Diff of the two buildlogs: -- --- b1/build.log 2024-12-22 06:05:04.679347926 +0000 +++ b2/build.log 2024-12-22 06:10:13.337349015 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Dec 21 17:57:17 -12 2024 -I: pbuilder-time-stamp: 1734847037 +I: Current time: Sun Jan 25 02:28:06 +14 2026 +I: pbuilder-time-stamp: 1769257686 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ 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/4140341/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1040544/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 Jan 24 12:28 /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/1040544/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1040544/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=20 ' - 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=42 ' + 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='681903bc60cc455592311f60114065f2' - 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='4140341' - PS1='# ' - PS2='> ' + INVOCATION_ID=1ff06c29619d49dd8fa0a882bd8da206 + 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=1040544 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.OtQT22mW/pbuilderrc_fIUz --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.OtQT22mW/b1 --logfile b1/build.log pairtools_1.1.2-1.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://46.16.76.132:3128' + 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.OtQT22mW/pbuilderrc_Ffvl --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.OtQT22mW/b2 --logfile b2/build.log pairtools_1.1.2-1.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://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4140341/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1040544/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -385,7 +417,7 @@ Get: 234 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.3.4-1 [250 kB] Get: 235 http://deb.debian.org/debian unstable/main amd64 python3-standard-pipes all 3.13.0-3 [7144 B] Get: 236 http://deb.debian.org/debian unstable/main amd64 python3-yaml amd64 6.0.2-1+b1 [178 kB] -Fetched 155 MB in 7s (23.4 MB/s) +Fetched 155 MB in 2s (102 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-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 ... 19967 files and directories currently installed.) @@ -1151,8 +1183,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Dec 22 05:58:39 UTC 2024. -Universal Time is now: Sun Dec 22 05:58:39 UTC 2024. +Local time is now: Sat Jan 24 12:29:10 UTC 2026. +Universal Time is now: Sat Jan 24 12:29:10 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... @@ -1370,7 +1402,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pairtools-1.1.2/ && 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_1.1.2-1_source.changes +I: user script /srv/workspace/pbuilder/1040544/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1040544/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pairtools-1.1.2/ && 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_1.1.2-1_source.changes dpkg-buildpackage: info: source package pairtools dpkg-buildpackage: info: source version 1.1.2-1 dpkg-buildpackage: info: source distribution unstable @@ -1401,9 +1437,9 @@ 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-1.1.2/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 @@ -1411,41 +1447,41 @@ running build running build_py creating build/lib.linux-x86_64-cpython-313/pairtools +copying pairtools/__main__.py -> build/lib.linux-x86_64-cpython-313/pairtools copying pairtools/__init__.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/stats.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/filterbycov.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/__init__.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/scaling.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/select.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/pairsam_format.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/headerops.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib creating 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/flip.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/restrict.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/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/markasdup.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/flip.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/scaling.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/parse.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/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/phase.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/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/__init__.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/merge.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/stats.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/header.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli +copying pairtools/cli/phase.py -> build/lib.linux-x86_64-cpython-313/pairtools/cli +creating 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/scaling.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/__init__.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/select.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/filterbycov.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/restrict.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib +copying pairtools/lib/phase.py -> build/lib.linux-x86_64-cpython-313/pairtools/lib running egg_info creating pairtools.egg-info writing pairtools.egg-info/PKG-INFO @@ -1472,8 +1508,24 @@ 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 -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/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-1.1.2=. -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 -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/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/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, + 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 pairtools/lib/dedup_cython.c:1240: +/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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-1.1.2=. -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/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/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/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, @@ -1492,74 +1544,58 @@ 10 | Py_DEPRECATED(3.13) typedef wchar_t Py_UNICODE; | ^~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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-1.1.2=. -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 -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/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/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, - 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 pairtools/lib/dedup_cython.c:1240: -/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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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 -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/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-1.1.2=. -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/__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/sort.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/dedup.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/scaling.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/sample.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/__init__.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/merge.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/stats.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/header.