Sun Apr 16 22:52:57 UTC 2023 I: starting to build hilive/bookworm/i386 on jenkins on '2023-04-16 22:52'
Sun Apr 16 22:52:57 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_12/10174/console.log
Sun Apr 16 22:52:57 UTC 2023 I: Downloading source for bookworm/hilive=2.0a-3
--2023-04-16 22:52:57-- http://cdn-fastly.deb.debian.org/debian/pool/main/h/hilive/hilive_2.0a-3.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2118 (2.1K) [text/prs.lines.tag]
Saving to: ‘hilive_2.0a-3.dsc’
0K .. 100% 19.8M=0s
2023-04-16 22:52:57 (19.8 MB/s) - ‘hilive_2.0a-3.dsc’ saved [2118/2118]
Sun Apr 16 22:52:57 UTC 2023 I: hilive_2.0a-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: hilive
Binary: hilive
Architecture: any
Version: 2.0a-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://gitlab.com/rki_bioinformatics/HiLive2
Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/hilive
Vcs-Git: https://salsa.debian.org/med-team/hilive.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, markdown
Package-List:
hilive deb science optional arch=any
Checksums-Sha1:
5705773f60eef87916fe3612b26df04ae3959d32 161788 hilive_2.0a.orig.tar.gz
fbe1ef06642fafe9547758eff3f8dde6ad874e66 9000 hilive_2.0a-3.debian.tar.xz
Checksums-Sha256:
a60e7675988b35d9ebf9472ca7515b40f790654c04e67d35fabf069d91d73bf6 161788 hilive_2.0a.orig.tar.gz
8da7ff9f1fa24befc2a2f14c190da2c1d1f0e924908adcd42710f8a53d97a4db 9000 hilive_2.0a-3.debian.tar.xz
Files:
8d393041a814071b4ac6a3db1f1f10e6 161788 hilive_2.0a.orig.tar.gz
455831bc062fe258d0d11b61f583b0d9 9000 hilive_2.0a-3.debian.tar.xz
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Sun Apr 16 22:52:57 UTC 2023 I: Checking whether the package is not for us
Sun Apr 16 22:52:57 UTC 2023 I: Starting 1st build on remote node ionos16-i386.debian.net.
Sun Apr 16 22:52:57 UTC 2023 I: Preparing to do remote build '1' on ionos16-i386.debian.net.
Sun Apr 16 22:54:38 UTC 2023 I: Deleting $TMPDIR on ionos16-i386.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sat May 18 17:15:57 -12 2024
I: pbuilder-time-stamp: 1716095757
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: using eatmydata during job
I: Copying source file
I: copying [hilive_2.0a-3.dsc]
I: copying [./hilive_2.0a.orig.tar.gz]
I: copying [./hilive_2.0a-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Wed Jan 15 23:17:41 2020 -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 ./hilive_2.0a-3.dsc: no acceptable signature found
dpkg-source: info: extracting hilive in hilive-2.0a
dpkg-source: info: unpacking hilive_2.0a.orig.tar.gz
dpkg-source: info: unpacking hilive_2.0a-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying do_not_set_rpath.patch
dpkg-source: info: applying use_FindSeQan.patch
dpkg-source: info: applying use_dynamic_linking.patch
dpkg-source: info: applying remove_march_native.patch
I: using fakeroot in build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/5724/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='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='21c2ee49b365446ab7c3e94cd4de250d'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='5724'
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.JoHne2yg/pbuilderrc_arCY --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.JoHne2yg/b1 --logfile b1/build.log hilive_2.0a-3.dsc'
SUDO_GID='112'
SUDO_UID='107'
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 ionos16-i386 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Feb 12 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 38404 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 38404 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 17892 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 42920 Sep 20 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 20 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 20 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 5 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 20 2022 date
-rwxr-xr-x 1 root root 100364 Sep 20 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 20 2022 df
-rwxr-xr-x 1 root root 162152 Sep 20 2022 dir
-rwxr-xr-x 1 root root 87760 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 38760 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 218680 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 100952 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 20 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 22 2023 login
-rwxr-xr-x 1 root root 162152 Sep 20 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 22 2023 more
-rwsr-xr-x 1 root root 58912 Mar 22 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 157932 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 38792 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 20 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 20 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 22 2023 su
-rwxr-xr-x 1 root root 38792 Sep 20 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 6 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 20 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 20 2022 true
-rwxr-xr-x 1 root root 17892 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 22 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 71216 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/5724/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: i386
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 (= 12), cmake, libboost-system-dev, libboost-filesystem-dev, libboost-iostreams-dev, libboost-program-options-dev, libhts-dev, libseqan2-dev, zlib1g-dev, liblz4-dev, chrpath, markdown
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19604 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 (= 12); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on libboost-system-dev; however:
Package libboost-system-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-filesystem-dev; however:
Package libboost-filesystem-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-iostreams-dev; however:
Package libboost-iostreams-dev is not installed.
