I: pbuilder: network access will be disabled during build I: Current time: Sun Nov 23 21:54:05 +14 2025 I: pbuilder-time-stamp: 1763884445 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [python-bx_0.13.0-1.dsc] I: copying [./python-bx_0.13.0.orig.tar.gz] I: copying [./python-bx_0.13.0-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sun Sep 22 12:26:19 2024 gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A gpgv: issuer "tchet@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./python-bx_0.13.0-1.dsc: no acceptable signature found dpkg-source: info: extracting python-bx in python-bx-0.13.0 dpkg-source: info: unpacking python-bx_0.13.0.orig.tar.gz dpkg-source: info: unpacking python-bx_0.13.0-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying spelling dpkg-source: info: applying shebang.patch dpkg-source: info: applying fix_BIN_OFFSETS_MAX I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2863652/tmp/hooks/D01_modify_environment starting debug: Running on infom02-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 Nov 23 07:54 /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/2863652/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2863652/tmp/hooks/D02_print_environment starting I: set 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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.32(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=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=a6f7bbcc5aa64a98bfb0b34d1a8991ed 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=2863652 PS4='+ ' 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.sG009pLB/pbuilderrc_IEpy --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.sG009pLB/b2 --logfile b2/build.log python-bx_0.13.0-1.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' I: uname -a Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2863652/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, zlib1g-dev, python3-setuptools, pybuild-plugin-pyproject, python3-all-dev:any, python3-lzo, python3-pyparsing, python3-pytest, python3-pytest-cython, python3-numpy, cython3 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19799 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev:any. pbuilder-satisfydepends-dummy depends on python3-lzo; however: Package python3-lzo is not installed. pbuilder-satisfydepends-dummy depends on python3-pyparsing; however: Package python3-pyparsing is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest; however: Package python3-pytest is not installed. pbuilder-satisfydepends-dummy depends on python3-pytest-cython; however: Package python3-pytest-cython is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on cython3; however: Package cython3 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cython3{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libcom-err2{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgssapi-krb5-2{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libnsl2{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libreadline8t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} pybuild-plugin-pyproject{a} python3{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-build{a} python3-dev{a} python3-inflect{a} python3-iniconfig{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-lzo{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytest-cython{a} python3-setuptools{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-wheel{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pygments wget 0 packages upgraded, 94 newly installed, 0 to remove and 0 not upgraded. Need to get 48.4 MB of archives. After unpacking 204 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 12 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-5 [1181 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.2-9 [97.2 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.72-3 [493 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 cython3 amd64 3.0.11+dfsg-1 [2449 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 45 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-2 [188 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5 [9396 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.1 [699 kB] Get: 49 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.20 [915 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 55 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 59 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 python3-zipp all 3.20.2-1 [10.3 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 python3-setuptools all 74.1.2-2 [736 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 dh-python all 6.20240824 [109 kB] Get: 64 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.3-1 [157 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-6 [836 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-3 [158 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 liblzo2-2 amd64 2.10-3 [54.4 kB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.6-1 [2147 kB] Get: 73 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 74 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.6-1 [5127 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get: 76 http://deb.debian.org/debian trixie/main amd64 libpython3-all-dev amd64 3.12.6-1 [1064 B] Get: 77 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 python3-pyproject-hooks all 1.1.0-2 [11.3 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 python3-wheel all 0.44.0-2 [53.4 kB] Get: 81 http://deb.debian.org/debian trixie/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get: 82 http://deb.debian.org/debian trixie/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 pybuild-plugin-pyproject all 6.20240824 [11.2 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 python3-all amd64 3.12.6-1 [1040 B] Get: 85 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.6-1 [506 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 python3-all-dev amd64 3.12.6-1 [1068 B] Get: 88 http://deb.debian.org/debian trixie/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 89 http://deb.debian.org/debian trixie/main amd64 python3-lzo amd64 1.15-2 [8472 B] Get: 90 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 python3-pluggy all 1.5.0-1 [26.9 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 python3-pytest all 8.3.3-1 [249 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 python3-pytest-cython all 0.1.1-1 [8068 B] Fetched 48.4 MB in 2s (23.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. 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Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (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 ... 20119 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package tzdata. Preparing to unpack .../03-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../05-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../06-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../12-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../14-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (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 ... 