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/__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/regions.pyx -> 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/parse_pysam.pyx -> 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/scaling.py -> 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/restrict.py -> 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/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/dedup_cython.pyx -> 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/fileio.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/dedup.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.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/select.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/pairsam_format.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/parse_pysam.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/select.py -> 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/headerops.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/stats.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/merge.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/parse2.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/markasdup.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/dedup.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/select.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/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/header.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/lib/regions.pyx -> 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/pairsio.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/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/restrict.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 running install_egg_info Copying pairtools.egg-info to build/bdist.linux-x86_64/wheel/./pairtools-1.1.2.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pairtools-1.1.2.dist-info/WHEEL -creating '/build/reproducible-path/pairtools-1.1.2/.pybuild/cpython3_3.13/.tmp-2gegi8rq/pairtools-1.1.2-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/pairtools-1.1.2/.pybuild/cpython3_3.13/.tmp-urn0uybs/pairtools-1.1.2-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' @@ -1616,41 +1652,41 @@ running build running build_py creating build/lib.linux-x86_64-cpython-312/pairtools +copying pairtools/__main__.py -> build/lib.linux-x86_64-cpython-312/pairtools copying pairtools/__init__.py -> build/lib.linux-x86_64-cpython-312/pairtools copying pairtools/_logging.py -> build/lib.linux-x86_64-cpython-312/pairtools -copying pairtools/__main__.py -> build/lib.linux-x86_64-cpython-312/pairtools -creating build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/stats.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/restrict.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/filterbycov.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/fileio.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/dedup.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/scaling.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/pairsio.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/select.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/parse.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/pairsam_format.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/phase.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib -copying pairtools/lib/headerops.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib creating build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/stats.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/flip.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/merge.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/restrict.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/parse2.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli copying pairtools/cli/sort.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/filterbycov.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/markasdup.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/__init__.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/flip.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli copying pairtools/cli/dedup.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/scaling.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/select.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli copying pairtools/cli/parse.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/scaling.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/markasdup.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli copying pairtools/cli/split.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/phase.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli -copying pairtools/cli/header.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli copying pairtools/cli/sample.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/parse2.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/__init__.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/select.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/merge.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/filterbycov.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/stats.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/restrict.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/header.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +copying pairtools/cli/phase.py -> build/lib.linux-x86_64-cpython-312/pairtools/cli +creating build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/dedup.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/parse.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/scaling.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/fileio.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/__init__.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/pairsam_format.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/select.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/headerops.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/filterbycov.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/pairsio.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/stats.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/restrict.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib +copying pairtools/lib/phase.py -> build/lib.linux-x86_64-cpython-312/pairtools/lib running egg_info writing pairtools.egg-info/PKG-INFO writing dependency_links to pairtools.egg-info/dependency_links.txt @@ -1675,82 +1711,82 @@ copying pairtools/lib/parse_pysam.pyx -> build/lib.linux-x86_64-cpython-312/pairtools/lib copying pairtools/lib/regions.pyx -> build/lib.linux-x86_64-cpython-312/pairtools/lib running build_ext -building 'pairtools.lib.regions' extension +building 'pairtools.lib.parse_pysam' extension creating build/temp.linux-x86_64-cpython-312/pairtools/lib -x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c pairtools/lib/regions.cpp -o build/temp.linux-x86_64-cpython-312/pairtools/lib/regions.o +x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c pairtools/lib/parse_pysam.c -o build/temp.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.o +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-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-312-x86_64-linux-gnu.so +building 'pairtools.lib.dedup_cython' extension +x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c pairtools/lib/dedup_cython.c -o build/temp.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 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 pairtools/lib/regions.cpp:1302: + from pairtools/lib/dedup_cython.c:1240: /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-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pairtools/lib/regions.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pairtools/lib/regions.cpython-312-x86_64-linux-gnu.so -building 'pairtools.lib.dedup_cython' extension -x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c pairtools/lib/dedup_cython.c -o build/temp.