Sun Mar  9 23:11:08 UTC 2025  I: starting to build vt/unstable/arm64 on jenkins on '2025-03-09 23:11'
Sun Mar  9 23:11:08 UTC 2025  I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_2/78111/console.log
Sun Mar  9 23:11:08 UTC 2025  I: Downloading source for unstable/vt=0.57721+ds-3
--2025-03-09 23:11:09--  http://deb.debian.org/debian/pool/main/v/vt/vt_0.57721%2bds-3.dsc
Connecting to 46.16.76.132:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2162 (2.1K) [text/prs.lines.tag]
Saving to: ‘vt_0.57721+ds-3.dsc’

     0K ..                                                    100%  322M=0s

2025-03-09 23:11:09 (322 MB/s) - ‘vt_0.57721+ds-3.dsc’ saved [2162/2162]

Sun Mar  9 23:11:09 UTC 2025  I: vt_0.57721+ds-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: vt
Binary: vt, vt-examples
Architecture: any all
Version: 0.57721+ds-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Antoni Villalonga <antoni@friki.cat>
Homepage: https://genome.sph.umich.edu/wiki/Vt
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/vt
Vcs-Git: https://salsa.debian.org/med-team/vt.git
Testsuite: autopkgtest
Build-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
Package-List:
 vt deb science optional arch=any
 vt-examples deb science optional arch=all
Checksums-Sha1:
 8d1f794a59a8497084272acc1d6d6d8e5557c961 18574416 vt_0.57721+ds.orig.tar.xz
 883ef66dd524310822a2ca0b1e9355515edb7f69 8092 vt_0.57721+ds-3.debian.tar.xz
Checksums-Sha256:
 ce6e49949e5a61cd8e06ebac2dea1db94e2df78881350aba1cd178a1e4f73865 18574416 vt_0.57721+ds.orig.tar.xz
 52295d9de36ef140fd0959a1220b85b7acd4e5c34e69a3b65abe56f9a2a3a95a 8092 vt_0.57721+ds-3.debian.tar.xz
Files:
 d431231e862dc0adaa30457001f064f0 18574416 vt_0.57721+ds.orig.tar.xz
 2ffd195b13c6e4b77b0d6673787fe57d 8092 vt_0.57721+ds-3.debian.tar.xz

