Tue May 9 01:18:44 UTC 2023 I: starting to build tiddit/bookworm/amd64 on jenkins on '2023-05-09 01:18'
Tue May 9 01:18:44 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/24037/console.log
Tue May 9 01:18:44 UTC 2023 I: Downloading source for bookworm/tiddit=3.5.2+dfsg-1
--2023-05-09 01:18:44-- http://cdn-fastly.deb.debian.org/debian/pool/main/t/tiddit/tiddit_3.5.2%2bdfsg-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2104 (2.1K) [text/prs.lines.tag]
Saving to: ‘tiddit_3.5.2+dfsg-1.dsc’
0K .. 100% 121M=0s
2023-05-09 01:18:44 (121 MB/s) - ‘tiddit_3.5.2+dfsg-1.dsc’ saved [2104/2104]
Tue May 9 01:18:45 UTC 2023 I: tiddit_3.5.2+dfsg-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: tiddit
Binary: tiddit
Architecture: any
Version: 3.5.2+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/SciLifeLab/TIDDIT
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/tiddit
Vcs-Git: https://salsa.debian.org/med-team/tiddit.git
Testsuite: autopkgtest
Testsuite-Triggers: samtools
Build-Depends: debhelper-compat (= 13), dh-python, cython3, python3-all-dev, python3-setuptools, python3-numpy, python3-pysam
Package-List:
tiddit deb science optional arch=any
Checksums-Sha1:
8d171afe35b7717eae6601b1f370079799802f04 19412 tiddit_3.5.2+dfsg.orig.tar.xz
60140498fd7cb2f20d36c7c4ad51e57347371fd6 1731628 tiddit_3.5.2+dfsg-1.debian.tar.xz
Checksums-Sha256:
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5788cc9356ba5688e7d5d877a0bb4e2e138020649c5c87a24128c07eccfc4be9 1731628 tiddit_3.5.2+dfsg-1.debian.tar.xz
Files:
e5b613d9604b5000d460758b2e138877 19412 tiddit_3.5.2+dfsg.orig.tar.xz
5ef1e747ef2d8f04c5015b91e5054a54 1731628 tiddit_3.5.2+dfsg-1.debian.tar.xz
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Tue May 9 01:18:45 UTC 2023 I: Checking whether the package is not for us
Tue May 9 01:18:45 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Tue May 9 01:18:45 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Tue May 9 01:24:49 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun Jun 9 19:41:51 -12 2024
I: pbuilder-time-stamp: 1718005311
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 [tiddit_3.5.2+dfsg-1.dsc]
I: copying [./tiddit_3.5.2+dfsg.orig.tar.xz]
I: copying [./tiddit_3.5.2+dfsg-1.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Feb 16 07:01:30 2023 -12
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@emlwks999.eu"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./tiddit_3.5.2+dfsg-1.dsc: no acceptable signature found
dpkg-source: info: extracting tiddit in tiddit-3.5.2+dfsg
dpkg-source: info: unpacking tiddit_3.5.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking tiddit_3.5.2+dfsg-1.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1804992/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='d8bc5a3e2c39467aada3515f7a19181c'
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='1804992'
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.2BrrAlxF/pbuilderrc_U2Xr --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.2BrrAlxF/b1 --logfile b1/build.log tiddit_3.5.2+dfsg-1.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.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) 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/1804992/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), dh-python, cython3, python3-all-dev, python3-setuptools, python3-numpy, python3-pysam
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19596 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 dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on cython3; however:
Package cython3 is not installed.
pbuilder-satisfydepends-dummy depends on python3-all-dev; however:
Package python3-all-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-setuptools; however:
Package python3-setuptools is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
pbuilder-satisfydepends-dummy depends on python3-pysam; however:
Package python3-pysam 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} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-dev{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-pysam{a} python3-setuptools{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget
0 packages upgraded, 77 newly installed, 0 to remove and 0 not upgraded.