pbuilder-satisfydepends-dummy depends on libboost-program-options-dev; however:
Package libboost-program-options-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libseqan2-dev; however:
Package libseqan2-dev is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on liblz4-dev; however:
Package liblz4-dev is not installed.
pbuilder-satisfydepends-dummy depends on chrpath; however:
Package chrpath is not installed.
pbuilder-satisfydepends-dummy depends on markdown; however:
Package markdown 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} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu-dev{a} libicu72{a} libjsoncpp25{a} libldap-2.5-0{a} liblz4-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libseqan2-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{a} markdown{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget
0 packages upgraded, 77 newly installed, 0 to remove and 0 not upgraded.
Need to get 62.8 MB of archives. After unpacking 362 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 chrpath i386 0.16-2+b1 [17.5 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.1+b3 [720 kB]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-8 [419 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 39 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 44 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 icu-devtools i386 72.1-3 [214 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-20 [9510 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74.0 i386 1.74.0+ds1-20 [264 kB]
Get: 53 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74.0 i386 1.74.0+ds1-20 [218 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74-dev i386 1.74.0+ds1-20 [219 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74-dev i386 1.74.0+ds1-20 [286 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem-dev i386 1.74.0.3 [4368 B]
Get: 57 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-20 [509 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libicu-dev i386 72.1-3 [10.6 MB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74-dev i386 1.74.0+ds1-20 [585 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams1.74-dev i386 1.74.0+ds1-20 [250 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B]
Get: 62 http://deb.debian.org/debian bookworm/main i386 libboost-program-options1.74.0 i386 1.74.0+ds1-20 [338 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libboost-program-options1.74-dev i386 1.74.0+ds1-20 [368 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libboost-program-options-dev i386 1.74.0.3 [4344 B]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libboost-system-dev i386 1.74.0.3 [4472 B]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-8 [412 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-8 [527 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB]
Get: 70 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 71 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB]
Get: 72 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB]
Get: 73 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 74 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB]
Get: 75 http://deb.debian.org/debian bookworm/main i386 liblz4-dev i386 1.9.4-1 [86.9 kB]
Get: 76 http://deb.debian.org/debian bookworm/main i386 libseqan2-dev all 2.4.0+dfsg-15 [1215 kB]
Get: 77 http://deb.debian.org/debian bookworm/main i386 markdown all 1.0.1-12 [17.7 kB]
Fetched 62.8 MB in 2s (31.0 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libexpat1:i386 (2.5.0-1) ...
Setting up libpipeline1:i386 (1.5.7-1) ...
Setting up libboost-system1.74.0:i386 (1.74.0+ds1-20) ...
Setting up libpsl5:i386 (0.21.2-1) ...
Setting up libboost1.74-dev:i386 (1.74.0+ds1-20) ...
Setting up libicu72:i386 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libboost-program-options1.74.0:i386 (1.74.0+ds1-20) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libbrotli1:i386 (1.0.9-2+b6) ...
Setting up libnghttp2-14:i386 (1.52.0-1) ...
Setting up libmagic1:i386 (1:5.44-3) ...
Setting up libdeflate0:i386 (1.14-1) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up libboost-filesystem1.74.0:i386 (1.74.0+ds1-20) ...
Setting up file (1:5.44-3) ...
Setting up libboost-program-options1.74-dev:i386 (1.74.0+ds1-20) ...
Setting up libseqan2-dev (2.4.0+dfsg-15) ...