21191 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package sensible-utils. 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Unpacking python3-pytest-cython (0.1.1-1) ... Setting up media-types (10.1.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-5) ... Setting up bsdextrautils (2.40.2-9) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.20) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.22.5-2) ... Setting up m4 (1.4.19-4) ... Setting up liblzo2-2:amd64 (2.10-3) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Nov 23 07:54:40 UTC 2025. Universal Time is now: Sun Nov 23 07:54:40 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libexpat1-dev:amd64 (2.6.3-1) ... Setting up autopoint (0.22.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-6) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libjs-sphinxdoc (7.4.7-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up debhelper (13.20) ... Setting up libpython3.12t64:amd64 (3.12.6-1) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.6-1) ... Setting up python3-zipp (3.20.2-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-wheel (0.44.0-2) ... Setting up python3-packaging (24.1-1) ... Setting up python3-pyproject-hooks (1.1.0-2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3.12-dev (3.12.6-1) ... Setting up cython3 (3.0.11+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-pluggy (1.5.0-1) ... Setting up python3-build (1.2.2-1) ... Setting up python3-lzo:amd64 (1.15-2) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pytest (8.3.3-1) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-all (3.12.6-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libpython3-all-dev:amd64 (3.12.6-1) ... Setting up python3-dev (3.12.6-1) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-all-dev (3.12.6-1) ... Setting up python3-setuptools (74.1.2-2) ... Setting up python3-pytest-cython (0.1.1-1) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up dh-python (6.20240824) ... Setting up pybuild-plugin-pyproject (6.20240824) ... Processing triggers for libc-bin (2.40-3) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2863652/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2863652/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/python-bx-0.13.0/ && 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 > ../python-bx_0.13.0-1_source.changes dpkg-buildpackage: info: source package python-bx dpkg-buildpackage: info: source version 0.13.0-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Alexandre Detiste dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/python-bx-0.13.0' find -name "*.pyx" | sed 's/pyx$/c/' | xargs rm -f grep -rli "Generated by Cython" lib/ | xargs -r rm rm -rf lib/bx_python.egg-info make[1]: Leaving directory '/build/reproducible-path/python-bx-0.13.0' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild dh_auto_build -O--buildsystem=pybuild I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python * Building wheel... running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-cpython-312 creating build/lib.linux-x86_64-cpython-312/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.linux-x86_64-cpython-312/bx_extras copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-312/bx_extras copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-312/bx_extras copying lib/bx_extras/pstat.py -> build/lib.linux-x86_64-cpython-312/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.linux-x86_64-cpython-312/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.linux-x86_64-cpython-312/bx_extras creating build/lib.linux-x86_64-cpython-312/bx copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/filter.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/bitset_tests.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/wiggle.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/interval_index_file_tests.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/binned_array.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-312/bx copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-312/bx creating build/lib.linux-x86_64-cpython-312/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/tabular copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-312/bx/tabular creating build/lib.linux-x86_64-cpython-312/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-312/bx/cookbook creating build/lib.linux-x86_64-cpython-312/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-312/bx/motif copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-312/bx/motif creating build/lib.linux-x86_64-cpython-312/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-312/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.linux-x86_64-cpython-312/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.linux-x86_64-cpython-312/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intervals copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-312/bx/intervals creating build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-312/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-312/bx/pwm creating build/lib.linux-x86_64-cpython-312/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-312/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.linux-x86_64-cpython-312/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-312/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-312/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/phylo creating build/lib.linux-x86_64-cpython-312/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intseq creating build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/nib.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/core.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/qdna.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-312/bx/seq copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-312/bx/seq creating build/lib.linux-x86_64-cpython-312/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-312/bx/bbi creating build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/lav_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/core.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/maf_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align copying lib/bx/align/epo_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align creating build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-312/bx/misc creating build/lib.linux-x86_64-cpython-312/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-312/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/arrays creating build/lib.linux-x86_64-cpython-312/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif/logo creating build/lib.linux-x86_64-cpython-312/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-312/bx/motif/io creating build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-312/bx/intervals/operations creating build/lib.linux-x86_64-cpython-312/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-312/bx/align/tools creating build/lib.linux-x86_64-cpython-312/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-312/bx/align/sitemask copying lib/bx/motif/logo/template.ps -> build/lib.linux-x86_64-cpython-312/bx/motif/logo running build_ext /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/python-bx-0.13.0/lib/bx/bitset.