Fri Jun 9 10:48:39 UTC 2023 I: starting to build freebayes/bookworm/amd64 on jenkins on '2023-06-09 10:48'
Fri Jun 9 10:48:39 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_4/470/console.log
Fri Jun 9 10:48:39 UTC 2023 I: Downloading source for bookworm/freebayes=1.3.6-2
--2023-06-09 10:48:40-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/freebayes/freebayes_1.3.6-2.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2232 (2.2K) [text/prs.lines.tag]
Saving to: ‘freebayes_1.3.6-2.dsc’
0K .. 100% 154M=0s
2023-06-09 10:48:40 (154 MB/s) - ‘freebayes_1.3.6-2.dsc’ saved [2232/2232]
Fri Jun 9 10:48:40 UTC 2023 I: freebayes_1.3.6-2.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: freebayes
Binary: freebayes
Architecture: any
Version: 1.3.6-2
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Brad Chapman <chapmanb@50mail.com>, Andreas Tille <tille@debian.org>
Homepage: https://github.com/ekg/freebayes
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/freebayes
Vcs-Git: https://salsa.debian.org/med-team/freebayes.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel <!nocheck>, libvcflib-tools <!nocheck>, debhelper
Package-List:
freebayes deb science optional arch=any
Checksums-Sha1:
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504b332ace3ff066468126e5559e058877bdfa0c 11440 freebayes_1.3.6-2.debian.tar.xz
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2fbada9aaa038dc048d99a28e91201f4b57f240a5119fd01e83bdf3224e63872 11440 freebayes_1.3.6-2.debian.tar.xz
Files:
e8fe2bf8bb0139bb313744e5fb8e4105 2898209 freebayes_1.3.6.orig.tar.gz
cd9f68ade2865de3a9d15cab4fce73fe 11440 freebayes_1.3.6-2.debian.tar.xz
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Fri Jun 9 10:48:40 UTC 2023 I: Checking whether the package is not for us
Fri Jun 9 10:48:40 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Fri Jun 9 10:48:40 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Fri Jun 9 10:50:24 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Jul 11 05:12:07 -12 2024
I: pbuilder-time-stamp: 1720717927
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [freebayes_1.3.6-2.dsc]
I: copying [./freebayes_1.3.6.orig.tar.gz]
I: copying [./freebayes_1.3.6-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Tue Nov 1 01:45:15 2022 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./freebayes_1.3.6-2.dsc: no acceptable signature found
dpkg-source: info: extracting freebayes in freebayes-1.3.6
dpkg-source: info: unpacking freebayes_1.3.6.orig.tar.gz
dpkg-source: info: unpacking freebayes_1.3.6-2.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/523057/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='5758ff9d261e40978537ce21ed901b70'
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='523057'
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.66tilOGj/pbuilderrc_kcTn --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.66tilOGj/b1 --logfile b1/build.log freebayes_1.3.6-2.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos15-amd64 6.1.0-0.deb11.7-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.20-2~bpo11+1 (2023-04-23) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/523057/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <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), meson, ninja-build, pkg-config, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools, debhelper
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19591 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 meson; however:
Package meson is not installed.
pbuilder-satisfydepends-dummy depends on ninja-build; however:
Package ninja-build is not installed.
pbuilder-satisfydepends-dummy depends on pkg-config; however:
Package pkg-config is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libbamtools-dev; however:
Package libbamtools-dev is not installed.
pbuilder-satisfydepends-dummy depends on libvcflib-dev (>= 1.0.0~rc2+dfsg-3~); however:
Package libvcflib-dev is not installed.
pbuilder-satisfydepends-dummy depends on libtabixpp-dev; however:
Package libtabixpp-dev is not installed.
pbuilder-satisfydepends-dummy depends on libseqlib-dev (>= 1.1.2+dfsg-5); however:
Package libseqlib-dev is not installed.
pbuilder-satisfydepends-dummy depends on bc; however:
Package bc is not installed.
pbuilder-satisfydepends-dummy depends on samtools; however:
Package samtools is not installed.
pbuilder-satisfydepends-dummy depends on parallel; however:
Package parallel is not installed.
pbuilder-satisfydepends-dummy depends on libvcflib-tools; however:
Package libvcflib-tools is not installed.
pbuilder-satisfydepends-dummy depends on debhelper; however:
Package debhelper is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bc{a} bsdextrautils{a} ca-certificates{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas3{a} libbrotli1{a} libbsd0{a} libbwa-dev{a} libcairo2{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdatrie1{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfastahack-dev{a} libfastahack0{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libharfbuzz0b{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libice6{a} libicu72{a} libjbig0{a} libjpeg62-turbo{a} libjsoncpp-dev{a} libjsoncpp25{a} liblapack3{a} libldap-2.5-0{a} liblerc4{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libseqlib-dev{a} libseqlib2{a} libsm6{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtabixpp-dev{a} libtabixpp0{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtk8.6{a} libtool{a} libuchardet0{a} libvcflib-dev{a} libvcflib-tools{a} libvcflib1{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} libxt6{a} littler{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} openssl{a} parallel{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-cli{a} r-cran-colorspace{a} r-cran-fansi{a} r-cran-farver{a} r-cran-ggplot2{a} r-cran-glue{a} r-cran-gridbase{a} r-cran-gtable{a} r-cran-isoband{a} r-cran-labeling{a} r-cran-lattice{a} r-cran-lifecycle{a} r-cran-littler{a} r-cran-magrittr{a} r-cran-mass{a} r-cran-matrix{a} r-cran-mgcv{a} r-cran-munsell{a} r-cran-nlme{a} r-cran-pillar{a} r-cran-pkgconfig{a} r-cran-pkgkitten{a} r-cran-plyr{a} r-cran-r6{a} r-cran-rcolorbrewer{a} r-cran-rcpp{a} r-cran-rlang{a} r-cran-scales{a} r-cran-tibble{a} r-cran-utf8{a} r-cran-vctrs{a} r-cran-viridislite{a} r-cran-withr{a} readline-common{a} samtools{a} sensible-utils{a} sysstat{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:
bcron cron curl libarchive-cpio-perl libfile-mimeinfo-perl libglib2.0-data libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lynx psmisc publicsuffix r-base-dev r-cran-abind r-cran-bit64 r-cran-covr r-cran-crayon r-cran-data.table r-cran-dbi r-cran-domc r-cran-dplyr r-cran-formattable r-cran-generics r-cran-hexbin r-cran-hmisc r-cran-hms r-cran-interp r-cran-knitr r-cran-lubridate r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mockery r-cran-mockr r-cran-multcomp r-cran-quantreg r-cran-ragg r-cran-rmarkdown r-cran-rpart r-cran-rsqlite r-cran-sf r-cran-stringi r-cran-svglite r-cran-testthat r-cran-vdiffr r-cran-waldo r-cran-xml2 r-doc-html r-recommended shared-mime-info systemd systemd-cron wget x11-utils x11-xserver-utils xdg-user-dirs
0 packages upgraded, 187 newly installed, 0 to remove and 0 not upgraded.