Setting up libsasl2-modules-db:i386 (2.1.28+dfsg-10) ...
Setting up autotools-dev (20220109.1) ...
Setting up libuv1:i386 (1.44.2-1) ...
Setting up libboost-program-options-dev:i386 (1.74.0.3) ...
Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libboost-system1.74-dev:i386 (1.74.0+ds1-20) ...
Setting up libboost-regex1.74.0:i386 (1.74.0+ds1-20) ...
Setting up libproc2-0:i386 (2:4.0.2-3) ...
Setting up autopoint (0.21-12) ...
Setting up libjsoncpp25:i386 (1.9.5-4) ...
Setting up icu-devtools (72.1-3) ...
Setting up liblz4-dev:i386 (1.9.4-1) ...
Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ...
Setting up autoconf (2.71-3) ...
Setting up liblzma-dev:i386 (5.4.1-0.2) ...
Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up librhash0:i386 (1.4.3-3) ...
Setting up libuchardet0:i386 (0.0.7-1) ...
Setting up procps (2:4.0.2-3) ...
Setting up libsub-override-perl (0.09-4) ...
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fakeroot is already the newest version (1.31-1.2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: Running cd /build/hilive-2.0a/ && 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 > ../hilive_2.0a-3_source.changes
dpkg-buildpackage: info: source package hilive
dpkg-buildpackage: info: source version 2.0a-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
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cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DSEQAN_PATH=/usr/lib/seqan/ ..
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[ 6%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o
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/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o -c /build/hilive-2.0a/lib/tools_static.cpp
[ 31%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o -c /build/hilive-2.0a/lib/tools.cpp
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o -c /build/hilive-2.0a/lib/alnstream.cpp
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o -c /build/hilive-2.0a/lib/alnread.cpp
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o -c /build/hilive-2.0a/lib/alnout.cpp
[ 37%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o
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[ 56%] Building CXX object CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o -c /build/hilive-2.0a/lib/illumina_parsers.cpp
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o -c /build/hilive-2.0a/lib/kindex.cpp
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o -c /build/hilive-2.0a/lib/parallel.cpp
/usr/bin/c++ -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -MF CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o.d -o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o -c /build/hilive-2.0a/lib/argument_parser.cpp
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/kindex.h:7,
from /build/hilive-2.0a/lib/kindex.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/kindex.h:4:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/tools.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/tools_static.h:10:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/parallel.h:6,
from /build/hilive-2.0a/lib/parallel.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/parallel.h:4:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools_static.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/tools_static.h:10:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/illumina_parsers.h:6,
from /build/hilive-2.0a/lib/illumina_parsers.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/illumina_parsers.h:4:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/kindex.h:7,
from /build/hilive-2.0a/lib/alnstream.h:7,
from /build/hilive-2.0a/lib/alnstream.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/alnstream.h:4:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/kindex.h:7,
from /build/hilive-2.0a/lib/alnread.h:6,
from /build/hilive-2.0a/lib/alnread.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/alnread.h:4:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/kindex.h:7,
from /build/hilive-2.0a/lib/alnout.h:7,
from /build/hilive-2.0a/lib/alnout.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/lib/headers.h:1,
from /build/hilive-2.0a/lib/alnout.h:4:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/lib/tools.h:11,
from /build/hilive-2.0a/lib/parallel.h:6,
from /build/hilive-2.0a/lib/argument_parser.h:5,
from /build/hilive-2.0a/lib/argument_parser.cpp:1:
/build/hilive-2.0a/lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/boost/program_options/errors.hpp:12,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from /build/hilive-2.0a/lib/argument_parser.h:1:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/lib/alnstream.cpp: In member function 'uint64_t oAlnStream::lz4write(const char*, uint64_t)':
