Diff of the two buildlogs:
--
--- b1/build.log 2025-03-13 11:07:13.632920466 +0000
+++ b2/build.log 2025-03-13 11:19:59.750414130 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Wed Apr 15 05:27:39 -12 2026
-I: pbuilder-time-stamp: 1776274059
+I: Current time: Fri Mar 14 01:07:16 +14 2025
+I: pbuilder-time-stamp: 1741864036
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -30,52 +30,84 @@
dpkg-source: info: applying syntax_warning.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3714857/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos11-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Mar 13 11:07 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build/reproducible-path'
- BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
- BUILDUSERNAME='pbuilder1'
- BUILD_ARCH='amd64'
- DEBIAN_FRONTEND='noninteractive'
- DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
- DISTRIBUTION='unstable'
- HOME='/root'
- HOST_ARCH='amd64'
+ BASH=/bin/sh
+ BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+ BASH_ALIASES=()
+ BASH_ARGC=()
+ BASH_ARGV=()
+ BASH_CMDS=()
+ BASH_LINENO=([0]="12" [1]="0")
+ BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+ BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+ BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+ BASH_VERSION='5.2.37(1)-release'
+ BUILDDIR=/build/reproducible-path
+ BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+ BUILDUSERNAME=pbuilder2
+ BUILD_ARCH=amd64
+ DEBIAN_FRONTEND=noninteractive
+ DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
+ DIRSTACK=()
+ DISTRIBUTION=unstable
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=x86_64
+ HOST_ARCH=amd64
IFS='
'
- INVOCATION_ID='f3e9c75927374212907c48cbfa348a9d'
- 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='3714857'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=be57ce4638374de88d01eebc9af2b5a7
+ LANG=C
+ LANGUAGE=et_EE:et
+ LC_ALL=C
+ MACHTYPE=x86_64-pc-linux-gnu
+ MAIL=/var/mail/root
+ OPTERR=1
+ OPTIND=1
+ OSTYPE=linux-gnu
+ PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+ PBCURRENTCOMMANDLINEOPERATION=build
+ PBUILDER_OPERATION=build
+ PBUILDER_PKGDATADIR=/usr/share/pbuilder
+ PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+ PBUILDER_SYSCONFDIR=/etc
+ PIPESTATUS=([0]="0")
+ POSIXLY_CORRECT=y
+ PPID=3092629
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.46pDLaR0/pbuilderrc_rVwY --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.46pDLaR0/b1 --logfile b1/build.log pairtools_1.1.3-1.dsc'
- SUDO_GID='110'
- SUDO_UID='105'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://213.165.73.152:3128'
+ PWD=/
+ SHELL=/bin/bash
+ SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+ SHLVL=3
+ SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.46pDLaR0/pbuilderrc_8LI1 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.46pDLaR0/b2 --logfile b2/build.log pairtools_1.1.3-1.dsc'
+ SUDO_GID=111
+ SUDO_UID=106
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ _='I: set'
+ http_proxy=http://46.16.76.132:3128
I: uname -a
- Linux ionos5-amd64 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/3714857/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -381,7 +413,7 @@
Get: 232 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.5-1 [250 kB]
Get: 233 http://deb.debian.org/debian unstable/main amd64 python3-standard-pipes all 3.13.0-5 [7376 B]
Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b2 [136 kB]
-Fetched 154 MB in 5s (31.1 MB/s)
+Fetched 154 MB in 6s (27.8 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpython3.13-minimal:amd64.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19783 files and directories currently installed.)
@@ -1138,8 +1170,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Wed Apr 15 17:28:25 UTC 2026.
-Universal Time is now: Wed Apr 15 17:28:25 UTC 2026.
+Local time is now: Thu Mar 13 11:11:14 UTC 2025.
+Universal Time is now: Thu Mar 13 11:11:14 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up unicode-data (15.1.0-1) ...
@@ -1356,7 +1388,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/pairtools-1.1.3/ && 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 > ../pairtools_1.1.3-1_source.changes
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/pairtools-1.1.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pairtools_1.1.3-1_source.changes
dpkg-buildpackage: info: source package pairtools
dpkg-buildpackage: info: source version 1.1.3-1
dpkg-buildpackage: info: source distribution unstable
@@ -1387,9 +1423,9 @@
tree = Parsing.p_module(s, pxd, full_module_name)
/usr/lib/python3/dist-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /build/reproducible-path/pairtools-1.1.3/pairtools/lib/regions.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
-Compiling pairtools/lib/regions.pyx because it changed.
-Compiling pairtools/lib/dedup_cython.pyx because it changed.
Compiling pairtools/lib/parse_pysam.pyx because it changed.