Need to get 115 MB of archives. After unpacking 287 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.9-1 [1416 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 bc amd64 1.07.1-3+b1 [110 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-4 [149 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libbamtools-dev amd64 2.5.2+dfsg-4 [214 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libbwa-dev amd64 0.7.17-7+b2 [156 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10 [381 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10 [386 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 libcurl4-gnutls-dev amd64 7.88.1-10 [481 kB]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 libdeflate-dev amd64 1.14-1 [53.3 kB]
Get: 85 http://deb.debian.org/debian bookworm/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B]
Get: 86 http://deb.debian.org/debian bookworm/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b1 [4860 B]
Get: 87 http://deb.debian.org/debian bookworm/main amd64 libfastahack0 amd64 1.0.0+dfsg-10 [25.7 kB]
Get: 88 http://deb.debian.org/debian bookworm/main amd64 libfastahack-dev amd64 1.0.0+dfsg-10 [27.0 kB]
Get: 89 http://deb.debian.org/debian bookworm/main amd64 libfml0 amd64 0.1+git20190320.b499514-1+b1 [71.4 kB]
Get: 90 http://deb.debian.org/debian bookworm/main amd64 libfml-dev amd64 0.1+git20190320.b499514-1+b1 [82.9 kB]
Get: 91 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get: 92 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 93 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB]
Get: 94 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get: 95 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB]
Get: 96 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 97 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get: 98 http://deb.debian.org/debian bookworm/main amd64 liblzma-dev amd64 5.4.1-0.2 [260 kB]
Get: 99 http://deb.debian.org/debian bookworm/main amd64 libhts-dev amd64 1.16+ds-3 [1601 kB]
Get: 100 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 101 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get: 102 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get: 103 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get: 104 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB]
Get: 105 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp-dev amd64 1.9.5-4 [26.4 kB]
Get: 106 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get: 107 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get: 108 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB]
Get: 109 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB]
Get: 110 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB]
Get: 111 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB]
Get: 112 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB]
Get: 113 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB]
Get: 114 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB]
Get: 115 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B]
Get: 116 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB]
Get: 117 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get: 118 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB]
Get: 119 http://deb.debian.org/debian bookworm/main amd64 libssw0 amd64 1.1-13 [19.7 kB]
Get: 120 http://deb.debian.org/debian bookworm/main amd64 libseqlib2 amd64 1.2.0+dfsg-9 [162 kB]
Get: 121 http://deb.debian.org/debian bookworm/main amd64 libssw-dev amd64 1.1-13 [22.4 kB]
Get: 122 http://deb.debian.org/debian bookworm/main amd64 libseqlib-dev amd64 1.2.0+dfsg-9 [209 kB]
Get: 123 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get: 124 http://deb.debian.org/debian bookworm/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB]
Get: 125 http://deb.debian.org/debian bookworm/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB]
Get: 126 http://deb.debian.org/debian bookworm/main amd64 libtabixpp0 amd64 1.1.2-1 [9532 B]
Get: 127 http://deb.debian.org/debian bookworm/main amd64 libtabixpp-dev amd64 1.1.2-1 [8936 B]
Get: 128 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB]
Get: 129 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2 [285 kB]
Get: 130 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6 [316 kB]
Get: 131 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB]
Get: 132 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB]
Get: 133 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB]
Get: 134 http://deb.debian.org/debian bookworm/main amd64 libvcflib1 amd64 1.0.3+dfsg-2 [153 kB]
Get: 135 http://deb.debian.org/debian bookworm/main amd64 libvcflib-dev amd64 1.0.3+dfsg-2 [85.2 kB]
Get: 136 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB]
Get: 137 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 138 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 139 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB]
Get: 140 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB]
Get: 141 http://deb.debian.org/debian bookworm/main amd64 r-cran-littler amd64 0.3.17-1 [96.3 kB]
Get: 142 http://deb.debian.org/debian bookworm/main amd64 littler all 0.3.17-1 [14.4 kB]