Need to get 47.9 MB of archives. After unpacking 195 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 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 cython3 amd64 0.29.32-2+b1 [1302 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 dh-python all 5.20230130 [104 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-9 [381 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB]
Fetched 47.9 MB in 2s (28.7 MB/s)
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update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode
Setting up libexpat1-dev:amd64 (2.5.0-1) ...
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Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up liblapack3:amd64 (3.11.0-2) ...
update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up libreadline8:amd64 (8.2-1.3) ...
Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libjs-sphinxdoc (5.3.0-4) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ...
Setting up libcurl3-gnutls:amd64 (7.88.1-9) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up libhts3:amd64 (1.16+ds-3) ...
Setting up libpython3.11:amd64 (3.11.2-6) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up libpython3.11-dev:amd64 (3.11.2-6) ...
Setting up cython3 (0.29.32-2+b1) ...
Setting up python3-lib2to3 (3.11.2-3) ...
Setting up python3-pkg-resources (66.1.1-1) ...
Setting up python3-distutils (3.11.2-3) ...
Setting up dh-python (5.20230130) ...
Setting up python3-pysam (0.20.0+ds-3+b1) ...
Setting up libpython3-dev:amd64 (3.11.2-1+b1) ...
Setting up python3-setuptools (66.1.1-1) ...
Setting up python3.11-dev (3.11.2-6) ...
Setting up python3-all (3.11.2-1+b1) ...
Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ...
Setting up python3-dev (3.11.2-1+b1) ...
Setting up python3-numpy (1:1.24.2-1) ...
Setting up python3-all-dev (3.11.2-1+b1) ...
Processing triggers for libc-bin (2.36-9) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/tiddit-3.5.2+dfsg/ && 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 > ../tiddit_3.5.2+dfsg-1_source.changes
dpkg-buildpackage: info: source package tiddit
dpkg-buildpackage: info: source version 3.5.2+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Lance Lin <lq27267@gmail.com>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --with python3 --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py clean
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_cluster.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_contig_analysis.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_coverage.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_coverage_analysis.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_signal.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_variant.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling tiddit/tiddit_signal.pyx because it changed.
Compiling tiddit/tiddit_coverage.pyx because it changed.
Compiling tiddit/tiddit_cluster.pyx because it changed.
Compiling tiddit/tiddit_coverage_analysis.pyx because it changed.
Compiling tiddit/tiddit_variant.pyx because it changed.
Compiling tiddit/tiddit_contig_analysis.pyx because it changed.
[1/6] Cythonizing tiddit/tiddit_cluster.pyx
[2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx
[3/6] Cythonizing tiddit/tiddit_coverage.pyx
[4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx
[5/6] Cythonizing tiddit/tiddit_signal.pyx
[6/6] Cythonizing tiddit/tiddit_variant.pyx
running clean
removing '/build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build' (and everything under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
'build/scripts-3.11' does not exist -- can't clean it
dh_autoreconf_clean -O--buildsystem=pybuild
debian/rules override_dh_clean
make[1]: Entering directory '/build/tiddit-3.5.2+dfsg'
dh_clean
rm -f tiddit/*.c
make[1]: Leaving directory '/build/tiddit-3.5.2+dfsg'
debian/rules binary
dh binary --with python3 --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
I: pybuild base:240: python3.11 setup.py config
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_cluster.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_contig_analysis.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_coverage.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_coverage_analysis.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_signal.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /build/tiddit-3.5.2+dfsg/tiddit/tiddit_variant.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
Compiling tiddit/tiddit_signal.pyx because it changed.
Compiling tiddit/tiddit_coverage.pyx because it changed.
Compiling tiddit/tiddit_cluster.pyx because it changed.
Compiling tiddit/tiddit_coverage_analysis.pyx because it changed.
Compiling tiddit/tiddit_variant.pyx because it changed.
Compiling tiddit/tiddit_contig_analysis.pyx because it changed.