+Compiling pairtools/lib/dedup_cython.pyx because it changed.
+Compiling pairtools/lib/regions.pyx because it changed.
[1/3] Cythonizing pairtools/lib/dedup_cython.pyx
[2/3] Cythonizing pairtools/lib/parse_pysam.pyx
[3/3] Cythonizing pairtools/lib/regions.pyx
@@ -1398,40 +1434,40 @@
running build_py
creating build/lib.linux-x86_64-cpython-313/pairtools
copying pairtools/__init__.py -> build/lib.linux-x86_64-cpython-313/pairtools
-copying pairtools/__main__.py -> build/lib.linux-x86_64-cpython-313/pairtools
copying pairtools/_logging.py -> build/lib.linux-x86_64-cpython-313/pairtools
+copying pairtools/__main__.py -> build/lib.linux-x86_64-cpython-313/pairtools
creating build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/filterbycov.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/stats.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/select.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/scaling.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/phase.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/restrict.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
copying pairtools/lib/__init__.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/headerops.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/pairsio.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/stats.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
copying pairtools/lib/pairsam_format.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
copying pairtools/lib/dedup.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
-copying pairtools/lib/parse.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/pairsio.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/restrict.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
copying pairtools/lib/fileio.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/filterbycov.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/scaling.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/parse.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/headerops.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/select.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
+copying pairtools/lib/phase.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib
creating build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/filterbycov.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/__init__.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/stats.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/select.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/header.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/scaling.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/split.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/phase.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/sort.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/dedup.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/restrict.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/flip.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/__init__.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/parse2.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/markasdup.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/split.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/header.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/merge.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/dedup.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
-copying pairtools/cli/sort.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/filterbycov.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/scaling.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/parse.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
copying pairtools/cli/sample.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/parse2.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/select.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
+copying pairtools/cli/phase.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli
running egg_info
creating pairtools.egg-info
writing pairtools.egg-info/PKG-INFO
@@ -1458,8 +1494,24 @@
copying pairtools/lib/parse_pysam.pyx -> build/lib.linux-x86_64-cpython-313/pairtools/lib
copying pairtools/lib/regions.pyx -> build/lib.linux-x86_64-cpython-313/pairtools/lib
running build_ext
-building 'pairtools.lib.regions' extension
+building 'pairtools.lib.parse_pysam' extension
creating build/temp.linux-x86_64-cpython-313/pairtools/lib
+x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipairtools/lib -I/usr/lib/python3/dist-packages/pysam -I/usr/lib/python3/dist-packages/pysam/include/samtools -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c pairtools/lib/parse_pysam.c -o build/temp.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.o
+pairtools/lib/parse_pysam.c:3259:9: warning: 'Py_UNICODE' is deprecated [-Wdeprecated-declarations]
+ 3259 | Py_UNICODE *as_pyunicodes;
+ | ^~~~~~~~~~
+x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-313-x86_64-linux-gnu.so
+building 'pairtools.lib.dedup_cython' extension
+x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c pairtools/lib/dedup_cython.c -o build/temp.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.o
+In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
+ from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
+ from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
+ from pairtools/lib/dedup_cython.c:1240:
+/usr/lib/x86_64-linux-gnu/python3-numpy/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.cpython-313-x86_64-linux-gnu.so
+building 'pairtools.lib.regions' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c pairtools/lib/regions.cpp -o build/temp.linux-x86_64-cpython-313/pairtools/lib/regions.o
In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
@@ -1478,74 +1530,58 @@
10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE;
| ^~~~~~~~~~
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pairtools/lib/regions.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pairtools/lib/regions.cpython-313-x86_64-linux-gnu.so
-building 'pairtools.lib.dedup_cython' extension
-x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c pairtools/lib/dedup_cython.c -o build/temp.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.o
-In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913,
- from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12,
- from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5,
- from pairtools/lib/dedup_cython.c:1240:
-/usr/lib/x86_64-linux-gnu/python3-numpy/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.cpython-313-x86_64-linux-gnu.so