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/bitset.pyx because it changed. [1/1] Cythonizing lib/bx/bitset.pyx building 'bx.bitset' extension creating build/temp.linux-x86_64-cpython-312 creating build/temp.linux-x86_64-cpython-312/lib creating build/temp.linux-x86_64-cpython-312/lib/bx creating build/temp.linux-x86_64-cpython-312/src creating build/temp.linux-x86_64-cpython-312/src/kent 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.12 -c lib/bx/bitset.c -o build/temp.linux-x86_64-cpython-312/lib/bx/bitset.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.12 -c src/binBits.c -o build/temp.linux-x86_64-cpython-312/src/binBits.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.12 -c src/kent/bits.c -o build/temp.linux-x86_64-cpython-312/src/kent/bits.o src/kent/bits.c:9:19: warning: ‘rcsid’ defined but not used [-Wunused-const-variable=] 9 | static char const rcsid[] = "$Id: bits.c,v 1.20 2008/03/25 16:32:31 angie Exp $"; | ^~~~~ 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/kent -Isrc -I/usr/include/python3.12 -c src/kent/common.c -o build/temp.linux-x86_64-cpython-312/src/kent/common.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/bitset.o build/temp.linux-x86_64-cpython-312/src/binBits.o build/temp.linux-x86_64-cpython-312/src/kent/bits.o build/temp.linux-x86_64-cpython-312/src/kent/common.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/bitset.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/intervals/intersection.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/intervals/intersection.pyx because it changed. [1/1] Cythonizing lib/bx/intervals/intersection.pyx building 'bx.intervals.intersection' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/intervals 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/intervals/intersection.c -o build/temp.linux-x86_64-cpython-312/lib/bx/intervals/intersection.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/intervals/intersection.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/intervals/intersection.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/align/_core.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/align/_core.pyx because it changed. [1/1] Cythonizing lib/bx/align/_core.pyx building 'bx.align._core' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/align 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/align/_core.c -o build/temp.linux-x86_64-cpython-312/lib/bx/align/_core.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/align/_core.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/align/_core.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/seq/_nib.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/seq/_nib.pyx because it changed. [1/1] Cythonizing lib/bx/seq/_nib.pyx building 'bx.seq._nib' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/seq 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/seq/_nib.c -o build/temp.linux-x86_64-cpython-312/lib/bx/seq/_nib.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/seq/_nib.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/seq/_nib.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/seq/_twobit.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/seq/_twobit.pyx because it changed. [1/1] Cythonizing lib/bx/seq/_twobit.pyx building 'bx.seq._twobit' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/seq/_twobit.c -o build/temp.linux-x86_64-cpython-312/lib/bx/seq/_twobit.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/seq/_twobit.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/seq/_twobit.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/_seqmapping.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/_seqmapping.pyx because it changed. [1/1] Cythonizing lib/bx/_seqmapping.pyx building 'bx._seqmapping' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/_seqmapping.c -o build/temp.linux-x86_64-cpython-312/lib/bx/_seqmapping.o In function ‘__pyx_pf_2bx_11_seqmapping_15IntToIntMapping___cinit__’, inlined from ‘__pyx_pw_2bx_11_seqmapping_15IntToIntMapping_1__cinit__’ at lib/bx/_seqmapping.c:5104:13, inlined from ‘__pyx_tp_new_2bx_11_seqmapping_IntToIntMapping’ at lib/bx/_seqmapping.c:8107:7: lib/bx/_seqmapping.c:5142:33: warning: argument 1 value ‘18446744073709551612’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 5142 | __pyx_v_self->table = ((int *)malloc((__pyx_v_in_size * (sizeof(int))))); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/python3.12/Python.h:23, from lib/bx/_seqmapping.c:29: /usr/include/stdlib.h: In function ‘__pyx_tp_new_2bx_11_seqmapping_IntToIntMapping’: /usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here 672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/_seqmapping.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/_seqmapping.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/misc/bgzf.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/misc/bgzf.pyx because it changed. [1/1] Cythonizing lib/bx/misc/bgzf.pyx building 'bx.misc.bgzf' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/misc creating build/temp.linux-x86_64-cpython-312/src/samtools 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/samtools -I/usr/include/python3.12 -c lib/bx/misc/bgzf.c -o build/temp.linux-x86_64-cpython-312/lib/bx/misc/bgzf.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/samtools -I/usr/include/python3.12 -c src/samtools/bgzf.c -o build/temp.linux-x86_64-cpython-312/src/samtools/bgzf.o src/samtools/bgzf.c: In function ‘cache_block’: src/samtools/bgzf.c:422:47: warning: comparison of integer expressions of different signedness: ‘khint_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 422 | if ((kh_size(h) + 1) * MAX_BLOCK_SIZE > fp->cache_size) { | ^ src/samtools/bgzf.c: In function ‘read_block’: src/samtools/bgzf.c:462:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 462 | if (count != sizeof(header)) { | ^~ src/samtools/bgzf.c: In function ‘bgzf_close’: src/samtools/bgzf.c:603:29: warning: variable ‘count’ set but not used [-Wunused-but-set-variable] 603 | int count, block_length = deflate_block(fp, 0); | ^~~~~ src/samtools/bgzf.c: In function ‘bgzf_check_EOF’: src/samtools/bgzf.c:662:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 662 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/misc/bgzf.o build/temp.linux-x86_64-cpython-312/src/samtools/bgzf.o -L/usr/lib/x86_64-linux-gnu -lz -o build/lib.linux-x86_64-cpython-312/bx/misc/bgzf.