[1/6] Cythonizing tiddit/tiddit_cluster.pyx
[2/6] Cythonizing tiddit/tiddit_contig_analysis.pyx
[3/6] Cythonizing tiddit/tiddit_coverage.pyx
[4/6] Cythonizing tiddit/tiddit_coverage_analysis.pyx
[5/6] Cythonizing tiddit/tiddit_signal.pyx
[6/6] Cythonizing tiddit/tiddit_variant.pyx
running config
dh_auto_build -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py build
running build
running build_py
creating /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit
copying tiddit/tiddit_vcf_header.py -> /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit
copying tiddit/tiddit_stats.py -> /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit
copying tiddit/__main__.py -> /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit
copying tiddit/__init__.py -> /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit
copying tiddit/DBSCAN.py -> /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit
running build_ext
building 'tiddit.tiddit_signal' extension
creating build
creating build/temp.linux-x86_64-cpython-311
creating build/temp.linux-x86_64-cpython-311/tiddit
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tiddit/tiddit_signal.c -o build/temp.linux-x86_64-cpython-311/tiddit/tiddit_signal.o
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tiddit/tiddit_signal.o -L/usr/lib/x86_64-linux-gnu -o /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_signal.cpython-311-x86_64-linux-gnu.so
building 'tiddit.tiddit_coverage' extension
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tiddit/tiddit_coverage.c -o build/temp.linux-x86_64-cpython-311/tiddit/tiddit_coverage.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from tiddit/tiddit_coverage.c:759:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tiddit/tiddit_coverage.o -L/usr/lib/x86_64-linux-gnu -o /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_coverage.cpython-311-x86_64-linux-gnu.so
building 'tiddit.tiddit_cluster' extension
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tiddit/tiddit_cluster.c -o build/temp.linux-x86_64-cpython-311/tiddit/tiddit_cluster.o
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tiddit/tiddit_cluster.o -L/usr/lib/x86_64-linux-gnu -o /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_cluster.cpython-311-x86_64-linux-gnu.so
building 'tiddit.tiddit_coverage_analysis' extension
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tiddit/tiddit_coverage_analysis.c -o build/temp.linux-x86_64-cpython-311/tiddit/tiddit_coverage_analysis.o
In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1940,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:5,
from tiddit/tiddit_coverage_analysis.c:759:
/usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
17 | #warning "Using deprecated NumPy API, disable it with " \
| ^~~~~~~
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tiddit/tiddit_coverage_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-311-x86_64-linux-gnu.so
building 'tiddit.tiddit_variant' extension
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tiddit/tiddit_variant.c -o build/temp.linux-x86_64-cpython-311/tiddit/tiddit_variant.o
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tiddit/tiddit_variant.o -L/usr/lib/x86_64-linux-gnu -o /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_variant.cpython-311-x86_64-linux-gnu.so
building 'tiddit.tiddit_contig_analysis' extension
x86_64-linux-gnu-gcc -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.11 -c tiddit/tiddit_contig_analysis.c -o build/temp.linux-x86_64-cpython-311/tiddit/tiddit_contig_analysis.o
x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/build/tiddit-3.5.2+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-311/tiddit/tiddit_contig_analysis.o -L/usr/lib/x86_64-linux-gnu -o /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_contig_analysis.cpython-311-x86_64-linux-gnu.so
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:240: cd /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build; python3.11 -m unittest discover -v
----------------------------------------------------------------------
Ran 0 tests in 0.000s
OK
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
dh_prep -O--buildsystem=pybuild
dh_auto_install --destdir=debian/tiddit/ -O--buildsystem=pybuild
I: pybuild base:240: /usr/bin/python3 setup.py install --root /build/tiddit-3.5.2+dfsg/debian/tiddit
running install
/usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
running build_ext
running install_lib
creating /build/tiddit-3.5.2+dfsg/debian/tiddit/usr
creating /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib
creating /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11
creating /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages
creating /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
creating /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/__pycache__
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/__pycache__/__init__.cpython-311.pyc -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/__pycache__
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_contig_analysis.cpython-311-x86_64-linux-gnu.so -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_variant.cpython-311-x86_64-linux-gnu.so -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_coverage_analysis.cpython-311-x86_64-linux-gnu.so -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_cluster.cpython-311-x86_64-linux-gnu.so -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_coverage.cpython-311-x86_64-linux-gnu.so -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_signal.cpython-311-x86_64-linux-gnu.so -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/DBSCAN.py -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/__init__.py -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/__main__.py -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_stats.py -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
copying /build/tiddit-3.5.2+dfsg/.pybuild/cpython3_3.11_tiddit/build/tiddit/tiddit_vcf_header.py -> /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit
byte-compiling /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/DBSCAN.py to DBSCAN.cpython-311.pyc
byte-compiling /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/__init__.py to __init__.cpython-311.pyc
byte-compiling /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/__main__.py to __main__.cpython-311.pyc
byte-compiling /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/tiddit_stats.py to tiddit_stats.cpython-311.pyc
byte-compiling /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit/tiddit_vcf_header.py to tiddit_vcf_header.cpython-311.pyc
running install_egg_info
running egg_info
creating tiddit.egg-info
writing tiddit.egg-info/PKG-INFO
writing dependency_links to tiddit.egg-info/dependency_links.txt
writing entry points to tiddit.egg-info/entry_points.txt
writing requirements to tiddit.egg-info/requires.txt
writing top-level names to tiddit.egg-info/top_level.txt
writing manifest file 'tiddit.egg-info/SOURCES.txt'
reading manifest file 'tiddit.egg-info/SOURCES.txt'
adding license file 'COPYING'
adding license file 'AUTHORS'
writing manifest file 'tiddit.egg-info/SOURCES.txt'
Copying tiddit.egg-info to /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/lib/python3.11/dist-packages/tiddit-3.5.2.egg-info
Skipping SOURCES.txt
running install_scripts
Installing tiddit script to /build/tiddit-3.5.2+dfsg/debian/tiddit/usr/bin
dh_installdocs -O--buildsystem=pybuild
dh_installchangelogs -O--buildsystem=pybuild
debian/rules override_dh_installman
make[1]: Entering directory '/build/tiddit-3.5.2+dfsg'
dh_installman --language=C
make[1]: Leaving directory '/build/tiddit-3.5.2+dfsg'
debian/rules override_dh_python3
make[1]: Entering directory '/build/tiddit-3.5.2+dfsg'
dh_python3 --shebang=/usr/bin/python3
I: dh_python3 tools:114: replacing shebang in debian/tiddit/usr/bin/tiddit
make[1]: Leaving directory '/build/tiddit-3.5.2+dfsg'
dh_installsystemduser -O--buildsystem=pybuild
dh_perl -O--buildsystem=pybuild
dh_link -O--buildsystem=pybuild
dh_strip_nondeterminism -O--buildsystem=pybuild
dh_compress -O--buildsystem=pybuild
dh_fixperms -O--buildsystem=pybuild
dh_missing -O--buildsystem=pybuild
dh_dwz -a -O--buildsystem=pybuild
dh_strip -a -O--buildsystem=pybuild
dh_makeshlibs -a -O--buildsystem=pybuild
dh_shlibdeps -a -O--buildsystem=pybuild
dh_installdeb -O--buildsystem=pybuild
dh_gencontrol -O--buildsystem=pybuild
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
dpkg-deb: building package 'tiddit' in '../tiddit_3.5.2+dfsg-1_amd64.deb'.
dpkg-deb: building package 'tiddit-dbgsym' in '../tiddit-dbgsym_3.5.2+dfsg-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../tiddit_3.5.2+dfsg-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../tiddit_3.5.2+dfsg-1_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: including full 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/1804992 and its subdirectories
I: Current time: Sun Jun 9 19:47:52 -12 2024
I: pbuilder-time-stamp: 1718005672
Tue May 9 01:24:49 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net.