Get: 143 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgkitten all 0.2.2-2 [27.0 kB]
Get: 144 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcpp amd64 1.0.10-1 [2059 kB]
Get: 145 http://deb.debian.org/debian bookworm/main amd64 r-cran-plyr amd64 1.8.8-1 [832 kB]
Get: 146 http://deb.debian.org/debian bookworm/main amd64 r-cran-cli amd64 3.6.0-1 [1287 kB]
Get: 147 http://deb.debian.org/debian bookworm/main amd64 r-cran-glue amd64 1.6.2-1 [152 kB]
Get: 148 http://deb.debian.org/debian bookworm/main amd64 r-cran-gtable all 0.3.1+dfsg-1 [165 kB]
Get: 149 http://deb.debian.org/debian bookworm/main amd64 r-cran-isoband amd64 0.2.7-1 [1614 kB]
Get: 150 http://deb.debian.org/debian bookworm/main amd64 r-cran-rlang amd64 1.0.6-1 [1618 kB]
Get: 151 http://deb.debian.org/debian bookworm/main amd64 r-cran-lifecycle all 1.0.3+dfsg-1 [109 kB]
Get: 152 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB]
Get: 153 http://deb.debian.org/debian bookworm/main amd64 r-cran-lattice amd64 0.20-45-3 [1177 kB]
Get: 154 http://deb.debian.org/debian bookworm/main amd64 r-cran-nlme amd64 3.1.162-1 [2260 kB]
Get: 155 http://deb.debian.org/debian bookworm/main amd64 r-cran-matrix amd64 1.5-3-1 [3822 kB]
Get: 156 http://deb.debian.org/debian bookworm/main amd64 r-cran-mgcv amd64 1.8-41-1 [3171 kB]
Get: 157 http://deb.debian.org/debian bookworm/main amd64 r-cran-farver amd64 2.1.1-1 [1404 kB]
Get: 158 http://deb.debian.org/debian bookworm/main amd64 r-cran-labeling all 0.4.2-1 [62.7 kB]
Get: 159 http://deb.debian.org/debian bookworm/main amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1692 kB]
Get: 160 http://deb.debian.org/debian bookworm/main amd64 r-cran-munsell all 0.5.0-2 [236 kB]
Get: 161 http://deb.debian.org/debian bookworm/main amd64 r-cran-r6 all 2.5.1-1 [105 kB]
Get: 162 http://deb.debian.org/debian bookworm/main amd64 r-cran-rcolorbrewer all 1.1-3-1 [54.7 kB]
Get: 163 http://deb.debian.org/debian bookworm/main amd64 r-cran-viridislite all 0.4.1-1 [1299 kB]
Get: 164 http://deb.debian.org/debian bookworm/main amd64 r-cran-scales all 1.2.1-1 [614 kB]
Get: 165 http://deb.debian.org/debian bookworm/main amd64 r-cran-fansi amd64 1.0.4-1 [619 kB]
Get: 166 http://deb.debian.org/debian bookworm/main amd64 r-cran-magrittr amd64 2.0.3-1 [201 kB]
Get: 167 http://deb.debian.org/debian bookworm/main amd64 r-cran-utf8 amd64 1.2.3-1 [133 kB]
Get: 168 http://deb.debian.org/debian bookworm/main amd64 r-cran-vctrs amd64 0.5.2-1 [1371 kB]
Get: 169 http://deb.debian.org/debian bookworm/main amd64 r-cran-pillar all 1.8.1+dfsg-1 [463 kB]
Get: 170 http://deb.debian.org/debian bookworm/main amd64 r-cran-pkgconfig all 2.0.3-2 [19.6 kB]
Get: 171 http://deb.debian.org/debian bookworm/main amd64 r-cran-tibble amd64 3.1.8+dfsg-1 [513 kB]
Get: 172 http://deb.debian.org/debian bookworm/main amd64 r-cran-withr all 2.5.0-1 [236 kB]
Get: 173 http://deb.debian.org/debian bookworm/main amd64 r-cran-ggplot2 all 3.4.1+dfsg-1 [3333 kB]
Get: 174 http://deb.debian.org/debian bookworm/main amd64 r-cran-gridbase all 0.4-7-5 [163 kB]
Get: 175 http://deb.debian.org/debian bookworm/main amd64 libvcflib-tools amd64 1.0.3+dfsg-2 [748 kB]
Get: 176 http://deb.debian.org/debian bookworm/main amd64 ninja-build amd64 1.11.1-1 [136 kB]
Get: 177 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 178 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 179 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB]
Get: 180 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB]
Get: 181 http://deb.debian.org/debian bookworm/main amd64 meson all 1.0.1-5 [548 kB]
Get: 182 http://deb.debian.org/debian bookworm/main amd64 sysstat amd64 12.6.1-1 [596 kB]
Get: 183 http://deb.debian.org/debian bookworm/main amd64 parallel all 20221122+ds-2 [1873 kB]
Get: 184 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB]
Get: 185 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB]
Get: 186 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB]
Get: 187 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB]
Fetched 115 MB in 2s (61.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
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(Reading database ... 19591 files and directories currently installed.)
Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ...
Selecting previously unselected package libexpat1:amd64.
Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ...
Unpacking libexpat1:amd64 (2.5.0-1) ...
Selecting previously unselected package python3.11-minimal.
Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ...
Unpacking python3.11-minimal (3.11.2-6) ...
Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
Setting up python3.11-minimal (3.11.2-6) ...
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Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up samtools (1.16.1-1) ...
Setting up r-base-core (4.2.2.20221110-2) ...
Creating config file /etc/R/Renviron with new version
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Setting up r-cran-magrittr (2.0.3-1) ...
Setting up libseqlib2:amd64 (1.2.0+dfsg-9) ...
Setting up r-cran-littler (0.3.17-1) ...
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done.
Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/freebayes-1.3.6/ && 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 > ../freebayes_1.3.6-2_source.changes
dpkg-buildpackage: info: source package freebayes
dpkg-buildpackage: info: source version 1.3.6-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --buildsystem=meson --builddir=build
dh_auto_clean -O--buildsystem=meson -O--builddir=build
dh_autoreconf_clean -O--buildsystem=meson -O--builddir=build
dh_clean -O--buildsystem=meson -O--builddir=build
debian/rules binary
dh binary --buildsystem=meson --builddir=build
dh_update_autotools_config -O--buildsystem=meson -O--builddir=build
dh_autoreconf -O--buildsystem=meson -O--builddir=build
dh_auto_configure -O--buildsystem=meson -O--builddir=build
cd build && LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/x86_64-linux-gnu
The Meson build system
Version: 1.0.1
Source dir: /build/freebayes-1.3.6
Build dir: /build/freebayes-1.3.6/build
Build type: native build
Project name: freebayes
Project version: 1.3.6
C compiler for the host machine: cc (gcc 12.2.0 "cc (Debian 12.2.0-14) 12.2.0")
C linker for the host machine: cc ld.bfd 2.40
C++ compiler for the host machine: c++ (gcc 12.2.0 "c++ (Debian 12.2.0-14) 12.2.0")
C++ linker for the host machine: c++ ld.bfd 2.40
Host machine cpu family: x86_64
Host machine cpu: x86_64
Found pkg-config: /usr/bin/pkg-config (1.8.1)
Run-time dependency zlib found: YES 1.2.13
Run-time dependency liblzma found: YES 5.4.1
Run-time dependency threads found: YES
Library tabixpp found: YES
Run-time dependency htslib found: YES 1.16
Library tabixpp found: YES
Run-time dependency libvcflib found: YES 1.0
Run-time dependency libseqlib found: YES 1.0
Compiler for C++ supports arguments -fpermissive: YES
Compiler for C++ supports arguments -Wno-reorder: YES
Compiler for C++ supports arguments -Wno-sign-compare: YES
Compiler for C++ supports arguments -Wno-unused-variable: YES
Compiler for C++ supports arguments -Wno-unused-but-set-variable: YES
Program prove found: YES (/usr/bin/prove)
Build targets in project: 3
freebayes 1.3.6
User defined options
buildtype : plain
libdir : lib/x86_64-linux-gnu
localstatedir: /var
prefix : /usr
sysconfdir : /etc
wrap_mode : nodownload
Found ninja-1.11.1 at /usr/bin/ninja
dh_auto_build -O--buildsystem=meson -O--builddir=build
cd build && LC_ALL=C.UTF-8 ninja -j16 -v
[1/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_IndelAllele.cpp.o -MF libfreebayes_common.a.p/src_IndelAllele.cpp.o.d -o libfreebayes_common.a.p/src_IndelAllele.cpp.o -c ../src/IndelAllele.cpp
[2/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Contamination.cpp.o -MF libfreebayes_common.a.p/src_Contamination.cpp.o.d -o libfreebayes_common.a.p/src_Contamination.cpp.o -c ../src/Contamination.cpp
[3/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Bias.cpp.o -MF libfreebayes_common.a.p/src_Bias.cpp.o.d -o libfreebayes_common.a.p/src_Bias.cpp.o -c ../src/Bias.cpp
[4/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Dirichlet.cpp.o -MF libfreebayes_common.a.p/src_Dirichlet.cpp.o.d -o libfreebayes_common.a.p/src_Dirichlet.cpp.o -c ../src/Dirichlet.cpp
[5/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Ewens.cpp.o -MF libfreebayes_common.a.p/src_Ewens.cpp.o.d -o libfreebayes_common.a.p/src_Ewens.cpp.o -c ../src/Ewens.cpp
[6/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_CNV.cpp.o -MF libfreebayes_common.a.p/src_CNV.cpp.o.d -o libfreebayes_common.a.p/src_CNV.cpp.o -c ../src/CNV.cpp
[7/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Multinomial.cpp.o -MF libfreebayes_common.a.p/src_Multinomial.cpp.o.d -o libfreebayes_common.a.p/src_Multinomial.cpp.o -c ../src/Multinomial.cpp
[8/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -MF libfreebayes_common.a.p/src_SegfaultHandler.cpp.o.d -o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o -c ../src/SegfaultHandler.cpp
[9/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_LeftAlign.cpp.o -MF libfreebayes_common.a.p/src_LeftAlign.cpp.o.d -o libfreebayes_common.a.p/src_LeftAlign.cpp.o -c ../src/LeftAlign.cpp
[10/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_BedReader.cpp.o -MF libfreebayes_common.a.p/src_BedReader.cpp.o.d -o libfreebayes_common.a.p/src_BedReader.cpp.o -c ../src/BedReader.cpp
[11/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_FBFasta.cpp.o -MF libfreebayes_common.a.p/src_FBFasta.cpp.o.d -o libfreebayes_common.a.p/src_FBFasta.cpp.o -c ../src/FBFasta.cpp
../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSequence(std::string)’:
../src/FBFasta.cpp:273:20: warning: pointer ‘seq’ used after ‘void free(void*)’ [-Wuse-after-free]
273 | s.resize((pend - pbegin)/sizeof(char));
| ~~~~~^~~~~~~~
../src/FBFasta.cpp:272:9: note: call to ‘void free(void*)’ here
272 | free(seq);
| ~~~~^~~~~
../src/FBFasta.cpp: In member function ‘std::string FB::FastaReference::getRawSubSequence(std::string, int, int)’:
../src/FBFasta.cpp:316:20: warning: pointer ‘seq’ used after ‘void free(void*)’ [-Wuse-after-free]
316 | s.resize((pend - pbegin)/sizeof(char));
| ~~~~~^~~~~~~~
../src/FBFasta.cpp:315:9: note: call to ‘void free(void*)’ here
315 | free(seq);
| ~~~~^~~~~
[12/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_NonCall.cpp.o -MF libfreebayes_common.a.p/src_NonCall.cpp.o.d -o libfreebayes_common.a.p/src_NonCall.cpp.o -c ../src/NonCall.cpp