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/intervals/cluster.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/intervals/cluster.pyx because it changed. [1/1] Cythonizing lib/bx/intervals/cluster.pyx building 'bx.intervals.cluster' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.12 -c lib/bx/intervals/cluster.c -o build/temp.linux-x86_64-cpython-312/lib/bx/intervals/cluster.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.12 -c src/cluster.c -o build/temp.linux-x86_64-cpython-312/src/cluster.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/intervals/cluster.o build/temp.linux-x86_64-cpython-312/src/cluster.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/intervals/cluster.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/pwm/_position_weight_matrix.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/pwm/_position_weight_matrix.pyx because it changed. [1/1] Cythonizing lib/bx/pwm/_position_weight_matrix.pyx building 'bx.pwm._position_weight_matrix' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/pwm 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.12 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.linux-x86_64-cpython-312/lib/bx/pwm/_position_weight_matrix.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.12 -c src/pwm_utils.c -o build/temp.linux-x86_64-cpython-312/src/pwm_utils.o src/pwm_utils.c: In function ‘main’: src/pwm_utils.c:12:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 12 | if (strlen(argv[2]) != string_size) { | ^~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/pwm/_position_weight_matrix.o build/temp.linux-x86_64-cpython-312/src/pwm_utils.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/pwm/_position_weight_matrix.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/motif/_pwm.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/motif/_pwm.pyx because it changed. [1/1] Cythonizing lib/bx/motif/_pwm.pyx building 'bx.motif._pwm' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/motif 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c lib/bx/motif/_pwm.c -o build/temp.linux-x86_64-cpython-312/lib/bx/motif/_pwm.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 lib/bx/motif/_pwm.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 " \ | ^~~~~~~ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:21: /usr/lib/python3/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1483:1: warning: ‘_import_array’ defined but not used [-Wunused-function] 1483 | _import_array(void) | ^~~~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/motif/_pwm.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/motif/_pwm.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/arrays/array_tree.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/arrays/array_tree.pyx because it changed. [1/1] Cythonizing lib/bx/arrays/array_tree.pyx building 'bx.arrays.array_tree' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/arrays 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c lib/bx/arrays/array_tree.c -o build/temp.linux-x86_64-cpython-312/lib/bx/arrays/array_tree.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 lib/bx/arrays/array_tree.c:1249: /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 -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/arrays/array_tree.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/bbi/bpt_file.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/bbi/bpt_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bpt_file.pyx building 'bx.bbi.bpt_file' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/bbi 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/bbi/bpt_file.c -o build/temp.linux-x86_64-cpython-312/lib/bx/bbi/bpt_file.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/bbi/bpt_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/bbi/bpt_file.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/bbi/cirtree_file.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/bbi/cirtree_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/cirtree_file.pyx building 'bx.bbi.cirtree_file' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/bbi/cirtree_file.c -o build/temp.linux-x86_64-cpython-312/lib/bx/bbi/cirtree_file.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/bbi/cirtree_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/bbi/cirtree_file.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/bbi/bbi_file.pxd tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/bbi/bbi_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bbi_file.pyx building 'bx.bbi.bbi_file' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c lib/bx/bbi/bbi_file.c -o build/temp.linux-x86_64-cpython-312/lib/bx/bbi/bbi_file.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 lib/bx/bbi/bbi_file.c:1249: /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 -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/bbi/bbi_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/bbi/bbi_file.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/bbi/bigwig_file.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/bbi/bigwig_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bigwig_file.pyx building 'bx.bbi.bigwig_file' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c lib/bx/bbi/bigwig_file.c -o build/temp.linux-x86_64-cpython-312/lib/bx/bbi/bigwig_file.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 lib/bx/bbi/bigwig_file.c:1249: /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 " \ | ^~~~~~~ lib/bx/bbi/bigwig_file.c: In function ‘__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_block’: lib/bx/bbi/bigwig_file.c:6522:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__pyx_t_2bx_3bbi_5types_bits32’ {aka ‘unsigned int’} [-Wsign-compare] 6522 | __pyx_t_12 = (__pyx_v_s < __pyx_v_self->start); | ^ lib/bx/bbi/bigwig_file.c:6551:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__pyx_t_2bx_3bbi_5types_bits32’ {aka ‘unsigned int’} [-Wsign-compare] 6551 | __pyx_t_12 = (__pyx_v_e > __pyx_v_self->end); | ^ lib/bx/bbi/bigwig_file.c: In function ‘__pyx_f_2bx_3bbi_11bigwig_file_29ArrayAccumulatingBlockHandler_handle_interval_value’: lib/bx/bbi/bigwig_file.c:8804:76: warning: comparison of integer expressions of different signedness: ‘int’ and ‘__pyx_t_2bx_3bbi_5types_bits32’ {aka ‘unsigned int’} [-Wsign-compare] 8804 | for (__pyx_v_i = (__pyx_v_s - __pyx_v_self->__pyx_base.start); __pyx_v_i < __pyx_t_2; __pyx_v_i++) { | ^ lib/bx/bbi/bigwig_file.c: In function ‘__pyx_f_2bx_3bbi_11bigwig_file_18BigWigBlockHandler_handle_block’: lib/bx/bbi/bigwig_file.c:6551:29: warning: ‘__pyx_v_e’ may be used uninitialized [-Wmaybe-uninitialized] 6551 | __pyx_t_12 = (__pyx_v_e > __pyx_v_self->end); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:5856:7: note: ‘__pyx_v_e’ was declared here 5856 | int __pyx_v_e; | ^~~~~~~~~ lib/bx/bbi/bigwig_file.c:6522:29: warning: ‘__pyx_v_s’ may be used uninitialized [-Wmaybe-uninitialized] 6522 | __pyx_t_12 = (__pyx_v_s < __pyx_v_self->start); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:5855:7: note: ‘__pyx_v_s’ was declared here 5855 | int __pyx_v_s; | ^~~~~~~~~ lib/bx/bbi/bigwig_file.c:6608:18: warning: ‘__pyx_v_val’ may be used uninitialized [-Wmaybe-uninitialized] 6608 | __pyx_t_2 = ((struct __pyx_vtabstruct_2bx_3bbi_11bigwig_file_BigWigBlockHandler *)__pyx_v_self->__pyx_base.