I: pbuilder: network access will be disabled during build I: Current time: Mon Mar 10 13:13:57 +14 2025 I: pbuilder-time-stamp: 1741562037 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [vt_0.57721+ds-3.dsc] I: copying [./vt_0.57721+ds.orig.tar.xz] I: copying [./vt_0.57721+ds-3.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./vt_0.57721+ds-3.dsc: unsupported subcommand dpkg-source: info: extracting vt in vt-0.57721+ds dpkg-source: info: unpacking vt_0.57721+ds.orig.tar.xz dpkg-source: info: unpacking vt_0.57721+ds-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying makefile dpkg-source: info: applying fix-spelling dpkg-source: info: applying test-fail-on-error dpkg-source: info: applying 0001-updated-faidx_fetch_uc_seq.patch dpkg-source: info: applying 0002-hts-1.11.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/D01_modify_environment starting debug: Running on codethink04-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Mar 9 23:14 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=56f58653b0d847dfa53880c2ad743579 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=3198746 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/pbuilderrc_e9yZ --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/b2 --logfile b2/build.log vt_0.57721+ds-3.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3198746/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: arm64 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), zlib1g-dev, libbz2-dev, liblzma-dev, libcurl4-gnutls-dev, libssl-dev, libdeflate-dev, libhts-dev, libpcre2-dev, libsvm-dev, libtclap-dev, r-mathlib, r-base-core dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19897 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 zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev; however: Package libcurl4-gnutls-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libpcre2-dev; however: Package libpcre2-dev is not installed. pbuilder-satisfydepends-dummy depends on libsvm-dev; however: Package libsvm-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on r-mathlib; however: Package r-mathlib is not installed. pbuilder-satisfydepends-dummy depends on r-base-core; however: Package r-base-core 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} ca-certificates{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} krb5-multidev{a} libarchive-zip-perl{a} libblas3{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo2{a} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libcurl4t64{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0t64{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgraphite2-3{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libharfbuzz0b{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libice6{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjbig0{a} libjpeg62-turbo{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack3{a} libldap-dev{a} libldap2{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper2{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16t64{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} libreadline8t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsharpyuv0{a} libsm6{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsvm-dev{a} libsvm3{a} libtasn1-6{a} libtasn1-6-dev{a} libtcl8.6{a} libtclap-dev{a} libtext-charwidth-perl{a} libtext-wrapi18n-perl{a} libthai-data{a} libthai0{a} libtiff6{a} libtirpc-common{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libwebp7{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libxt6t64{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} openssl{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} r-base-core{a} r-mathlib{a} readline-common{a} sensible-utils{a} tzdata{a} ucf{a} unzip{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc curl krb5-locales libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libtasn1-doc libx11-protocol-perl linux-sysctl-defaults lynx psmisc publicsuffix r-base-dev r-doc-html r-recommended shared-mime-info wget x11-utils x11-xserver-utils xdg-user-dirs 0 packages upgraded, 167 newly installed, 0 to remove and 0 not upgraded. Need to get 92.5 MB of archives. After unpacking 272 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025a-2 [259 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 openssl arm64 3.4.1-1 [1390 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 ca-certificates all 20241223 [164 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtext-charwidth-perl arm64 0.04-11+b4 [9652 B] Get: 18 http://deb.debian.org/debian unstable/main arm64 libtext-wrapi18n-perl all 0.06-10 [8808 B] Get: 19 http://deb.debian.org/debian unstable/main arm64 ucf all 3.0050 [42.7 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 33 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b2 [630 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libpng16-16t64 arm64 1.6.47-1 [274 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libfreetype6 arm64 2.13.3+dfsg-1 [422 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 fontconfig-config arm64 2.15.0-2.1 [318 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libfontconfig1 arm64 2.15.0-2.1 [387 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 fontconfig arm64 2.15.0-2.1 [463 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 54 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b7 [308 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 libpixman-1-0 arm64 0.44.0-3 [168 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 libxau6 arm64 1:1.0.11-1 [20.6 kB] Get: 66 http://deb.debian.org/debian unstable/main arm64 libxdmcp6 arm64 1:1.1.5-1 [27.8 kB] Get: 67 http://deb.debian.org/debian unstable/main arm64 libxcb1 arm64 1.17.0-2+b1 [143 kB] Get: 68 http://deb.debian.org/debian unstable/main arm64 libx11-data all 2:1.8.10-2 [337 kB] Get: 69 http://deb.debian.org/debian unstable/main arm64 libx11-6 arm64 2:1.8.10-2 [789 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 libxcb-render0 arm64 1.17.0-2+b1 [115 kB] Get: 71 