[13/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Result.cpp.o -MF libfreebayes_common.a.p/src_Result.cpp.o.d -o libfreebayes_common.a.p/src_Result.cpp.o -c ../src/Result.cpp
[14/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Marginals.cpp.o -MF libfreebayes_common.a.p/src_Marginals.cpp.o.d -o libfreebayes_common.a.p/src_Marginals.cpp.o -c ../src/Marginals.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/ResultData.h:10,
from ../src/Marginals.h:7,
from ../src/Marginals.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/Marginals.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[15/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Sample.cpp.o -MF libfreebayes_common.a.p/src_Sample.cpp.o.d -o libfreebayes_common.a.p/src_Sample.cpp.o -c ../src/Sample.cpp
[16/27] c++ -Ibamleftalign.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ bamleftalign.p/src_bamleftalign.cpp.o -MF bamleftalign.p/src_bamleftalign.cpp.o.d -o bamleftalign.p/src_bamleftalign.cpp.o -c ../src/bamleftalign.cpp
[17/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Parameters.cpp.o -MF libfreebayes_common.a.p/src_Parameters.cpp.o.d -o libfreebayes_common.a.p/src_Parameters.cpp.o -c ../src/Parameters.cpp
[18/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_DataLikelihood.cpp.o -MF libfreebayes_common.a.p/src_DataLikelihood.cpp.o.d -o libfreebayes_common.a.p/src_DataLikelihood.cpp.o -c ../src/DataLikelihood.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/DataLikelihood.h:20,
from ../src/DataLikelihood.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/DataLikelihood.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[19/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Utility.cpp.o -MF libfreebayes_common.a.p/src_Utility.cpp.o.d -o libfreebayes_common.a.p/src_Utility.cpp.o -c ../src/Utility.cpp
In file included from ../ttmath/ttmathint.h:48,
from ../ttmath/ttmathbig.h:46,
from ../ttmath/ttmath.h:58,
from ../src/Utility.h:18,
from ../src/Utility.cpp:3:
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with long unsigned int value_size = 1]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<4, 1>::mantissa.ttmath::UInt<1>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
In member function ‘ttmath::uint ttmath::Int<value_size>::FromUIntOrInt(const ttmath::UInt<result_size>&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’,
inlined from ‘ttmath::uint ttmath::Int<value_size>::FromInt(const ttmath::Int<argument_size>&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23,
inlined from ‘ttmath::Int<value_size>& ttmath::Int<value_size>::operator=(const ttmath::Int<value_size>&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::<unnamed>.ttmath::UInt<4>::table[0]))’ may be used uninitialized [-Wmaybe-uninitialized]
652 | UInt<value_size>::table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
In member function ‘ttmath::uint ttmath::Int<value_size>::FromUIntOrInt(const ttmath::UInt<result_size>&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’,
inlined from ‘ttmath::uint ttmath::Int<value_size>::FromInt(const ttmath::Int<argument_size>&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23,
inlined from ‘ttmath::Int<value_size>& ttmath::Int<value_size>::operator=(const ttmath::Int<value_size>&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::<unnamed>.ttmath::UInt<4>::table[2]))’ may be used uninitialized [-Wmaybe-uninitialized]
652 | UInt<value_size>::table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
In member function ‘ttmath::UInt<value_size>& ttmath::UInt<value_size>::operator=(const ttmath::UInt<value_size>&) [with long unsigned int value_size = 1]’,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3648:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathuint.h:2740:43: warning: ‘result.ttmath::Big<4, 1>::mantissa.ttmath::UInt<1>::table[0]’ may be used uninitialized [-Wmaybe-uninitialized]
2740 | table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
In member function ‘ttmath::uint ttmath::Int<value_size>::FromUIntOrInt(const ttmath::UInt<result_size>&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’,
inlined from ‘ttmath::uint ttmath::Int<value_size>::FromInt(const ttmath::Int<argument_size>&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23,
inlined from ‘ttmath::Int<value_size>& ttmath::Int<value_size>::operator=(const ttmath::Int<value_size>&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::<unnamed>.ttmath::UInt<4>::table[0]))’ may be used uninitialized [-Wmaybe-uninitialized]
652 | UInt<value_size>::table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
In member function ‘ttmath::uint ttmath::Int<value_size>::FromUIntOrInt(const ttmath::UInt<result_size>&, bool) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’,
inlined from ‘ttmath::uint ttmath::Int<value_size>::FromInt(const ttmath::Int<argument_size>&) [with long unsigned int argument_size = 4; long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:698:23,
inlined from ‘ttmath::Int<value_size>& ttmath::Int<value_size>::operator=(const ttmath::Int<value_size>&) [with long unsigned int value_size = 4]’ at ../ttmath/ttmathint.h:772:10,
inlined from ‘ttmath::Big<exp, man>& ttmath::Big<exp, man>::operator=(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3647:12,
inlined from ‘ttmath::Big<exp, man>::Big(const ttmath::Big<exp, man>&) [with long unsigned int exp = 4; long unsigned int man = 1]’ at ../ttmath/ttmathbig.h:3660:12,