__pyx_vtab)->handle_interval_value(__pyx_v_self, __pyx_v_s, __pyx_v_e, __pyx_v_val); if (unlikely(!__pyx_t_2)) __PYX_ERR(0, 88, __pyx_L1_error) | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ lib/bx/bbi/bigwig_file.c:5857:9: note: ‘__pyx_v_val’ was declared here 5857 | float __pyx_v_val; | ^~~~~~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/bbi/bigwig_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_file.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/bbi/bigbed_file.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/bbi/bigbed_file.pyx because it changed. [1/1] Cythonizing lib/bx/bbi/bigbed_file.pyx building 'bx.bbi.bigbed_file' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c lib/bx/bbi/bigbed_file.c -o build/temp.linux-x86_64-cpython-312/lib/bx/bbi/bigbed_file.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 lib/bx/bbi/bigbed_file.c:1249: /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 -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/bbi/bigbed_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/bbi/bigbed_file.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/align/_epo.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/align/_epo.pyx because it changed. [1/1] Cythonizing lib/bx/align/_epo.pyx building 'bx.align._epo' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.12 -c lib/bx/align/_epo.c -o build/temp.linux-x86_64-cpython-312/lib/bx/align/_epo.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 lib/bx/align/_epo.c:1249: /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 " \ | ^~~~~~~ lib/bx/align/_epo.c: In function ‘__pyx_f_2bx_5align_4_epo_bed_union’: lib/bx/align/_epo.c:8904:236: warning: comparison of integer expressions of different signedness: ‘__pyx_t_5numpy_uint64_t’ {aka ‘long unsigned int’} and ‘Py_ssize_t’ {aka ‘long int’} [-Wsign-compare] 8904 | __pyx_t_5 = ((*__Pyx_BufPtrStrided2d(__pyx_t_5numpy_uint64_t *, __pyx_pybuffernd_elements.rcbuffer->pybuffer.buf, __pyx_t_12, __pyx_pybuffernd_elements.diminfo[0].strides, __pyx_t_13, __pyx_pybuffernd_elements.diminfo[1].strides)) <= __pyx_v_cen); | ^~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/align/_epo.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/align/_epo.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/arrays/bed.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/arrays/bed.pyx because it changed. [1/1] Cythonizing lib/bx/arrays/bed.pyx building 'bx.arrays.bed' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/arrays/bed.c -o build/temp.linux-x86_64-cpython-312/lib/bx/arrays/bed.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/arrays/bed.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/arrays/bed.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/arrays/wiggle.pxd tree = Parsing.p_module(s, pxd, full_module_name) warning: lib/bx/arrays/wiggle.pyx:94:20: Unreachable code Compiling lib/bx/arrays/wiggle.pyx because it changed. [1/1] Cythonizing lib/bx/arrays/wiggle.pyx building 'bx.arrays.wiggle' 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/arrays/wiggle.c -o build/temp.linux-x86_64-cpython-312/lib/bx/arrays/wiggle.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/arrays/wiggle.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/arrays/wiggle.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/align/sitemask/_cpg.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/align/sitemask/_cpg.pyx because it changed. [1/1] Cythonizing lib/bx/align/sitemask/_cpg.pyx building 'bx.align.sitemask._cpg' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/align/sitemask 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/align/sitemask/_cpg.c -o build/temp.linux-x86_64-cpython-312/lib/bx/align/sitemask/_cpg.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.12 -c lib/bx/align/sitemask/find_cpg.c -o build/temp.linux-x86_64-cpython-312/lib/bx/align/sitemask/find_cpg.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/align/sitemask/_cpg.o build/temp.linux-x86_64-cpython-312/lib/bx/align/sitemask/find_cpg.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/align/sitemask/_cpg.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/intseq/ngramcount.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/intseq/ngramcount.pyx because it changed. [1/1] Cythonizing lib/bx/intseq/ngramcount.pyx building 'bx.intseq.ngramcount' extension creating build/temp.linux-x86_64-cpython-312/lib/bx/intseq 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc -I/usr/include/python3.12 -c lib/bx/intseq/ngramcount.c -o build/temp.linux-x86_64-cpython-312/lib/bx/intseq/ngramcount.o x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/intseq/ngramcount.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/intseq/ngramcount.cpython-312-x86_64-linux-gnu.so /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/python-bx-0.13.0/lib/bx/misc/_seekbzip2.pyx tree = Parsing.p_module(s, pxd, full_module_name) Compiling lib/bx/misc/_seekbzip2.pyx because it changed. [1/1] Cythonizing lib/bx/misc/_seekbzip2.pyx building 'bx.misc._seekbzip2' extension creating build/temp.linux-x86_64-cpython-312/src/bunzip 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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/bunzip -I/usr/include/python3.12 -c lib/bx/misc/_seekbzip2.c -o build/temp.linux-x86_64-cpython-312/lib/bx/misc/_seekbzip2.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/python-bx-0.13.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Isrc/bunzip -I/usr/include/python3.12 -c src/bunzip/micro-bunzip.c -o build/temp.linux-x86_64-cpython-312/src/bunzip/micro-bunzip.o src/bunzip/micro-bunzip.c: In function ‘get_bits’: src/bunzip/micro-bunzip.c:99:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘char’ [-Wsign-compare] 99 | while (bd->inbufBitCount dbufSize) return RETVAL_DATA_ERROR; | ^ src/bunzip/micro-bunzip.c:298:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 298 | while (bd->inbufBitCountmaxLen) { | ^ src/bunzip/micro-bunzip.c:400:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 400 | if(origPtr>=dbufCount) return RETVAL_DATA_ERROR; | ^~ src/bunzip/micro-bunzip.c: In function ‘start_bunzip’: src/bunzip/micro-bunzip.c:629:26: warning: pointer targets in assignment from ‘char *’ to ‘unsigned char *’ differ in signedness [-Wpointer-sign] 629 | bd->inbuf=inbuf; | ^ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/python-bx-0.13.0=. -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/lib/bx/misc/_seekbzip2.o build/temp.linux-x86_64-cpython-312/src/bunzip/micro-bunzip.