/build/hilive-2.0a/lib/alnstream.cpp:23:43: warning: 'int LZ4_compress(const char*, char*, int)' is deprecated: use LZ4_compress_default() instead [-Wdeprecated-declarations]
23 | uint32_t compressed_size = LZ4_compress (source, buf.data(), size);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /build/hilive-2.0a/lib/headers.h:5:
/usr/include/lz4.h:765:75: note: declared here
765 | LZ4_DEPRECATED("use LZ4_compress_default() instead") LZ4LIB_API int LZ4_compress (const char* src, char* dest, int srcSize);
| ^~~~~~~~~~~~
/build/hilive-2.0a/lib/alnstream.cpp: In member function 'ReadAlignment* iAlnStream::get_alignment()':
/build/hilive-2.0a/lib/alnstream.cpp:359:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
359 | fread(buffer.data(),1,buf_size,fstream);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/hilive-2.0a/lib/alnstream.cpp:389:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
389 | fread(buffer.data(),1,buf_size,fstream);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 62%] Linking CXX static library libHiLiveLibs.a
/usr/bin/cmake -P CMakeFiles/HiLiveLibs.dir/cmake_clean_target.cmake
/usr/bin/cmake -E cmake_link_script CMakeFiles/HiLiveLibs.dir/link.txt --verbose=1
/usr/bin/ar qc libHiLiveLibs.a CMakeFiles/HiLiveLibs.dir/lib/tools_static.cpp.o CMakeFiles/HiLiveLibs.dir/lib/tools.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnread.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnstream.cpp.o CMakeFiles/HiLiveLibs.dir/lib/alnout.cpp.o CMakeFiles/HiLiveLibs.dir/lib/illumina_parsers.cpp.o CMakeFiles/HiLiveLibs.dir/lib/kindex.cpp.o CMakeFiles/HiLiveLibs.dir/lib/parallel.cpp.o CMakeFiles/HiLiveLibs.dir/lib/argument_parser.cpp.o
/usr/bin/ranlib libHiLiveLibs.a
make[3]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
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make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/depend
make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/depend
make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/depend
make[3]: Entering directory '/build/hilive-2.0a/obj-i686-linux-gnu'
cd /build/hilive-2.0a/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hilive-2.0a /build/hilive-2.0a /build/hilive-2.0a/obj-i686-linux-gnu /build/hilive-2.0a/obj-i686-linux-gnu /build/hilive-2.0a/obj-i686-linux-gnu/CMakeFiles/hilive-build.dir/DependInfo.cmake --color=
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make[3]: Entering directory '/build/hilive-2.0a/obj-i686-linux-gnu'
cd /build/hilive-2.0a/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/hilive-2.0a /build/hilive-2.0a /build/hilive-2.0a/obj-i686-linux-gnu /build/hilive-2.0a/obj-i686-linux-gnu /build/hilive-2.0a/obj-i686-linux-gnu/CMakeFiles/hilive.dir/DependInfo.cmake --color=
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make[3]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
make -f CMakeFiles/hilive-out.dir/build.make CMakeFiles/hilive-out.dir/build
make[3]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
make -f CMakeFiles/hilive-build.dir/build.make CMakeFiles/hilive-build.dir/build
make -f CMakeFiles/hilive.dir/build.make CMakeFiles/hilive.dir/build
make[3]: Entering directory '/build/hilive-2.0a/obj-i686-linux-gnu'
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make[3]: Entering directory '/build/hilive-2.0a/obj-i686-linux-gnu'
[ 68%] Building CXX object CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o
[ 75%] Building CXX object CMakeFiles/hilive.dir/tools/hilive.cpp.o
[ 81%] Building CXX object CMakeFiles/hilive-build.dir/tools/build_index.cpp.o
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -MF CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o.d -o CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o -c /build/hilive-2.0a/tools/hilive_out.cpp
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/hilive.dir/tools/hilive.cpp.o -MF CMakeFiles/hilive.dir/tools/hilive.cpp.o.d -o CMakeFiles/hilive.dir/tools/hilive.cpp.o -c /build/hilive-2.0a/tools/hilive.cpp
/usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_FILESYSTEM_DYN_LINK -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PROGRAM_OPTIONS_DYN_LINK -DBOOST_SYSTEM_DYN_LINK -DHiLive_VERSION_MAJOR=2 -DHiLive_VERSION_MINOR=0 -I/build/hilive-2.0a/obj-i686-linux-gnu -I/build/hilive-2.0a/lib -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_ZLIB=1 -std=c++14 -MD -MT CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -MF CMakeFiles/hilive-build.dir/tools/build_index.cpp.o.d -o CMakeFiles/hilive-build.dir/tools/build_index.cpp.o -c /build/hilive-2.0a/tools/build_index.cpp
In file included from /build/hilive-2.0a/tools/../lib/tools.h:11,
from /build/hilive-2.0a/tools/../lib/kindex.h:7,
from /build/hilive-2.0a/tools/hilive.cpp:4:
/build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/tools/../lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
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 /build/hilive-2.0a/tools/../lib/headers.h:1,
from /build/hilive-2.0a/tools/hilive.cpp:1:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/tools/../lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/tools/../lib/tools.h:11,
from /build/hilive-2.0a/tools/../lib/kindex.h:7,
from /build/hilive-2.0a/tools/build_index.cpp:5:
/build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/tools/../lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/boost/program_options/errors.hpp:12,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from /build/hilive-2.0a/tools/build_index.cpp:1:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/tools/../lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
In file included from /build/hilive-2.0a/tools/../lib/tools.h:11,
from /build/hilive-2.0a/tools/../lib/kindex.h:7,
from /build/hilive-2.0a/tools/hilive_out.cpp:5:
/build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void ltrim(std::string&)':
/build/hilive-2.0a/tools/../lib/tools_static.h:304:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
304 | std::not1(std::ptr_fun<int, int>(std::isspace))));
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/boost/program_options/errors.hpp:12,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from /build/hilive-2.0a/tools/hilive_out.cpp:1:
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
/build/hilive-2.0a/tools/../lib/tools_static.h: In function 'void rtrim(std::string&)':
/build/hilive-2.0a/tools/../lib/tools_static.h:314:45: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
314 | std::not1(std::ptr_fun<int, int>(std::isspace))).base(), s.end());
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
[ 87%] Linking CXX executable hilive-build
/usr/bin/cmake -E cmake_link_script CMakeFiles/hilive-build.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive "CMakeFiles/hilive-build.dir/tools/build_index.cpp.o" -o hilive-build libHiLiveLibs.a /usr/lib/i386-linux-gnu/libz.so -llz4 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.74.0 -lrt /usr/lib/i386-linux-gnu/libz.so -llz4 -lrt
make[3]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
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[ 93%] Linking CXX executable hilive-out
/usr/bin/cmake -E cmake_link_script CMakeFiles/hilive-out.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive "CMakeFiles/hilive-out.dir/tools/hilive_out.cpp.o" -o hilive-out libHiLiveLibs.a /usr/lib/i386-linux-gnu/libz.so -llz4 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.74.0 -lrt /usr/lib/i386-linux-gnu/libz.so -llz4 -lrt
make[3]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
[ 93%] Built target hilive-out
[100%] Linking CXX executable hilive
/usr/bin/cmake -E cmake_link_script CMakeFiles/hilive.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/hilive-2.0a=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive CMakeFiles/hilive.dir/tools/hilive.cpp.o -o hilive libHiLiveLibs.a /usr/lib/i386-linux-gnu/libz.so -llz4 /usr/lib/i386-linux-gnu/libboost_system.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_program_options.so.1.74.0 /usr/lib/i386-linux-gnu/libboost_iostreams.so.1.74.0 -lrt /usr/lib/i386-linux-gnu/libz.so -llz4 -lrt
make[3]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
[100%] Built target hilive
make[2]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/hilive-2.0a/obj-i686-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/hilive-2.0a/obj-i686-linux-gnu'
dh_auto_test
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary
dh binary
dh_testroot
dh_prep
dh_auto_install --destdir=debian/hilive/
debian/rules override_dh_install
make[1]: Entering directory '/build/hilive-2.0a'
chrpath --delete obj-i686-linux-gnu/hilive*
dh_install
make[1]: Leaving directory '/build/hilive-2.0a'
debian/rules override_dh_installdocs
make[1]: Entering directory '/build/hilive-2.0a'
markdown README.md > README.html
dh_installdocs
rm README.html
make[1]: Leaving directory '/build/hilive-2.0a'
dh_installchangelogs
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
dh_missing
dh_dwz
dh_strip
dh_makeshlibs
dh_shlibdeps
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'hilive-dbgsym' in '../hilive-dbgsym_2.0a-3_i386.deb'.
dpkg-deb: building package 'hilive' in '../hilive_2.0a-3_i386.deb'.
dpkg-genbuildinfo --build=binary -O../hilive_2.0a-3_i386.buildinfo
dpkg-genchanges --build=binary -O../hilive_2.0a-3_i386.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/5724 and its subdirectories
I: Current time: Sat May 18 17:17:37 -12 2024
I: pbuilder-time-stamp: 1716095857
Sun Apr 16 22:54:38 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net.