inlined from ‘ValueType ttmath::Log(const ValueType&, const ValueType&, ErrorCode*) [with ValueType = Big<4, 1>]’ at ../ttmath/ttmath.h:311:9,
inlined from ‘long double big2phred(const BigFloat&)’ at ../src/Utility.cpp:58:44:
../ttmath/ttmathint.h:652:61: warning: ‘*(const __vector(2) long unsigned int*)((char*)&result + offsetof(ttmath::Big<4, 1>,ttmath::Big<4, 1>::exponent.ttmath::Int<4>::<unnamed>.ttmath::UInt<4>::table[2]))’ may be used uninitialized [-Wmaybe-uninitialized]
652 | UInt<value_size>::table[i] = p.table[i];
| ~~~~~~~^
../ttmath/ttmath.h: In function ‘long double big2phred(const BigFloat&)’:
../ttmath/ttmath.h:288:27: note: ‘result’ declared here
288 | ValueType result;
| ^~~~~~
[20/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Allele.cpp.o -MF libfreebayes_common.a.p/src_Allele.cpp.o.d -o libfreebayes_common.a.p/src_Allele.cpp.o -c ../src/Allele.cpp
../src/Allele.cpp: In member function ‘const short int Allele::currentQuality() const’:
../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_GENOTYPE’ not handled in switch [-Wswitch]
160 | switch (this->type) {
| ^
../src/Allele.cpp:160:12: warning: enumeration value ‘ALLELE_NULL’ not handled in switch [-Wswitch]
[21/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_Genotype.cpp.o -MF libfreebayes_common.a.p/src_Genotype.cpp.o.d -o libfreebayes_common.a.p/src_Genotype.cpp.o -c ../src/Genotype.cpp
[22/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_ResultData.cpp.o -MF libfreebayes_common.a.p/src_ResultData.cpp.o.d -o libfreebayes_common.a.p/src_ResultData.cpp.o -c ../src/ResultData.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/ResultData.h:10,
from ../src/ResultData.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/ResultData.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[23/27] c++ -Ifreebayes.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ freebayes.p/src_freebayes.cpp.o -MF freebayes.p/src_freebayes.cpp.o.d -o freebayes.p/src_freebayes.cpp.o -c ../src/freebayes.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/freebayes.cpp:29:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/freebayes.cpp:9:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[24/27] c++ -Ilibfreebayes_common.a.p -I. -I.. -I../src -I../ttmath -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -pthread -fpermissive -Wno-reorder -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable -MD -MQ libfreebayes_common.a.p/src_AlleleParser.cpp.o -MF libfreebayes_common.a.p/src_AlleleParser.cpp.o.d -o libfreebayes_common.a.p/src_AlleleParser.cpp.o -c ../src/AlleleParser.cpp
In file included from ../src/AlleleParser.h:32,
from ../src/AlleleParser.cpp:1:
/usr/include/vcflib/Variant.h:651:28: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/AlleleParser.h:4:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/vcflib/Variant.h:652:42: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[25/27] rm -f libfreebayes_common.a && gcc-ar csrDT libfreebayes_common.a libfreebayes_common.a.p/src_Allele.cpp.o libfreebayes_common.a.p/src_AlleleParser.cpp.o libfreebayes_common.a.p/src_BedReader.cpp.o libfreebayes_common.a.p/src_Bias.cpp.o libfreebayes_common.a.p/src_CNV.cpp.o libfreebayes_common.a.p/src_Contamination.cpp.o libfreebayes_common.a.p/src_DataLikelihood.cpp.o libfreebayes_common.a.p/src_Dirichlet.cpp.o libfreebayes_common.a.p/src_Ewens.cpp.o libfreebayes_common.a.p/src_FBFasta.cpp.o libfreebayes_common.a.p/src_Genotype.cpp.o libfreebayes_common.a.p/src_IndelAllele.cpp.o libfreebayes_common.a.p/src_LeftAlign.cpp.o libfreebayes_common.a.p/src_Marginals.cpp.o libfreebayes_common.a.p/src_Multinomial.cpp.o libfreebayes_common.a.p/src_NonCall.cpp.o libfreebayes_common.a.p/src_Parameters.cpp.o libfreebayes_common.a.p/src_Result.cpp.o libfreebayes_common.a.p/src_ResultData.cpp.o libfreebayes_common.a.p/src_Sample.cpp.o libfreebayes_common.a.p/src_SegfaultHandler.cpp.o libfreebayes_common.a.p/src_Utility.cpp.o
[26/27] c++ -o bamleftalign bamleftalign.p/src_bamleftalign.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libvcflib.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libdisorder.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libtabixpp.so -Wl,--end-group
[27/27] c++ -o freebayes freebayes.p/src_freebayes.cpp.o -Wl,--as-needed -Wl,--no-undefined -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/freebayes-1.3.6=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--start-group libfreebayes_common.a /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/liblzma.so -pthread /usr/lib/x86_64-linux-gnu/libhts.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libtabixpp.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libvcflib.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libsmithwaterman.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libdisorder.so /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/libfastahack.so /usr/lib/x86_64-linux-gnu/libseqlib.so /usr/lib/libbwa.a -Wl,--end-group
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/freebayes-1.3.6'
mkdir -p test/bash-tap/
ln -s -t test/bash-tap /build/freebayes-1.3.6/debian/bash-tap/*
mkdir -p test/test-simple-bash
ln -s -t test/test-simple-bash /build/freebayes-1.3.6/debian/test-simple-bash/*
dh_auto_test -- -v --timeout-multiplier 100
cd build && LC_ALL=C.UTF-8 MESON_TESTTHREADS=16 meson test -v --timeout-multiplier 100
ninja: no work to do.
ninja: Entering directory `/build/freebayes-1.3.6/build'
ninja: no work to do.