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Sun Mar  9 23:11:09 UTC 2025  I: Checking whether the package is not for us
Sun Mar  9 23:11:09 UTC 2025  I: Starting 1st build on remote node codethink03-arm64.debian.net.
Sun Mar  9 23:11:09 UTC 2025  I: Preparing to do remote build '1' on codethink03-arm64.debian.net.
Sun Mar  9 23:13:54 UTC 2025  I: Deleting $TMPDIR on codethink03-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat Apr 11 17:34:09 -12 2026
I: pbuilder-time-stamp: 1775972049
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/2024554/tmp/hooks/D02_print_environment starting
I: set
  BUILDDIR='/build/reproducible-path'
  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
  BUILDUSERNAME='pbuilder1'
  BUILD_ARCH='arm64'
  DEBIAN_FRONTEND='noninteractive'
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
  DISTRIBUTION='unstable'
  HOME='/root'
  HOST_ARCH='arm64'
  IFS=' 	
  '
  INVOCATION_ID='a7054556d7ec47b39b300f6f3d5441b2'
  LANG='C'
  LANGUAGE='en_US:en'
  LC_ALL='C'
  MAIL='/var/mail/root'
  OPTIND='1'
  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
  PBCURRENTCOMMANDLINEOPERATION='build'
  PBUILDER_OPERATION='build'
  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
  PBUILDER_SYSCONFDIR='/etc'
  PPID='2024554'
  PS1='# '
  PS2='> '
  PS4='+ '
  PWD='/'
  SHELL='/bin/bash'
  SHLVL='2'
  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/pbuilderrc_P6Bq --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/b1 --logfile b1/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+12'
  USER='root'
  _='/usr/bin/systemd-run'
  http_proxy='http://192.168.101.4:3128'
I: uname -a
  Linux codethink03-arm64 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  2025 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/2024554/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 <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), 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 1s (117 MB/s)
Preconfiguring packages ...
Selecting previously unselected package tzdata.
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(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.
Preparing to unpack .../002-procps_2%3a4.0.4-7_arm64.deb ...
Unpacking procps (2:4.0.4-7) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../003-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../004-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package openssl.
Preparing to unpack .../005-openssl_3.4.1-1_arm64.deb ...
Unpacking openssl (3.4.1-1) ...
Selecting previously unselected package ca-certificates.
Preparing to unpack .../006-ca-certificates_20241223_all.deb ...
Unpacking ca-certificates (20241223) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../007-libmagic-mgc_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../008-libmagic1t64_1%3a5.45-3+b1_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../009-file_1%3a5.45-3+b1_arm64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../010-gettext-base_0.23.1-1_arm64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../011-libuchardet0_0.0.8-1+b2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../012-groff-base_1.23.0-7_arm64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../013-bsdextrautils_2.40.4-5_arm64.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../014-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../015-man-db_2.13.0-1_arm64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package libtext-charwidth-perl:arm64.
Preparing to unpack .../016-libtext-charwidth-perl_0.04-11+b4_arm64.deb ...
Unpacking libtext-charwidth-perl:arm64 (0.04-11+b4) ...
Selecting previously unselected package libtext-wrapi18n-perl.
Preparing to unpack .../017-libtext-wrapi18n-perl_0.06-10_all.deb ...
Unpacking libtext-wrapi18n-perl (0.06-10) ...
Selecting previously unselected package ucf.
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Moving old data out of the way
Unpacking ucf (3.0050) ...
Selecting previously unselected package m4.
Preparing to unpack .../019-m4_1.4.19-7_arm64.deb ...
Unpacking m4 (1.4.19-7) ...
Selecting previously unselected package autoconf.
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Unpacking autoconf (2.72-3) ...
Selecting previously unselected package autotools-dev.
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Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../022-automake_1%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../023-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libcom-err2:arm64.
Preparing to unpack .../024-libcom-err2_1.47.2-1_arm64.deb ...
Unpacking libcom-err2:arm64 (1.47.2-1) ...
Selecting previously unselected package comerr-dev:arm64.
Preparing to unpack .../025-comerr-dev_2.1-1.47.2-1_arm64.deb ...
Unpacking comerr-dev:arm64 (2.1-1.47.2-1) ...
Selecting previously unselected package libdebhelper-perl.
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Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
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Unpacking libtool (2.5.4-4) ...
Selecting previously unselected package dh-autoreconf.
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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.
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Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
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Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:arm64.
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Unpacking libelf1t64:arm64 (0.192-4) ...
Selecting previously unselected package dwz.
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Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:arm64.
Preparing to unpack .../034-libunistring5_1.3-1_arm64.deb ...
Unpacking libunistring5:arm64 (1.3-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../035-libicu72_72.1-6_arm64.deb ...
Unpacking libicu72:arm64 (72.1-6) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../036-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_arm64.deb ...
Unpacking libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
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Unpacking gettext (0.23.1-1) ...
Selecting previously unselected package intltool-debian.
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Unpacking intltool-debian (0.35.0+20060710.6) ...
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Unpacking po-debconf (1.0.21+nmu1) ...
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Unpacking debhelper (13.24.1) ...
Selecting previously unselected package libexpat1:arm64.
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Unpacking libexpat1:arm64 (2.6.4-1) ...
Selecting previously unselected package libbrotli1:arm64.
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Unpacking libbrotli1:arm64 (1.1.0-2+b7) ...
Selecting previously unselected package libpng16-16t64:arm64.
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Unpacking libpng16-16t64:arm64 (1.6.47-1) ...
Selecting previously unselected package libfreetype6:arm64.
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Unpacking libfreetype6:arm64 (2.13.3+dfsg-1) ...
Selecting previously unselected package fonts-dejavu-mono.
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Unpacking fonts-dejavu-mono (2.37-8) ...
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Unpacking fonts-dejavu-core (2.37-8) ...
Selecting previously unselected package fontconfig-config.
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Unpacking fontconfig-config (2.15.0-2.1) ...
Selecting previously unselected package libfontconfig1:arm64.
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Unpacking libfontconfig1:arm64 (2.15.0-2.1) ...
Selecting previously unselected package fontconfig.
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Unpacking fontconfig (2.15.0-2.1) ...
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.
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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.
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I: Building the package
I: Running cd /build/reproducible-path/vt-0.57721+ds/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../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 <antoni@friki.cat>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
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	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
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	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
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
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 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
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
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 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
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 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
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
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
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_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
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 genotype.o -c genotype.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 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
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
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 hfilter.o -c hfilter.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_annotator.o -c indel_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 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
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
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 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
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);
      |         ~~~~~~~~~~~~^~~~~~~~~~
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 multi_partition.o -c multi_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 multiallelics_consolidator.o -c multiallelics_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 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
ordered_bcf_overlap_matcher.cpp: In constructor 'OrderedBCFOverlapMatcher::OrderedBCFOverlapMatcher(std::string&, std::vector<GenomeInterval>&)':
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<GenomeInterval>&, 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 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
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
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
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_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
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
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 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
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
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;
      |                 ^~~
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
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 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: 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/2024554 and its subdirectories
I: Current time: Sat Apr 11 17:36:40 -12 2026
I: pbuilder-time-stamp: 1775972200
Sun Mar  9 23:13:55 UTC 2025  I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net.
Sun Mar  9 23:13:55 UTC 2025  I: Preparing to do remote build '2' on codethink04-arm64.debian.net.
Sun Mar  9 23:16:18 UTC 2025  I: Deleting $TMPDIR on codethink04-arm64.debian.net.
Sun Mar  9 23:16:20 UTC 2025  I: vt_0.57721+ds-3_arm64.changes:
Format: 1.8
Date: Mon, 09 Nov 2020 09:29:40 +0100
Source: vt
Binary: vt vt-dbgsym vt-examples
Architecture: arm64 all
Version: 0.57721+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Antoni Villalonga <antoni@friki.cat>
Description:
 vt         - toolset for short variant discovery in genetic sequence data
 vt-examples - toolset for short variant discovery in genetic sequence data (exa
Changes:
 vt (0.57721+ds-3) unstable; urgency=medium
 .
   * patch 0001: Get rid of commented code
   * Add patch 0002-hts-1.11.patch
Checksums-Sha1:
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 28c6592ec18137f999bf47cc24a47fbabe452965 18358872 vt-examples_0.57721+ds-3_all.deb
 ebf530731325d2e1adc5d418121de0b980597fc8 9237 vt_0.57721+ds-3_arm64.buildinfo
 62697aed8395458843e8a4247da0dc2ef31901fa 721880 vt_0.57721+ds-3_arm64.deb
Checksums-Sha256:
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 277c0ef50f4cda40f2dd837f90b6d837155ecd5b8889797683fe63375b017b56 18358872 vt-examples_0.57721+ds-3_all.deb
 8748b3a12fdd796536e8459a2e88c62aae931ea97cccffb3d01b6578065ac9d6 9237 vt_0.57721+ds-3_arm64.buildinfo
 0fb3ae6985fd1c768b5c4b6beb1596d6010572fa66569ce7f1df5527550f9499 721880 vt_0.57721+ds-3_arm64.deb
Files:
 1833fa068a0c1596dde1ffc98d04d502 28916604 debug optional vt-dbgsym_0.57721+ds-3_arm64.deb
 d527ae3f7ec7028b6007a44b3ec74128 18358872 science optional vt-examples_0.57721+ds-3_all.deb
 9f65f6027fb67829bd8bff93b66e2ab7 9237 science optional vt_0.57721+ds-3_arm64.buildinfo
 ad5d38cce1a116b5d86c65daf8c953cc 721880 science optional vt_0.57721+ds-3_arm64.deb
Sun Mar  9 23:16:21 UTC 2025  I: diffoscope 289 will be used to compare the two builds:
Running as unit: rb-diffoscope-arm64_2-78111.service
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/vt_0.57721+ds-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/vt_0.57721+ds-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/vt_0.57721+ds-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/b1/vt_0.57721+ds-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.hzTNiFQl/b2/vt_0.57721+ds-3_arm64.changes