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-312/bx/misc/_seekbzip2.cpython-312-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.12 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.12 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.12 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.12 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.12 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.12 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.12 copying and adjusting scripts/pretty_table.py -> build/scripts-3.12 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.12 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.12 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.12 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.12 copying and adjusting scripts/nib_length.py -> build/scripts-3.12 copying and adjusting scripts/maf_chunk.py -> build/scripts-3.12 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.12 copying and adjusting scripts/bed_coverage.py -> build/scripts-3.12 copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.12 copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.12 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.12 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.12 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.12 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.12 copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.12 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.12 copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.12 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.12 copying and adjusting scripts/random_lines.py -> build/scripts-3.12 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.12 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.12 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.12 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.12 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.12 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.12 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.12 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.12 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.12 copying and adjusting scripts/bed_intersect.py -> build/scripts-3.12 copying and adjusting scripts/prefix_lines.py -> build/scripts-3.12 copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.12 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.12 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.12 copying and adjusting scripts/maf_count.py -> build/scripts-3.12 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.12 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.12 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.12 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.12 copying and adjusting scripts/bed_complement.py -> build/scripts-3.12 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.12 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.12 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.12 copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.12 copying and adjusting scripts/align_print_template.py -> build/scripts-3.12 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.12 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.12 copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.12 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.12 copying and adjusting scripts/maf_chop.py -> build/scripts-3.12 copying and adjusting scripts/out_to_chain.py -> build/scripts-3.12 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.12 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.12 copying and adjusting scripts/table_filter.py -> build/scripts-3.12 copying and adjusting scripts/maf_filter.py -> build/scripts-3.12 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.12 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.12 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.12 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.12 copying and adjusting scripts/maf_truncate.py -> build/scripts-3.12 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.12 copying and adjusting scripts/interval_join.py -> build/scripts-3.12 copying and adjusting scripts/table_add_column.py -> build/scripts-3.12 copying and adjusting scripts/line_select.py -> build/scripts-3.12 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.12 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.12 copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.12 copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.12 copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.12 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.12 copying and adjusting scripts/bnMapper.py -> build/scripts-3.12 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.12 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.12 copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.12 copying and adjusting scripts/mask_quality.py -> build/scripts-3.12 copying and adjusting scripts/maf_select.py -> build/scripts-3.12 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.12 copying and adjusting scripts/maf_randomize.py -> build/scripts-3.12 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.12 copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.12 copying and adjusting scripts/maf_tile.py -> build/scripts-3.12 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.12 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.12 copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.12 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.12 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.12 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.12 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.12 changing mode of build/scripts-3.12/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-3.12/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-3.12/lzop_build_offset_table.py from 644 to 755 changing mode of build/scripts-3.12/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-3.12/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-3.12/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-3.12/pretty_table.py from 644 to 755 changing mode of build/scripts-3.12/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.12/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-3.12/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-3.12/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-3.12/nib_length.py from 644 to 755 changing mode of build/scripts-3.12/maf_chunk.py from 644 to 755 changing mode of build/scripts-3.12/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-3.12/bed_coverage.py from 644 to 755 changing mode of build/scripts-3.12/maf_print_scores.py from 644 to 755 changing mode of build/scripts-3.12/maf_div_sites.py