Sun Apr 16 22:54:38 UTC 2023 I: Preparing to do remote build '2' on ionos2-i386.debian.net.
Sun Apr 16 22:57:42 UTC 2023 I: Deleting $TMPDIR on ionos2-i386.debian.net.
Sun Apr 16 22:57:43 UTC 2023 I: hilive_2.0a-3_i386.changes:
Format: 1.8
Date: Thu, 16 Jan 2020 11:56:44 +0100
Source: hilive
Binary: hilive hilive-dbgsym
Architecture: i386
Version: 2.0a-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
hilive - realtime alignment of Illumina reads
Changes:
hilive (2.0a-3) unstable; urgency=medium
.
[ Andreas Tille ]
* Really install documentation
.
[ Juhani Numminen ]
* Remove undesired build flag -march=native
.
[ Andreas Tille ]
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Remove obsolete field Name from debian/upstream/metadata (already
present in machine-readable debian/copyright).
Checksums-Sha1:
23de47ac21992e4eecfb48d95f58e5e56c1932b3 9847728 hilive-dbgsym_2.0a-3_i386.deb
999015fee790f1cb3be3b4dabe906f1a633070d1 6834 hilive_2.0a-3_i386.buildinfo
30a38570947ea64905e2216d6f43f8b3eafb2f91 537996 hilive_2.0a-3_i386.deb
Checksums-Sha256:
33d2c57d509b9561c0fd2485c7a81eea4710d5a95a7a20de7df3c967e71a6f3b 9847728 hilive-dbgsym_2.0a-3_i386.deb
bc059e711d67736b12c3fe45ef9f86ea6d000953768acbd22cf57fefd215b330 6834 hilive_2.0a-3_i386.buildinfo
19c2c47bccff116a58f520f38d4d23d2359528edfd8a872aaa3e7d0640a6c6a4 537996 hilive_2.0a-3_i386.deb
Files:
9232153e42360faf2f24d9c51f231908 9847728 debug optional hilive-dbgsym_2.0a-3_i386.deb
a447c6e4fa6394e2ac0bbe3162a8b0f5 6834 science optional hilive_2.0a-3_i386.buildinfo
c95ebd5366bfba825eae10754f9c3ac1 537996 science optional hilive_2.0a-3_i386.deb
Sun Apr 16 22:57:45 UTC 2023 I: diffoscope 240 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.JoHne2yg/hilive_2.0a-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.JoHne2yg/hilive_2.0a-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.JoHne2yg/hilive_2.0a-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.JoHne2yg/b1/hilive_2.0a-3_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.JoHne2yg/b2/hilive_2.0a-3_i386.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: 0.589s)
0.589s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.253s)
0.252s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Sun Apr 16 22:57:48 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists.
Sun Apr 16 22:57:48 UTC 2023 I: hilive from bookworm built successfully and reproducibly on i386.
Sun Apr 16 22:57:51 UTC 2023 I: Submitting .buildinfo files to external archives:
Sun Apr 16 22:57:51 UTC 2023 I: Submitting 8.0K b1/hilive_2.0a-3_i386.buildinfo.asc
Sun Apr 16 22:57:56 UTC 2023 I: Submitting 8.0K b2/hilive_2.0a-3_i386.buildinfo.asc
Sun Apr 16 22:57:57 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Sun Apr 16 22:57:57 UTC 2023 I: Done submitting .buildinfo files.
Sun Apr 16 22:57:57 UTC 2023 I: Removing signed hilive_2.0a-3_i386.buildinfo.asc files:
removed './b1/hilive_2.0a-3_i386.buildinfo.asc'
removed './b2/hilive_2.0a-3_i386.buildinfo.asc'