http://deb.debian.org/debian unstable/main arm64 libxcb-shm0 arm64 1.17.0-2+b1 [105 kB] Get: 72 http://deb.debian.org/debian unstable/main arm64 libxext6 arm64 2:1.3.4-1+b3 [49.2 kB] Get: 73 http://deb.debian.org/debian unstable/main arm64 libxrender1 arm64 1:0.9.10-1.1+b4 [27.2 kB] Get: 74 http://deb.debian.org/debian unstable/main arm64 libcairo2 arm64 1.18.2-2 [483 kB] Get: 75 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-1 [107 kB] Get: 76 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 77 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 78 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 79 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 80 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 81 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 82 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB] Get: 83 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 84 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 85 http://deb.debian.org/debian unstable/main arm64 libngtcp2-16 arm64 1.11.0-1 [121 kB] Get: 86 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls8 arm64 1.11.0-1 [28.2 kB] Get: 87 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 88 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 89 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 90 http://deb.debian.org/debian unstable/main arm64 libcurl3t64-gnutls arm64 8.12.1-3 [336 kB] Get: 91 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB] Get: 92 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB] Get: 93 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB] Get: 94 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB] Get: 95 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.8-1 [101 kB] Get: 96 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB] Get: 97 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB] Get: 98 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB] Get: 99 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB] Get: 100 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB] Get: 101 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB] Get: 102 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB] Get: 103 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB] Get: 104 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB] Get: 105 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB] Get: 106 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB] Get: 107 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB] Get: 108 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.8.0-1 [89.4 kB] Get: 109 http://deb.debian.org/debian unstable/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.11.0-1 [33.9 kB] Get: 110 http://deb.debian.org/debian unstable/main arm64 libngtcp2-dev arm64 1.11.0-1 [174 kB] Get: 111 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB] Get: 112 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 113 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB] Get: 114 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB] Get: 115 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB] Get: 116 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB] Get: 117 http://deb.debian.org/debian unstable/main arm64 libcurl4-gnutls-dev arm64 8.12.1-3 [465 kB] Get: 118 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-3 [339 kB] Get: 119 http://deb.debian.org/debian unstable/main arm64 libdatrie1 arm64 0.2.13-3+b1 [37.6 kB] Get: 120 http://deb.debian.org/debian unstable/main arm64 libdeflate0 arm64 1.23-1+b1 [42.5 kB] Get: 121 http://deb.debian.org/debian unstable/main arm64 libdeflate-dev arm64 1.23-1+b1 [51.4 kB] Get: 122 http://deb.debian.org/debian unstable/main arm64 libfribidi0 arm64 1.0.16-1 [26.5 kB] Get: 123 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB] Get: 124 http://deb.debian.org/debian unstable/main arm64 libglib2.0-0t64 arm64 2.83.5-1 [1422 kB] Get: 125 http://deb.debian.org/debian unstable/main arm64 libgraphite2-3 arm64 1.3.14-2+b1 [70.4 kB] Get: 126 http://deb.debian.org/debian unstable/main arm64 libharfbuzz0b arm64 10.2.0-1 [443 kB] Get: 127 http://deb.debian.org/debian unstable/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 128 http://deb.debian.org/debian unstable/main arm64 libhts3t64 arm64 1.21+ds-1 [426 kB] Get: 129 http://deb.debian.org/debian unstable/main arm64 liblzma-dev arm64 5.6.4-1 [319 kB] Get: 130 http://deb.debian.org/debian unstable/main arm64 libhts-dev arm64 1.21+ds-1 [1658 kB] Get: 131 http://deb.debian.org/debian unstable/main arm64 x11-common all 1:7.7+24 [217 kB] Get: 132 http://deb.debian.org/debian unstable/main arm64 libice6 arm64 2:1.1.1-1 [62.1 kB] Get: 133 http://deb.debian.org/debian unstable/main arm64 libjbig0 arm64 2.1-6.1+b2 [30.4 kB] Get: 134 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB] Get: 135 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 136 http://deb.debian.org/debian unstable/main arm64 liblerc4 arm64 4.0.0+ds-5 [146 kB] Get: 137 http://deb.debian.org/debian unstable/main arm64 libthai-data all 0.1.29-2 [168 kB] Get: 138 http://deb.debian.org/debian unstable/main arm64 libthai0 arm64 0.1.29-2+b1 [48.4 kB] Get: 139 http://deb.debian.org/debian unstable/main arm64 libpango-1.0-0 arm64 1.56.1-1 [213 kB] Get: 140 http://deb.debian.org/debian unstable/main arm64 libpangoft2-1.0-0 arm64 1.56.1-1 [52.8 kB] Get: 141 http://deb.debian.org/debian unstable/main arm64 libpangocairo-1.0-0 arm64 1.56.1-1 [33.8 kB] Get: 142 http://deb.debian.org/debian unstable/main arm64 libpaper2 arm64 2.2.5-0.3+b1 [16.6 kB] Get: 143 http://deb.debian.org/debian unstable/main arm64 libpaper-utils arm64 2.2.5-0.3+b1 [16.3 kB] Get: 144 http://deb.debian.org/debian unstable/main arm64 libpcre2-16-0 arm64 10.45-1 [247 kB] Get: 145 http://deb.debian.org/debian unstable/main arm64 libpcre2-32-0 arm64 10.45-1 [237 kB] Get: 146 http://deb.debian.org/debian unstable/main arm64 libpcre2-posix3 arm64 10.45-1 [63.7 kB] Get: 147 http://deb.debian.org/debian unstable/main arm64 libpcre2-dev arm64 10.45-1 [749 kB] Get: 148 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 149 http://deb.debian.org/debian unstable/main arm64 libsharpyuv0 arm64 1.5.0-0.1 [114 kB] Get: 150 http://deb.debian.org/debian unstable/main arm64 libsm6 arm64 2:1.2.4-1 [34.2 kB] Get: 151 http://deb.debian.org/debian unstable/main arm64 libsvm3 arm64 3.24+ds-6+b1 [38.3 kB] Get: 152 http://deb.debian.org/debian unstable/main arm64 libsvm-dev arm64 3.24+ds-6+b1 [59.4 kB] Get: 153 http://deb.debian.org/debian unstable/main arm64 libtcl8.6 arm64 8.6.16+dfsg-1 [984 kB] Get: 154 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Get: 155 http://deb.debian.org/debian unstable/main arm64 libwebp7 arm64 1.5.0-0.1 [271 kB] Get: 156 http://deb.debian.org/debian unstable/main arm64 libtiff6 arm64 4.5.1+git230720-5 [309 kB] Get: 157 http://deb.debian.