from 644 to 755 changing mode of build/scripts-3.12/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-3.12/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-3.12/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-3.12/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-3.12/axt_to_maf.py from 644 to 755 changing mode of build/scripts-3.12/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-3.12/mMK_bitset.py from 644 to 755 changing mode of build/scripts-3.12/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-3.12/random_lines.py from 644 to 755 changing mode of build/scripts-3.12/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-3.12/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-3.12/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.12/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-3.12/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-3.12/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-3.12/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-3.12/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-3.12/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-3.12/bed_intersect.py from 644 to 755 changing mode of build/scripts-3.12/prefix_lines.py from 644 to 755 changing mode of build/scripts-3.12/maf_col_counts.py from 644 to 755 changing mode of build/scripts-3.12/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-3.12/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-3.12/maf_count.py from 644 to 755 changing mode of build/scripts-3.12/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-3.12/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-3.12/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.12/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.12/bed_complement.py from 644 to 755 changing mode of build/scripts-3.12/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-3.12/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-3.12/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-3.12/one_field_per_line.py from 644 to 755 changing mode of build/scripts-3.12/align_print_template.py from 644 to 755 changing mode of build/scripts-3.12/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-3.12/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-3.12/maf_gc_content.py from 644 to 755 changing mode of build/scripts-3.12/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-3.12/maf_chop.py from 644 to 755 changing mode of build/scripts-3.12/out_to_chain.py from 644 to 755 changing mode of build/scripts-3.12/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-3.12/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-3.12/table_filter.py from 644 to 755 changing mode of build/scripts-3.12/maf_filter.py from 644 to 755 changing mode of build/scripts-3.12/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-3.12/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-3.12/bed_build_windows.py from 644 to 755 changing mode of build/scripts-3.12/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-3.12/maf_truncate.py from 644 to 755 changing mode of build/scripts-3.12/wiggle_to_simple.py from 644 to 755 changing mode of build/scripts-3.12/interval_join.py from 644 to 755 changing mode of build/scripts-3.12/table_add_column.py from 644 to 755 changing mode of build/scripts-3.12/line_select.py from 644 to 755 changing mode of build/scripts-3.12/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-3.12/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-3.12/maf_to_axt.py from 644 to 755 changing mode of build/scripts-3.12/lav_to_maf.py from 644 to 755 changing mode of build/scripts-3.12/maf_tile_2.py from 644 to 755 changing mode of build/scripts-3.12/maf_build_index.py from 644 to 755 changing mode of build/scripts-3.12/bnMapper.py from 644 to 755 changing mode of build/scripts-3.12/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-3.12/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.12/tfloc_summary.py from 644 to 755 changing mode of build/scripts-3.12/mask_quality.py from 644 to 755 changing mode of build/scripts-3.12/maf_select.py from 644 to 755 changing mode of build/scripts-3.12/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-3.12/maf_randomize.py from 644 to 755 changing mode of build/scripts-3.12/axt_to_lav.py from 644 to 755 changing mode of build/scripts-3.12/bed_extend_to.py from 644 to 755 changing mode of build/scripts-3.12/maf_tile.py from 644 to 755 changing mode of build/scripts-3.12/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-3.12/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-3.12/lav_to_axt.py from 644 to 755 changing mode of build/scripts-3.12/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-3.12/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-3.12/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.12/maf_covered_regions.py from 644 to 755 installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/bx_extras copying build/lib.linux-x86_64-cpython-312/bx_extras/fpconst_tests.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-312/bx_extras/stats.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-312/bx_extras/__init__.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-312/bx_extras/pstat.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-312/bx_extras/fpconst.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-312/bx_extras/lrucache.py -> build/bdist.linux-x86_64/wheel/./bx_extras creating build/bdist.linux-x86_64/wheel/bx copying build/lib.linux-x86_64-cpython-312/bx/bitset_utils.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/filter.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/wiggle_tests.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/tabular copying build/lib.linux-x86_64-cpython-312/bx/tabular/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/tabular copying build/lib.linux-x86_64-cpython-312/bx/tabular/io.py -> build/bdist.linux-x86_64/wheel/./bx/tabular creating build/bdist.linux-x86_64/wheel/bx/cookbook copying build/lib.linux-x86_64-cpython-312/bx/cookbook/doc_optparse.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook copying build/lib.linux-x86_64-cpython-312/bx/cookbook/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook copying build/lib.linux-x86_64-cpython-312/bx/cookbook/attribute.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook copying build/lib.linux-x86_64-cpython-312/bx/bitset.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/motif copying build/lib.linux-x86_64-cpython-312/bx/motif/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif creating build/bdist.linux-x86_64/wheel/bx/motif/logo copying build/lib.linux-x86_64-cpython-312/bx/motif/logo/template.ps -> build/bdist.linux-x86_64/wheel/./bx/motif/logo copying build/lib.linux-x86_64-cpython-312/bx/motif/logo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/logo creating build/bdist.linux-x86_64/wheel/bx/motif/io copying build/lib.linux-x86_64-cpython-312/bx/motif/io/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io copying build/lib.linux-x86_64-cpython-312/bx/motif/io/transfac.