1/5 T00 RUNNING
>>> MALLOC_PERTURB_=46 /usr/bin/prove -e bash -v t/00_region_and_target_handling.t
2/5 T01 RUNNING
>>> MALLOC_PERTURB_=117 /usr/bin/prove -e bash -v t/01_call_variants.t
3/5 T01b RUNNING
>>> MALLOC_PERTURB_=59 /usr/bin/prove -e bash -v t/01b_call_variants.t
4/5 T02 RUNNING
>>> MALLOC_PERTURB_=251 /usr/bin/prove -e bash -v t/02_multi_bam.t
5/5 T03 RUNNING
>>> MALLOC_PERTURB_=194 /usr/bin/prove -e bash -v t/03_reference_bases.t
5/5 T03 OK 0.21s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/03_reference_bases.t ..
1..3
ok 1 - freebayes rejects invalid reference
ok 2 - freebayes does not put uppercase IUPAC bases in VCFs
ok 3 - freebayes does not put lowercase IUPAC bases in VCFs
ok
All tests successful.
Files=1, Tests=3, 0 wallclock secs ( 0.03 usr 0.01 sys + 0.04 cusr 0.05 csys = 0.13 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
1/5 T00 OK 0.35s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/00_region_and_target_handling.t ..
1..12
ok 1 - ref:4-5 ref:6-7 are empty
ok 2 - ref:4 ref:6 are empty
ok 3 - ref:5-6 ref:7-8
ok 4 - ref:5 ref:7
ok 5 - ref:5-
ok 6 - full output
ok 7 - --targets t/../00_region_and_target_handling.t.bed
ok 8 - --region ref
ok 9 - ref:1,0-
ok 10 - ref:1,0-1,1
ok 11 - ref:0-1
ok 12 - region outside of bounds error
ok
All tests successful.
Files=1, Tests=12, 0 wallclock secs ( 0.04 usr 0.00 sys + 0.15 cusr 0.12 csys = 0.31 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
4/5 T02 OK 0.39s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/02_multi_bam.t ..
1..7
ok 1 - freebayes calls from two identical BAMs
ok 2 - freebayes calls from two BAMs with different samples for different read groups
ok 3 - freebayes calls from two BAMs with different technologies for different read groups
ok 4 - freebayes rejects two BAMs with different samples for same read groups
ok 5 - freebayes rejects two BAMs with different technologies for same read groups
ok 6 - freebayes calls multiple alts from two different BAMs
ok 7 - freebayes rejects two BAMs with the same name
ok
All tests successful.
Files=1, Tests=7, 0 wallclock secs ( 0.03 usr 0.00 sys + 0.12 cusr 0.17 csys = 0.32 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
3/5 T01b OK 5.59s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
t/01b_call_variants.t ..
1..10
ok 1 - running in parallel makes no difference
ok 2 - freebayes handles spaces in file names
ok 3 - freebayes handles region and variant input even with : in contig names
ok 4 - freebayes can handle spliced reads
ok 5 - freebayes produces the expected number of lines of gVCF output
ok 6 - freebayes produces the expected number of lines of gVCF output
ok 7 - freebayes produces the expected number of lines of gVCF output
ok 8 - the CNV map may be used to specify per-sample copy numbers
ok 9 - freebayes makes the expected number of calls when capping coverage
ok 10 - freebayes correctly uses CNV map with multiple entries
ok
All tests successful.
Files=1, Tests=10, 5 wallclock secs ( 0.02 usr 0.02 sys + 5.73 cusr 0.68 csys = 6.45 CPU)
Result: PASS
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
2/5 T01 OK 14.50s
――――――――――――――――――――――――――――――――――――― ✀ ―――――――――――――――――――――――――――――――――――――
stdout:
t/01_call_variants.t ..
1..16
ok 1 - variant calling recovers most of the GiAB variants in a test region
ok 2 - freebayes produces the same number of calls if targeted per site or called without targets
ok 3 - a targets bed file can be used with the same effect as running by region
ok 4 - reading from stdin or not makes no difference
ok 5 - freebayes processes all alignments in BAM input
ok 6 - freebayes processes all alignments in CRAM input
ok 7 - freebayes correctly handles variant input
ok 8 - freebayes puts required variants in output
ok 9 - freebayes limits calls to input variants correctly
ok 10 - freebayes reports all input variants even when there is no input data
ok 11 - freebayes handles region and variant input
ok 12 - freebayes limits to variant input correctly when region is given
ok 13 - freebayes handles variant input and reading from stdin
ok 14 - freebayes limits to variant input when reading from stdin
ok 15 - freebayes handles region, stdin, and variant input
ok 16 - !
ok
All tests successful.
Files=1, Tests=16, 14 wallclock secs ( 0.03 usr 0.00 sys + 10.16 cusr 7.85 csys = 18.04 CPU)
Result: PASS
stderr:
[E::idx_find_and_load] Could not retrieve index file for '-'
Random access with SetRegion not available for STDIN reading (no index file)
ERROR(freebayes): Could not SetRegion to q:1..10000
t/01_call_variants.t: line 107: 535760 Aborted freebayes -f tiny/q.fa.gz -@ tiny/q_spiked.vcf.gz -r q:1-10000 -l - < tiny/NA12878.chr22.tiny.bam > /dev/null 2> /dev/null
――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――
Ok: 5
Expected Fail: 0
Fail: 0
Unexpected Pass: 0
Skipped: 0
Timeout: 0
Full log written to /build/freebayes-1.3.6/build/meson-logs/testlog.txt
rm test/bash-tap/*
rm test/test-simple-bash/*
make[1]: Leaving directory '/build/freebayes-1.3.6'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=meson -O--builddir=build
dh_prep -O--buildsystem=meson -O--builddir=build
dh_auto_install --destdir=debian/freebayes/ -O--buildsystem=meson -O--builddir=build
cd build && DESTDIR=/build/freebayes-1.3.6/debian/freebayes LC_ALL=C.UTF-8 ninja install
[0/1] Installing files.