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 158 http://deb.debian.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.3+b1 [78.7 kB] Get: 159 http://deb.debian.org/debian unstable/main arm64 libxft2 arm64 2.3.6-1+b4 [51.6 kB] Get: 160 http://deb.debian.org/debian unstable/main arm64 libxss1 arm64 1:1.2.3-1+b3 [17.1 kB] Get: 161 http://deb.debian.org/debian unstable/main arm64 libtk8.6 arm64 8.6.16-1 [741 kB] Get: 162 http://deb.debian.org/debian unstable/main arm64 libxt6t64 arm64 1:1.2.1-1.2+b2 [173 kB] Get: 163 http://deb.debian.org/debian unstable/main arm64 zip arm64 3.0-14+b1 [227 kB] Get: 164 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB] Get: 165 http://deb.debian.org/debian unstable/main arm64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 166 http://deb.debian.org/debian unstable/main arm64 r-base-core arm64 4.4.3-1 [28.1 MB] Get: 167 http://deb.debian.org/debian unstable/main arm64 r-mathlib arm64 4.4.3-1 [2594 kB] Fetched 92.5 MB in 0s (222 MB/s) Preconfiguring packages ... Selecting previously unselected package tzdata. (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 ... 19897 files and directories currently installed.) Preparing to unpack .../000-tzdata_2025a-2_all.deb ... Unpacking tzdata (2025a-2) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-7_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-7) ... Selecting previously unselected package procps. 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Unpacking libdebhelper-perl (13.24.1) ... Selecting previously unselected package libtool. Preparing to unpack .../027-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../028-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../029-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../030-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../031-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. 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Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../050-libkrb5support0_1.21.3-4_arm64.deb ... Unpacking libkrb5support0:arm64 (1.21.3-4) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../051-libk5crypto3_1.21.3-4_arm64.deb ... Unpacking libk5crypto3:arm64 (1.21.3-4) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../052-libkeyutils1_1.6.3-4_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../053-libkrb5-3_1.21.3-4_arm64.deb ... Unpacking libkrb5-3:arm64 (1.21.3-4) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../054-libgssapi-krb5-2_1.21.3-4_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.21.3-4) ... Selecting previously unselected package libgssrpc4t64:arm64. Preparing to unpack .../055-libgssrpc4t64_1.21.3-4_arm64.deb ... Unpacking libgssrpc4t64:arm64 (1.21.3-4) ... Selecting previously unselected package libkadm5clnt-mit12:arm64. Preparing to unpack .../056-libkadm5clnt-mit12_1.21.3-4_arm64.deb ... Unpacking libkadm5clnt-mit12:arm64 (1.21.3-4) ... Selecting previously unselected package libkdb5-10t64:arm64. Preparing to unpack .../057-libkdb5-10t64_1.21.3-4_arm64.deb ... Unpacking libkdb5-10t64:arm64 (1.21.3-4) ... Selecting previously unselected package libkadm5srv-mit12:arm64. Preparing to unpack .../058-libkadm5srv-mit12_1.21.3-4_arm64.deb ... Unpacking libkadm5srv-mit12:arm64 (1.21.3-4) ... Selecting previously unselected package krb5-multidev:arm64. Preparing to unpack .../059-krb5-multidev_1.21.3-4_arm64.deb ... Unpacking krb5-multidev:arm64 (1.21.3-4) ... Selecting previously unselected package libblas3:arm64. Preparing to unpack .../060-libblas3_3.12.1-2_arm64.deb ... Unpacking libblas3:arm64 (3.12.1-2) ... Selecting previously unselected package libbrotli-dev:arm64. 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Unpacking libpangocairo-1.0-0:arm64 (1.56.1-1) ... Selecting previously unselected package libpaper2:arm64. Preparing to unpack .../141-libpaper2_2.2.5-0.3+b1_arm64.deb ... Unpacking libpaper2:arm64 (2.2.5-0.3+b1) ... Selecting previously unselected package libpaper-utils. Preparing to unpack .../142-libpaper-utils_2.2.5-0.3+b1_arm64.deb ... Unpacking libpaper-utils (2.2.5-0.3+b1) ... Selecting previously unselected package libpcre2-16-0:arm64. Preparing to unpack .../143-libpcre2-16-0_10.45-1_arm64.deb ... Unpacking libpcre2-16-0:arm64 (10.45-1) ... Selecting previously unselected package libpcre2-32-0:arm64. Preparing to unpack .../144-libpcre2-32-0_10.45-1_arm64.deb ... Unpacking libpcre2-32-0:arm64 (10.45-1) ... Selecting previously unselected package libpcre2-posix3:arm64. Preparing to unpack .../145-libpcre2-posix3_10.45-1_arm64.deb ... Unpacking libpcre2-posix3:arm64 (10.45-1) ... Selecting previously unselected package libpcre2-dev:arm64. Preparing to unpack .../146-libpcre2-dev_10.45-1_arm64.deb ... Unpacking libpcre2-dev:arm64 (10.45-1) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../147-libreadline8t64_8.2-6_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-6) ... Selecting previously unselected package libsharpyuv0:arm64. Preparing to unpack .../148-libsharpyuv0_1.5.0-0.1_arm64.deb ... 