9+dfsg1-3_amd64.buildinfo.asc Tue May 7 18:50:28 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue May 7 18:50:28 UTC 2024 I: Done submitting .buildinfo files. Tue May 7 18:50:28 UTC 2024 I: Removing signed libvcflib_1.0.9+dfsg1-3_amd64.buildinfo.asc files: removed './b1/libvcflib_1.0.9+dfsg1-3_amd64.buildinfo.asc' removed './b2/libvcflib_1.0.9+dfsg1-3_amd64.buildinfo.asc'