Installing freebayes to /build/freebayes-1.3.6/debian/freebayes/usr/bin
Installing bamleftalign to /build/freebayes-1.3.6/debian/freebayes/usr/bin
dh_install -O--buildsystem=meson -O--builddir=build
dh_installdocs -O--buildsystem=meson -O--builddir=build
dh_installchangelogs -O--buildsystem=meson -O--builddir=build
dh_installexamples -O--buildsystem=meson -O--builddir=build
dh_installsystemduser -O--buildsystem=meson -O--builddir=build
dh_perl -O--buildsystem=meson -O--builddir=build
dh_link -O--buildsystem=meson -O--builddir=build
dh_strip_nondeterminism -O--buildsystem=meson -O--builddir=build
dh_compress -O--buildsystem=meson -O--builddir=build
dh_fixperms -O--buildsystem=meson -O--builddir=build
dh_missing -O--buildsystem=meson -O--builddir=build
dh_dwz -a -O--buildsystem=meson -O--builddir=build
dh_strip -a -O--buildsystem=meson -O--builddir=build
dh_makeshlibs -a -O--buildsystem=meson -O--builddir=build
dh_shlibdeps -a -O--buildsystem=meson -O--builddir=build
dh_installdeb -O--buildsystem=meson -O--builddir=build
dh_gencontrol -O--buildsystem=meson -O--builddir=build
dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package freebayes: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -O--buildsystem=meson -O--builddir=build
dh_builddeb -O--buildsystem=meson -O--builddir=build
dpkg-deb: building package 'freebayes' in '../freebayes_1.3.6-2_amd64.deb'.
dpkg-deb: building package 'freebayes-dbgsym' in '../freebayes-dbgsym_1.3.6-2_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../freebayes_1.3.6-2_amd64.buildinfo
dpkg-genchanges --build=binary -O../freebayes_1.3.6-2_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/523057 and its subdirectories
I: Current time: Thu Jul 11 05:13:49 -12 2024
I: pbuilder-time-stamp: 1720718029
Fri Jun 9 10:50:24 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Fri Jun 9 10:50:24 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Fri Jun 9 10:53:13 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Fri Jun 9 10:53:14 UTC 2023 I: freebayes_1.3.6-2_amd64.changes:
Format: 1.8
Date: Tue, 01 Nov 2022 14:38:51 +0100
Source: freebayes
Binary: freebayes freebayes-dbgsym
Architecture: amd64
Version: 1.3.6-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
freebayes - Bayesian haplotype-based polymorphism discovery and genotyping
Changes:
freebayes (1.3.6-2) unstable; urgency=medium
.
* install scripts (+ python3 dependency accordingly)
* Standards-Version: 4.6.1 (routine-update)
Checksums-Sha1:
13d0f91999da4e7ab02034f5b2b2510d2c433265 6577892 freebayes-dbgsym_1.3.6-2_amd64.deb
d3ac3d07d4a78880c2170abc7605e9655e7e3e22 10003 freebayes_1.3.6-2_amd64.buildinfo
ef7232bde3a7c6edc1044a83d0ca1045460f41e7 1483220 freebayes_1.3.6-2_amd64.deb
Checksums-Sha256:
2e5f5ed238677c43df1121bcb5af97202118799643dd0f5eaac7633c97e2e059 6577892 freebayes-dbgsym_1.3.6-2_amd64.deb
8e7545e2981e968dccf50d6a2d1af82cff820cc64d8f89e6a7e09f64f0069315 10003 freebayes_1.3.6-2_amd64.buildinfo
7985ce6e7733d4dd680943924028523d9506fedd177eef0022cc49b46dbd1f7a 1483220 freebayes_1.3.6-2_amd64.deb
Files:
bb20b5c2ef2b1dd3a4d66f861217740f 6577892 debug optional freebayes-dbgsym_1.3.6-2_amd64.deb
a9f4789c77ae3fad9511783c3344adde 10003 science optional freebayes_1.3.6-2_amd64.buildinfo
c9b241960beeb16b09a8406241cd5716 1483220 science optional freebayes_1.3.6-2_amd64.deb
Fri Jun 9 10:53:15 UTC 2023 I: diffoscope 242 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.66tilOGj/freebayes_1.3.6-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.66tilOGj/freebayes_1.3.6-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.66tilOGj/freebayes_1.3.6-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.66tilOGj/b1/freebayes_1.3.6-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.66tilOGj/b2/freebayes_1.3.6-2_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.462s)
0.462s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.118s)
0.117s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.001s)
0.001s 1 call specialize
Fri Jun 9 10:53:16 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Fri Jun 9 10:53:16 UTC 2023 I: freebayes from bookworm built successfully and reproducibly on amd64.
Fri Jun 9 10:53:18 UTC 2023 I: Submitting .buildinfo files to external archives:
Fri Jun 9 10:53:18 UTC 2023 I: Submitting 12K b1/freebayes_1.3.6-2_amd64.buildinfo.asc
Fri Jun 9 10:53:19 UTC 2023 I: Submitting 12K b2/freebayes_1.3.6-2_amd64.buildinfo.asc
Fri Jun 9 10:53:19 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Jun 9 10:53:20 UTC 2023 I: Done submitting .buildinfo files.
Fri Jun 9 10:53:20 UTC 2023 I: Removing signed freebayes_1.3.6-2_amd64.buildinfo.asc files:
removed './b1/freebayes_1.3.6-2_amd64.buildinfo.asc'
removed './b2/freebayes_1.3.6-2_amd64.buildinfo.asc'