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Unpacking libwebp7:arm64 (1.5.0-0.1) ... Selecting previously unselected package libtiff6:arm64. Preparing to unpack .../155-libtiff6_4.5.1+git230720-5_arm64.deb ... Unpacking libtiff6:arm64 (4.5.1+git230720-5) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../156-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:arm64. Preparing to unpack .../157-libtirpc3t64_1.3.4+ds-1.3+b1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../158-libxft2_2.3.6-1+b4_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1+b4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/vt-0.57721+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../vt_0.57721+ds-3_source.changes dpkg-buildpackage: info: source package vt dpkg-buildpackage: info: source version 0.57721+ds-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Antoni Villalonga dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 clean make[1]: Entering directory '/build/reproducible-path/vt-0.57721+ds' rm -rf vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o make[1]: Leaving directory '/build/reproducible-path/vt-0.57721+ds' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/vt-0.57721+ds' g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ahmm.o -c ahmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o align.o -c align.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o allele.o -c allele.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_1000g.o -c annotate_1000g.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_indels.o -c annotate_indels.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_indels2.o -c annotate_indels2.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_regions.o -c annotate_regions.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_variants.o -c annotate_variants.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o annotate_vntrs.o -c annotate_vntrs.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o augmented_bam_record.o -c augmented_bam_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_genotyping_buffered_reader.o -c bcf_genotyping_buffered_reader.cpp ahmm.cpp: In member function 'void AHMM::collect_statistics(int32_t, int32_t, int32_t)': ahmm.cpp:687:35: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 687 | rflank_start[MODEL] = NAN; | ^~~ ahmm.cpp:688:34: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 688 | rflank_start[READ] = NAN; | ^~~ ahmm.cpp:689:33: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+Inff' to '2147483647' [-Woverflow] 689 | rflank_end[MODEL] = INFINITY; | ^~~~~~~~ ahmm.cpp:690:32: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+Inff' to '2147483647' [-Woverflow] 690 | rflank_end[READ] = INFINITY; | ^~~~~~~~ ahmm.cpp: In member function 'void AHMM::clear_statistics()': ahmm.cpp:737:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 737 | lflank_start[MODEL] = NAN; | ^~~ ahmm.cpp:738:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 738 | lflank_start[READ] = NAN; | ^~~ ahmm.cpp:739:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 739 | lflank_end[MODEL] = NAN; | ^~~ ahmm.cpp:740:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 740 | lflank_end[READ] = NAN; | ^~~ ahmm.cpp:741:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 741 | motif_start[MODEL] = NAN; | ^~~ ahmm.cpp:742:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 742 | motif_start[READ] = NAN; | ^~~ ahmm.cpp:743:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 743 | motif_end[MODEL] = NAN; | ^~~ ahmm.cpp:744:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 744 | motif_end[READ] = NAN; | ^~~ ahmm.cpp:745:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 745 | motif_count = NAN; | ^~~ ahmm.cpp:746:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 746 | exact_motif_count = NAN; | ^~~ ahmm.cpp:747:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 747 | motif_m = NAN; | ^~~ ahmm.cpp:748:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 748 | motif_xid = NAN; | ^~~ ahmm.cpp:750:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 750 | rflank_start[MODEL] = NAN; | ^~~ ahmm.cpp:751:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 751 | rflank_start[READ] = NAN; | ^~~ ahmm.cpp:752:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 752 | rflank_end[MODEL] = NAN; | ^~~ ahmm.cpp:753:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 753 | rflank_end[READ] = NAN; | ^~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_single_genotyping_buffered_reader.o -c bcf_single_genotyping_buffered_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bam_ordered_reader.o -c bam_ordered_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bcf_synced_reader.o -c bcf_synced_reader.cpp bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)': bcf_ordered_writer.cpp:162:114: warning: format '%d' expects argument of type 'int', but argument 8 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 162 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~^ | | | int | %ld bcf_ordered_writer.cpp:162:123: warning: format '%d' expects argument of type 'int', but argument 10 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 162 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~^ | | | int | %ld bcf_ordered_writer.cpp:162:187: warning: format '%d' expects argument of type 'int', but argument 12 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 162 | fprintf(stderr, "[%s:%d %s] Might not be sorted for window size %d at current record %s:%d < %d (%d [last record] - %d), please increase window size to at least %d.\n", | ~^ | | | int | %ld bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write_hdr()': bcf_ordered_writer.cpp:129:18: warning: ignoring return value of 'int bcf_hdr_write(htsFile*, bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | bcf_hdr_write(file, hdr); | ~~~~~~~~~~~~~^~~~~~~~~~~ bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::write(bcf1_t*)': bcf_ordered_writer.cpp:195:18: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 195 | bcf_write(file, hdr, v); | ~~~~~~~~~^~~~~~~~~~~~~~ bcf_ordered_writer.cpp: In member function 'void BCFOrderedWriter::flush(bool)': bcf_ordered_writer.cpp:245:22: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 245 | bcf_write(file, hdr, buffer.back()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ bcf_ordered_writer.cpp:261:30: warning: ignoring return value of 'int bcf_write(htsFile*, bcf_hdr_t*, bcf1_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 261 | bcf_write(file, hdr, buffer.back()); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o bed.o -c bed.