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       0.000s      1 call     cmp (internal)

## has_same_content_as (total time: 0.000s)
       0.000s      1 call     diffoscope.comparators.binary.FilesystemFile

## main (total time: 0.003s)
       0.003s      2 calls    outputs
       0.000s      1 call     cleanup
Finished with result: success
Main processes terminated with: code=exited/status=0
Service runtime: 267ms
CPU time consumed: 254ms
Sun Mar  9 23:16:22 UTC 2025  I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists.
Sun Mar  9 23:16:22 UTC 2025  I: vt from unstable built successfully and reproducibly on arm64.
Sun Mar  9 23:16:23 UTC 2025  I: Submitting .buildinfo files to external archives:
Sun Mar  9 23:16:23 UTC 2025  I: Submitting 12K	b1/vt_0.57721+ds-3_arm64.buildinfo.asc
Sun Mar  9 23:16:24 UTC 2025  I: Submitting 12K	b2/vt_0.57721+ds-3_arm64.buildinfo.asc
Sun Mar  9 23:16:25 UTC 2025  I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Mar  9 23:16:25 UTC 2025  I: Done submitting .buildinfo files.
Sun Mar  9 23:16:25 UTC 2025  I: Removing signed vt_0.57721+ds-3_arm64.buildinfo.asc files:
removed './b1/vt_0.57721+ds-3_arm64.buildinfo.asc'
removed './b2/vt_0.57721+ds-3_arm64.buildinfo.asc'