Tue May 9 01:24:49 UTC 2023 I: Preparing to do remote build '2' on ionos11-amd64.debian.net.
Tue May 9 01:29:23 UTC 2023 I: Deleting $TMPDIR on ionos11-amd64.debian.net.
Tue May 9 01:29:23 UTC 2023 I: tiddit_3.5.2+dfsg-1_amd64.changes:
Format: 1.8
Date: Mon, 13 Feb 2023 20:39:25 +0700
Source: tiddit
Binary: tiddit tiddit-dbgsym
Architecture: amd64
Version: 3.5.2+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Lance Lin <lq27267@gmail.com>
Description:
tiddit - structural variant calling
Changes:
tiddit (3.5.2+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version 3.5.2+dfsg
* d/copyright: Update year to 2023
Checksums-Sha1:
5838b7205766406d84383f8cffa06ef17500042b 1517576 tiddit-dbgsym_3.5.2+dfsg-1_amd64.deb
3ef91e97afb2f3c07d8b13a8832a49edf1f12442 6849 tiddit_3.5.2+dfsg-1_amd64.buildinfo
672672220bbcf95ee107b4b476fc1221689b58c2 271684 tiddit_3.5.2+dfsg-1_amd64.deb
Checksums-Sha256:
f56f01e0bb25bfd2c3f6f74083adba4037f835eadc84d8958bbbafec511014f4 1517576 tiddit-dbgsym_3.5.2+dfsg-1_amd64.deb
2ec8c68a92219389d99196abfd7d892104efaee11231b5c4a6a4d2562d307acf 6849 tiddit_3.5.2+dfsg-1_amd64.buildinfo
60a964bfd857190d8208e4e82c3a6a9758d106ee0e9f313caf4777fd8574a208 271684 tiddit_3.5.2+dfsg-1_amd64.deb
Files:
0a7fc1824cb182d268d9a297871c8441 1517576 debug optional tiddit-dbgsym_3.5.2+dfsg-1_amd64.deb
d0523106d68ed3fac4a638bbd422bb6a 6849 science optional tiddit_3.5.2+dfsg-1_amd64.buildinfo
19222ae77edcd494f0b1a40cd342f80d 271684 science optional tiddit_3.5.2+dfsg-1_amd64.deb
Tue May 9 01:29:25 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.2BrrAlxF/tiddit_3.5.2+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.2BrrAlxF/tiddit_3.5.2+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.2BrrAlxF/tiddit_3.5.2+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.2BrrAlxF/b1/tiddit_3.5.2+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.2BrrAlxF/b2/tiddit_3.5.2+dfsg-1_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: 0.791s)
0.791s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.035s)
0.035s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Tue May 9 01:29:27 UTC 2023 I: diffoscope 242 found no differences in the changes files, and a .buildinfo file also exists.
Tue May 9 01:29:27 UTC 2023 I: tiddit from bookworm built successfully and reproducibly on amd64.
Tue May 9 01:29:28 UTC 2023 I: Submitting .buildinfo files to external archives:
Tue May 9 01:29:28 UTC 2023 I: Submitting 8.0K b1/tiddit_3.5.2+dfsg-1_amd64.buildinfo.asc
Tue May 9 01:29:28 UTC 2023 I: Submitting 8.0K b2/tiddit_3.5.2+dfsg-1_amd64.buildinfo.asc
Tue May 9 01:29:29 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Tue May 9 01:29:29 UTC 2023 I: Done submitting .buildinfo files.
Tue May 9 01:29:29 UTC 2023 I: Removing signed tiddit_3.5.2+dfsg-1_amd64.buildinfo.asc files:
removed './b1/tiddit_3.5.2+dfsg-1_amd64.buildinfo.asc'
removed './b2/tiddit_3.5.2+dfsg-1_amd64.buildinfo.asc'