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_motif_picker.o -c candidate_motif_picker.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o candidate_region_extractor.o -c candidate_region_extractor.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o cat.o -c cat.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o chmm.o -c chmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o complex_genotyping_record.o -c complex_genotyping_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_concordance.o -c compute_concordance.cpp chmm.cpp: In member function 'void CHMM::clear_statistics()': chmm.cpp:1106:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1106 | lflank_start[MODEL] = NAN; | ^~~ chmm.cpp:1107:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1107 | lflank_start[READ] = NAN; | ^~~ chmm.cpp:1108:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1108 | lflank_end[MODEL] = NAN; | ^~~ chmm.cpp:1109:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1109 | lflank_end[READ] = NAN; | ^~~ chmm.cpp:1110:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1110 | motif_start[MODEL] = NAN; | ^~~ chmm.cpp:1111:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1111 | motif_start[READ] = NAN; | ^~~ chmm.cpp:1112:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1112 | motif_end[MODEL] = NAN; | ^~~ chmm.cpp:1113:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1113 | motif_end[READ] = NAN; | ^~~ chmm.cpp:1114:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1114 | rflank_start[MODEL] = NAN; | ^~~ chmm.cpp:1115:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1115 | rflank_start[READ] = NAN; | ^~~ chmm.cpp:1116:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1116 | rflank_end[MODEL] = NAN; | ^~~ chmm.cpp:1117:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1117 | rflank_end[READ] = NAN; | ^~~ chmm.cpp:1118:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1118 | motif_count = NAN; | ^~~ chmm.cpp:1119:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1119 | exact_motif_count = NAN; | ^~~ chmm.cpp:1120:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1120 | motif_m = NAN; | ^~~ chmm.cpp:1121:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 1121 | motif_xid = NAN; | ^~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features.o -c compute_features.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_features2.o -c compute_features2.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o compute_rl_dist.o -c compute_rl_dist.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o config.o -c config.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_multiallelics.o -c consolidate_multiallelics.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate_vntrs.o -c consolidate_vntrs.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o consolidate.o -c consolidate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o construct_probes.o -c construct_probes.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose.o -c decompose.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose2.o -c decompose2.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o decompose_blocksub.o -c decompose_blocksub.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o discover.o -c discover.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o duplicate.o -c duplicate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimate.o -c estimate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o estimator.o -c estimator.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o extract_vntrs.o -c extract_vntrs.cpp In file included from bcf_ordered_reader.h:27, from program.h:32, from discover.h:27, from discover.cpp:24: discover.cpp: In member function 'bool {anonymous}::Igor::filter_read(bam1_t*)': hts_utils.h:124:40: warning: narrowing conversion of '(s->bam1_t::core.bam1_core_t::pos + 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 124 | #define bam_get_pos1(s) ((s)->core.pos + 1) | ~~~~~~~~~~~~~~~^~~~ discover.cpp:355:45: note: in expansion of macro 'bam_get_pos1' 355 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; | ^~~~~~~~~~~~ discover.cpp:355:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 355 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter.o -c filter.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o filter_overlap.o -c filter_overlap.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o flank_detector.o -c flank_detector.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_aligner.o -c fuzzy_aligner.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o fuzzy_partition.o -c fuzzy_partition.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o gencode.o -c gencode.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genome_interval.o -c genome_interval.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotype.o -c genotype.cpp fuzzy_partition.cpp: In member function 'void {anonymous}::Igor::initialize()': fuzzy_partition.cpp:153:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 153 | bcf_hdr_sync(odr->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o genotyping_record.o -c genotyping_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ghmm.o -c ghmm.cpp In file included from bam_ordered_reader.h:27, from genotype.h:27, from genotype.cpp:24: genotype.cpp: In member function 'bool {anonymous}::Igor::filter_read(bam1_t*)': hts_utils.h:124:40: warning: narrowing conversion of '(s->bam1_t::core.bam1_core_t::pos + 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 124 | #define bam_get_pos1(s) ((s)->core.pos + 1) | ~~~~~~~~~~~~~~~^~~~ genotype.cpp:304:45: note: in expansion of macro 'bam_get_pos1' 304 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; | ^~~~~~~~~~~~ genotype.cpp:304:95: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 304 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hts_utils.o -c hts_utils.