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.o +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-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.cpython-312-x86_64-linux-gnu.so +building 'pairtools.lib.regions' extension +x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c pairtools/lib/regions.cpp -o build/temp.linux-x86_64-cpython-312/pairtools/lib/regions.o In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1929, 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 pairtools/lib/dedup_cython.c:1240: + from pairtools/lib/regions.cpp:1302: /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 -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.cpython-312-x86_64-linux-gnu.so -building 'pairtools.lib.parse_pysam' extension -x86_64-linux-gnu-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/lib/python3/dist-packages/numpy/core/include -c pairtools/lib/parse_pysam.c -o build/temp.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.o -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-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabixproxies.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcfaidx.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcsamfile.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcvcf.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libcbcf.cpython-312-x86_64-linux-gnu.so /usr/lib/python3/dist-packages/pysam/libctabix.cpython-312-x86_64-linux-gnu.so +x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/pairtools-1.1.2=. -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-1.1.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-cpython-312/pairtools/lib/regions.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/pairtools/lib/regions.cpython-312-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-312/pairtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools -copying build/lib.linux-x86_64-cpython-312/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-312/pairtools/lib/regions.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/stats.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/fileio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/pairsio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/regions.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/pairsam_format.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.pxd -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib -copying build/lib.linux-x86_64-cpython-312/pairtools/lib/headerops.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib copying build/lib.linux-x86_64-cpython-312/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-312/pairtools/cli/stats.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/flip.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/merge.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/parse2.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli copying build/lib.linux-x86_64-cpython-312/pairtools/cli/sort.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/markasdup.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/flip.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli copying build/lib.linux-x86_64-cpython-312/pairtools/cli/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli copying build/lib.linux-x86_64-cpython-312/pairtools/cli/parse.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/markasdup.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli copying build/lib.linux-x86_64-cpython-312/pairtools/cli/split.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli -copying build/lib.linux-x86_64-cpython-312/pairtools/cli/header.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli copying build/lib.linux-x86_64-cpython-312/pairtools/cli/sample.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/parse2.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/merge.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/stats.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/header.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/cli/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/cli +copying build/lib.linux-x86_64-cpython-312/pairtools/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools +copying build/lib.linux-x86_64-cpython-312/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-312/pairtools/lib/parse_pysam.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/regions.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/scaling.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.pxd -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/fileio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/__init__.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/pairsam_format.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/select.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/dedup_cython.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/headerops.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/regions.pyx -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/filterbycov.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/pairsio.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/stats.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/restrict.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/phase.py -> build/bdist.linux-x86_64/wheel/./pairtools/lib +copying build/lib.linux-x86_64-cpython-312/pairtools/lib/parse_pysam.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./pairtools/lib running install_egg_info Copying pairtools.egg-info to build/bdist.linux-x86_64/wheel/./pairtools-1.1.2.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/pairtools-1.1.2.dist-info/WHEEL -creating '/build/reproducible-path/pairtools-1.1.2/.pybuild/cpython3_3.12/.tmp-4rdgyqkh/pairtools-1.1.2-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it +creating '/build/reproducible-path/pairtools-1.1.2/.pybuild/cpython3_3.12/.tmp-bjoghwe0/pairtools-1.1.2-cp312-cp312-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' @@ -1872,7 +1908,7 @@ 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 71.20s (0:01:11) ============ +================ 31 passed, 3 deselected, 6 warnings in 34.41s ================= I: pybuild base:311: export CURPY=python3.12; cd /build/reproducible-path/pairtools-1.1.2/.pybuild/cpython3_3.12/build && python3.12 -m pytest -v -k 'not test_dedup and not test_mock_pysam_parse2_single_end' ============================= test session starts ============================== platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0 -- /usr/bin/python3.12 @@ -1941,7 +1977,7 @@ 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 74.13s (0:01:14) ============ +================ 31 passed, 3 deselected, 6 warnings in 36.75s ================= make[1]: Leaving directory '/build/reproducible-path/pairtools-1.1.2' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild @@ -1975,9 +2011,9 @@ dpkg-gencontrol: warning: package python3-pairtools-examples: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild +dpkg-deb: building package 'python3-pairtools-dbgsym' in '../python3-pairtools-dbgsym_1.1.2-1_amd64.deb'. dpkg-deb: building package 'python3-pairtools' in '../python3-pairtools_1.1.2-1_amd64.deb'. dpkg-deb: building package 'python3-pairtools-examples' in '../python3-pairtools-examples_1.1.2-1_amd64.deb'. -dpkg-deb: building package 'python3-pairtools-dbgsym' in '../python3-pairtools-dbgsym_1.1.2-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../pairtools_1.1.2-1_amd64.buildinfo dpkg-genchanges --build=binary -O../pairtools_1.1.2-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -1985,12 +2021,14 @@ 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/1040544/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1040544/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/4140341 and its subdirectories -I: Current time: Sat Dec 21 18:05:04 -12 2024 -I: pbuilder-time-stamp: 1734847504 +I: removing directory /srv/workspace/pbuilder/1040544 and its subdirectories +I: Current time: Sun Jan 25 02:33:12 +14 2026 +I: pbuilder-time-stamp: 1769257992