-building 'pairtools.lib.parse_pysam' extension
-x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Ipairtools/lib -I/usr/lib/python3/dist-packages/pysam -I/usr/lib/python3/dist-packages/pysam/include/samtools -I/usr/include/python3.13 -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include -c pairtools/lib/parse_pysam.c -o build/temp.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.o
-pairtools/lib/parse_pysam.c:3259:9: warning: 'Py_UNICODE' is deprecated [-Wdeprecated-declarations]
- 3259 | Py_UNICODE *as_pyunicodes;
- | ^~~~~~~~~~
-x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-313-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-313-x86_64-linux-gnu.so
installing to build/bdist.linux-x86_64/wheel
running install
running install_lib
creating build/bdist.linux-x86_64/wheel
creating build/bdist.linux-x86_64/wheel/pairtools
+copying build/lib.linux-x86_64-cpython-313/pairtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools
+copying build/lib.linux-x86_64-cpython-313/pairtools/_logging.py -> build/bdist.linux-x86_64/wheel/./pairtools
creating build/bdist.linux-x86_64/wheel/pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
copying build/lib.linux-x86_64-cpython-313/pairtools/lib/stats.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/pairsam_format.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/pairsio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/fileio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
copying build/lib.linux-x86_64-cpython-313/pairtools/lib/regions.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/regions.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib
copying build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/headerops.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib
copying build/lib.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/regions.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
copying build/lib.linux-x86_64-cpython-313/pairtools/lib/parse_pysam.pxd -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup_cython.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/pairsio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/pairsam_format.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
copying build/lib.linux-x86_64-cpython-313/pairtools/lib/parse.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
-copying build/lib.linux-x86_64-cpython-313/pairtools/lib/fileio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/headerops.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/lib/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib
+copying build/lib.linux-x86_64-cpython-313/pairtools/__main__.py -> build/bdist.linux-x86_64/wheel/./pairtools
creating build/bdist.linux-x86_64/wheel/pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/stats.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/header.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/split.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/sort.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/flip.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/parse2.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/markasdup.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/split.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/header.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/merge.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/cli/sort.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/parse.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
copying build/lib.linux-x86_64-cpython-313/pairtools/cli/sample.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
-copying build/lib.linux-x86_64-cpython-313/pairtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools
-copying build/lib.linux-x86_64-cpython-313/pairtools/__main__.py -> build/bdist.linux-x86_64/wheel/./pairtools
-copying build/lib.linux-x86_64-cpython-313/pairtools/_logging.py -> build/bdist.linux-x86_64/wheel/./pairtools
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/parse2.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
+copying build/lib.linux-x86_64-cpython-313/pairtools/cli/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli
running install_egg_info
Copying pairtools.egg-info to build/bdist.linux-x86_64/wheel/./pairtools-1.1.3.egg-info
running install_scripts
creating build/bdist.linux-x86_64/wheel/pairtools-1.1.3.dist-info/WHEEL
-creating '/build/reproducible-path/pairtools-1.1.3/.pybuild/cpython3_3.13_pairtools/.tmp-3af41rvi/pairtools-1.1.3-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
+creating '/build/reproducible-path/pairtools-1.1.3/.pybuild/cpython3_3.13_pairtools/.tmp-r7o_zgzg/pairtools-1.1.3-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it
adding 'pairtools/__init__.py'
adding 'pairtools/__main__.py'
adding 'pairtools/_logging.py'
@@ -1667,7 +1703,7 @@
sum(list(n_cis_pairs_above_convergence_dist.values())) / norm_factor )
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
-================ 31 passed, 3 deselected, 6 warnings in 41.20s =================
+=========== 31 passed, 3 deselected, 6 warnings in 155.39s (0:02:35) ===========
make[1]: Leaving directory '/build/reproducible-path/pairtools-1.1.3'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=pybuild
@@ -1703,8 +1739,8 @@
dpkg-gencontrol: warning: Depends field of package python3-pairtools-examples: substitution variable ${shlibs:Depends} used, but is not defined
dh_md5sums -O--buildsystem=pybuild
dh_builddeb -O--buildsystem=pybuild
-dpkg-deb: building package 'python3-pairtools' in '../python3-pairtools_1.1.3-1_amd64.deb'.
dpkg-deb: building package 'python3-pairtools-dbgsym' in '../python3-pairtools-dbgsym_1.1.3-1_amd64.deb'.
+dpkg-deb: building package 'python3-pairtools' in '../python3-pairtools_1.1.3-1_amd64.deb'.
dpkg-deb: building package 'python3-pairtools-examples' in '../python3-pairtools-examples_1.1.3-1_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../pairtools_1.1.3-1_amd64.buildinfo
dpkg-genchanges --build=binary -O../pairtools_1.1.3-1_amd64.changes
@@ -1713,12 +1749,14 @@
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: including full source code in upload
I: copying local configuration
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3092629/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
-I: removing directory /srv/workspace/pbuilder/3714857 and its subdirectories
-I: Current time: Wed Apr 15 05:30:12 -12 2026
-I: pbuilder-time-stamp: 1776274212
+I: removing directory /srv/workspace/pbuilder/3092629 and its subdirectories
+I: Current time: Fri Mar 14 01:19:58 +14 2025
+I: pbuilder-time-stamp: 1741864798