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o hfilter.o -c hfilter.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_annotator.o -c indel_annotator.cpp hts_utils.cpp: In function 'void bcf_hdr_print(bcf_hdr_t*)': hts_utils.cpp:406:33: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 406 | if ( h->dirty ) bcf_hdr_sync(h); | ~~~~~~~~~~~~^~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o indel_genotyping_record.o -c indel_genotyping_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o index.o -c index.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o info2tab.o -c info2tab.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval_tree.o -c interval_tree.cpp info2tab.cpp: In member function 'void {anonymous}::Igor::info2tab()': info2tab.cpp:278:32: warning: format '%d' expects argument of type 'int', but argument 4 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 278 | fprintf(out, "%s\t%d", bcf_get_chrom(h, v), bcf_get_pos1(v)); | ~^ | | | int | %ld g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o interval.o -c interval.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lfhmm.o -c lfhmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm.o -c lhmm.cpp lfhmm.cpp: In member function 'void LFHMM::collect_statistics(int32_t, int32_t, int32_t)': lfhmm.cpp:761:33: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 761 | rflank_end[MODEL] = NAN; | ^~~ lfhmm.cpp: In member function 'void LFHMM::clear_statistics()': lfhmm.cpp:868:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 868 | lflank_start[MODEL] = NAN; | ^~~ lfhmm.cpp:869:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 869 | lflank_start[READ] = NAN; | ^~~ lfhmm.cpp:870:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 870 | lflank_end[MODEL] = NAN; | ^~~ lfhmm.cpp:871:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 871 | lflank_end[READ] = NAN; | ^~~ lfhmm.cpp:872:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 872 | motif_start[MODEL] = NAN; | ^~~ lfhmm.cpp:873:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 873 | motif_start[READ] = NAN; | ^~~ lfhmm.cpp:874:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 874 | motif_end[MODEL] = NAN; | ^~~ lfhmm.cpp:875:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 875 | motif_end[READ] = NAN; | ^~~ lfhmm.cpp:876:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 876 | motif_count = NAN; | ^~~ lfhmm.cpp:877:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 877 | exact_motif_count = NAN; | ^~~ lfhmm.cpp:878:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 878 | motif_m = NAN; | ^~~ lfhmm.cpp:879:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 879 | motif_xid = NAN; | ^~~ lfhmm.cpp:881:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 881 | rflank_start[MODEL] = NAN; | ^~~ lfhmm.cpp:882:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 882 | rflank_start[READ] = NAN; | ^~~ lfhmm.cpp:883:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 883 | rflank_end[MODEL] = NAN; | ^~~ lfhmm.cpp:884:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 884 | rflank_end[READ] = NAN; | ^~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o lhmm1.o -c lhmm1.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o liftover.o -c liftover.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o log_tool.o -c log_tool.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge.o -c merge.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_candidate_variants.o -c merge_candidate_variants.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o merge_genotypes.o -c merge_genotypes.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o milk_filter.o -c milk_filter.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o motif_tree.o -c motif_tree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o motif_map.o -c motif_map.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multi_partition.o -c multi_partition.cpp milk_filter.cpp: In member function 'void {anonymous}::Igor::milk_filter()': milk_filter.cpp:456:53: warning: format '%d' expects argument of type 'int', but argument 5 has type 'hts_pos_t' {aka 'long int'} [-Wformat=] 456 | fprintf(stderr,"Processing %d variants at %s:%d\n", nread + 1, bcf_seqname(odw->hdr,nv), nv->pos); | ~^ ~~~~~~~ | | | | int hts_pos_t {aka long int} | %ld g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp merge_genotypes.cpp: In member function 'void {anonymous}::Igor::initialize()': merge_genotypes.cpp:215:21: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 215 | bcf_hdr_sync(odw->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o needle.o -c needle.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o normalize.o -c normalize.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o nuclear_pedigree.o -c nuclear_pedigree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o partition.o -c partition.cpp ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector&)': ordered_bcf_overlap_matcher.cpp:34:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 34 | bcf_hdr_sync(odr->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector&, std::string)': ordered_bcf_overlap_matcher.cpp:52:17: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 52 | bcf_hdr_sync(odr->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste.o -c paste.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o paste_genotypes.o -c paste_genotypes.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pedigree.o -c pedigree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o peek.o -c peek.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pileup.o -c pileup.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o pregex.o -c pregex.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_afs.o -c profile_afs.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_chm1.o -c profile_chm1.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_chrom.o -c profile_chrom.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_fic_hwe.o -c profile_fic_hwe.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_hwe.o -c profile_hwe.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_indels.o -c profile_indels.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_len.o -c profile_len.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_mendelian.o -c profile_mendelian.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_na12878.o -c profile_na12878.cpp profile_mendelian.cpp: In member function 'void {anonymous}::Igor::initialize()': profile_mendelian.cpp:191:25: warning: ignoring return value of 'int bcf_hdr_sync(bcf_hdr_t*)' declared with attribute 'warn_unused_result' [-Wunused-result] 191 | bcf_hdr_sync(odw->hdr); | ~~~~~~~~~~~~^~~~~~~~~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_snps.o -c profile_snps.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o profile_vntrs.o -c profile_vntrs.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o program.o -c program.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o read_filter.o -c read_filter.cpp In file included from read_filter.h:30, from read_filter.cpp:24: read_filter.cpp: In member function 'bool ReadFilter::filter_read(bam_hdr_t*, bam1_t*)': hts_utils.h:124:40: warning: narrowing conversion of '(s->bam1_t::core.bam1_core_t::pos + 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 124 | #define bam_get_pos1(s) ((s)->core.pos + 1) | ~~~~~~~~~~~~~~~^~~~ read_filter.cpp:95:41: note: in expansion of macro 'bam_get_pos1' 95 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; | ^~~~~~~~~~~~ read_filter.cpp:95:91: warning: narrowing conversion of '(((s->bam1_t::core.bam1_core_t::pos + 1) + ((hts_pos_t)s->bam1_t::core.bam1_core_t::l_qseq)) - 1)' from 'hts_pos_t' {aka 'long int'} to 'int32_t' {aka 'int'} [-Wnarrowing] 95 | kh_val(reads, k) = {bam_get_pos1(s), bam_get_pos1(s)+bam_get_l_qseq(s)-1}; g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o reference_sequence.o -c reference_sequence.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm.o -c rfhmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rfhmm_x.o -c rfhmm_x.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o rminfo.o -c rminfo.cpp rfhmm.cpp: In member function 'void RFHMM::clear_statistics()': rfhmm.cpp:833:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 833 | lflank_start[MODEL] = NAN; | ^~~ rfhmm.cpp:834:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 834 | lflank_start[READ] = NAN; | ^~~ rfhmm.cpp:835:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 835 | lflank_end[MODEL] = NAN; | ^~~ rfhmm.cpp:836:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 836 | lflank_end[READ] = NAN; | ^~~ rfhmm.cpp:837:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 837 | motif_start[MODEL] = NAN; | ^~~ rfhmm.cpp:838:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 838 | motif_start[READ] = NAN; | ^~~ rfhmm.cpp:839:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 839 | motif_end[MODEL] = NAN; | ^~~ rfhmm.cpp:840:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 840 | motif_end[READ] = NAN; | ^~~ rfhmm.cpp:841:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 841 | rflank_start[MODEL] = NAN; | ^~~ rfhmm.cpp:842:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 842 | rflank_start[READ] = NAN; | ^~~ rfhmm.cpp:843:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 843 | rflank_end[MODEL] = NAN; | ^~~ rfhmm.cpp:844:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 844 | rflank_end[READ] = NAN; | ^~~ rfhmm.cpp:845:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 845 | motif_count = NAN; | ^~~ rfhmm.cpp:846:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 846 | exact_motif_count = NAN; | ^~~ rfhmm.cpp:847:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 847 | motif_m = NAN; | ^~~ rfhmm.cpp:848:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 848 | motif_xid = NAN; | ^~~ rfhmm_x.cpp: In member function 'void RFHMM_X::clear_statistics()': rfhmm_x.cpp:928:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 928 | lflank_start[MODEL] = NAN; | ^~~ rfhmm_x.cpp:929:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 929 | lflank_start[READ] = NAN; | ^~~ rfhmm_x.cpp:930:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 930 | lflank_end[MODEL] = NAN; | ^~~ rfhmm_x.cpp:931:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 931 | lflank_end[READ] = NAN; | ^~~ rfhmm_x.cpp:932:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 932 | motif_start[MODEL] = NAN; | ^~~ rfhmm_x.cpp:933:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 933 | motif_start[READ] = NAN; | ^~~ rfhmm_x.cpp:934:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 934 | motif_end[MODEL] = NAN; | ^~~ rfhmm_x.cpp:935:23: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 935 | motif_end[READ] = NAN; | ^~~ rfhmm_x.cpp:936:27: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 936 | rflank_start[MODEL] = NAN; | ^~~ rfhmm_x.cpp:937:26: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 937 | rflank_start[READ] = NAN; | ^~~ rfhmm_x.cpp:938:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 938 | rflank_end[MODEL] = NAN; | ^~~ rfhmm_x.cpp:939:24: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 939 | rflank_end[READ] = NAN; | ^~~ rfhmm_x.cpp:940:19: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 940 | motif_count = NAN; | ^~~ rfhmm_x.cpp:941:25: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 941 | exact_motif_count = NAN; | ^~~ rfhmm_x.cpp:942:15: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 942 | motif_m = NAN; | ^~~ rfhmm_x.cpp:943:17: warning: overflow in conversion from 'float' to 'int32_t' {aka 'int'} changes value from '+QNaNf' to '0' [-Woverflow] 943 | motif_xid = NAN; | ^~~ g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o seq.o -c seq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o set_ref.o -c set_ref.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o snp_genotyping_record.o -c snp_genotyping_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sort.o -c sort.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o subset.o -c subset.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o sv_tree.o -c sv_tree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o svm_train.o -c svm_train.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o svm_predict.o -c svm_predict.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o tbx_ordered_reader.o -c tbx_ordered_reader.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o test.o -c test.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o trio.o -c trio.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o union_variants.o -c union_variants.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o uniq.o -c uniq.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o utils.o -c utils.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o validate.o -c validate.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o variant.o -c variant.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o variant_manip.o -c variant_manip.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o variant_filter.o -c variant_filter.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o view.o -c view.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr.o -c vntr.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_annotator.o -c vntr_annotator.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_consolidator.o -c vntr_consolidator.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_extractor.o -c vntr_extractor.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_genotyping_record.o -c vntr_genotyping_record.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntr_tree.o -c vntr_tree.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vntrize.o -c vntrize.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o wdp_ahmm.o -c wdp_ahmm.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o main.o -c main.cpp g++ -Wl,-z,relro -Wl,-z,now -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/vt-0.57721+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -pipe -std=c++0x -O3 -I. -I/usr/share/R/include -D__STDC_LIMIT_MACROS -DPCRE2_CODE_UNIT_WIDTH=8 -o vt ahmm.o align.o allele.o annotate_1000g.o annotate_dbsnp_rsid.o annotate_indels.o annotate_indels2.o annotate_regions.o annotate_variants.o annotate_vntrs.o augmented_bam_record.o bcf_genotyping_buffered_reader.o bcf_single_genotyping_buffered_reader.o bam_ordered_reader.o bcf_ordered_reader.o bcf_ordered_writer.o bcf_synced_reader.o bed.o candidate_motif_picker.o candidate_region_extractor.o cat.o chmm.o complex_genotyping_record.o compute_concordance.o compute_features.o compute_features2.o compute_rl_dist.o config.o consolidate_multiallelics.o consolidate_vntrs.o consolidate.o construct_probes.o decompose.o decompose2.o decompose_blocksub.o discover.o duplicate.o estimate.o estimator.o extract_vntrs.o filter.o filter_overlap.o flank_detector.o fuzzy_aligner.o fuzzy_partition.o gencode.o genome_interval.o genotype.o genotyping_record.o ghmm.o hts_utils.o hfilter.o indel_annotator.o indel_genotyping_record.o index.o info2tab.o interval_tree.o interval.o lfhmm.o lhmm.o lhmm1.o liftover.o log_tool.o merge.o merge_candidate_variants.o merge_genotypes.o milk_filter.o motif_tree.o motif_map.o multi_partition.o multiallelics_consolidator.o needle.o normalize.o nuclear_pedigree.o ordered_bcf_overlap_matcher.o ordered_region_overlap_matcher.o partition.o paste.o paste_and_compute_features_sequential.o paste_genotypes.o pedigree.o peek.o pileup.o pregex.o profile_afs.o profile_chm1.o profile_chrom.o profile_fic_hwe.o profile_hwe.o profile_indels.o profile_len.o profile_mendelian.o profile_na12878.o profile_snps.o profile_vntrs.o program.o read_filter.o reference_sequence.o rfhmm.o rfhmm_x.o rminfo.o seq.o set_ref.o snp_genotyping_record.o sort.o subset.o sv_tree.o svm_train.o svm_predict.o tbx_ordered_reader.o test.o trio.o union_variants.o uniq.o utils.o validate.o variant.o variant_manip.o variant_filter.o view.o vntr.o vntr_annotator.o vntr_consolidator.o vntr_extractor.o vntr_genotyping_record.o vntr_tree.o vntrize.o wdp_ahmm.o main.o -lz -lpthread -lbz2 -llzma -lcurl -lcrypto -lhts -lpcre2-8 -lsvm -lRmath -lR make[1]: Leaving directory '/build/reproducible-path/vt-0.57721+ds' dh_auto_test make -j12 test make[1]: Entering directory '/build/reproducible-path/vt-0.57721+ds' test/test.sh ++++++++++++++++++++++ Tests for vt normalize ++++++++++++++++++++++ testing normalize output VCF file : ok output logs : ok +++++++++++++++++++++++++++++++ Tests for vt decompose_blocksub +++++++++++++++++++++++++++++++ testing decompose_blocksub of even-length blocks output VCF file : ok output logs : ok testing decompose_blocksub with alignment output VCF file : ok output logs : ok testing decompose_blocksub of phased even-length blocks output VCF file : ok output logs : ok ++++++++++++++++++++++ Tests for vt decompose ++++++++++++++++++++++ testing decompose for a triallelic variant output VCF file : ok output logs : ok Passed tests : 5 / 5 make[1]: Leaving directory '/build/reproducible-path/vt-0.57721+ds' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install dh_install dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'vt' in '../vt_0.57721+ds-3_arm64.deb'. dpkg-deb: building package 'vt-dbgsym' in '../vt-dbgsym_0.57721+ds-3_arm64.deb'. dpkg-deb: building package 'vt-examples' in '../vt-examples_0.57721+ds-3_all.deb'. dpkg-genbuildinfo --build=binary -O../vt_0.57721+ds-3_arm64.buildinfo dpkg-genchanges --build=binary -O../vt_0.57721+ds-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3198746/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/3198746 and its subdirectories I: Current time: Mon Mar 10 13:15:58 +14 2025 I: pbuilder-time-stamp: 1741562158