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io copying build/lib.linux-x86_64-cpython-312/bx/motif/io/transfac_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io copying build/lib.linux-x86_64-cpython-312/bx/motif/_pwm.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/motif copying build/lib.linux-x86_64-cpython-312/bx/motif/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif copying build/lib.linux-x86_64-cpython-312/bx/motif/pwm.py -> build/bdist.linux-x86_64/wheel/./bx/motif creating build/bdist.linux-x86_64/wheel/bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/cluster_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/intersection_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/random_intervals.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/cluster.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/intersection.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-312/bx/intervals/io.py -> build/bdist.linux-x86_64/wheel/./bx/intervals creating build/bdist.linux-x86_64/wheel/bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/base_coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/complement.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/find_clusters.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/concat.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/intersect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/subtract.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/merge.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/quicksect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/intervals/operations/join.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-312/bx/bitset_tests.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/wiggle.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/bitset_builders.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_positions.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/maf_select_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/bed_score_aligned_string.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/pwm_score_maf.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/position_weight_matrix.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-312/bx/pwm/_position_weight_matrix.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/pwm creating build/bdist.linux-x86_64/wheel/bx/phylo copying build/lib.linux-x86_64-cpython-312/bx/phylo/phast.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-312/bx/phylo/phast_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-312/bx/phylo/newick.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-312/bx/phylo/newick_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-312/bx/phylo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/phylo creating build/bdist.linux-x86_64/wheel/bx/intseq copying build/lib.linux-x86_64-cpython-312/bx/intseq/ngramcount.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intseq copying build/lib.linux-x86_64-cpython-312/bx/intseq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intseq creating build/bdist.linux-x86_64/wheel/bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/nib_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/qdna_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/nib.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/core.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/seq_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/qdna.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/_nib.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/fasta_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/twobit_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/_twobit.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/twobit.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/seq.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-312/bx/seq/fasta.py -> build/bdist.linux-x86_64/wheel/./bx/seq creating build/bdist.linux-x86_64/wheel/bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/bpt_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigbed_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/bigwig_tests.py -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/bbi_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/bbi/cirtree_file.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-312/bx/seqmapping_tests.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/interval_index_file.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/_epo.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align creating build/bdist.linux-x86_64/wheel/bx/align/tools copying build/lib.linux-x86_64-cpython-312/bx/align/tools/fuse.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-312/bx/align/tools/thread.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-312/bx/align/tools/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-312/bx/align/tools/chop.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-312/bx/align/tools/tile.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-312/bx/align/lav_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/lav.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/epo.py -> build/bdist.linux-x86_64/wheel/./bx/align creating build/bdist.linux-x86_64/wheel/bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/sitemask_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/quality.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/core.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/_cpg.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/sitemask/cpg.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-312/bx/align/core.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/score.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/maf.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/maf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/_core.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/axt.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/score_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-312/bx/align/epo_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align creating build/bdist.linux-x86_64/wheel/bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/cdb_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/_seekbzip2.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/seekbzip2_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/cdb.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/seeklzop_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/bgzf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/filecache.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/binary_file.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/seekbzip2.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/filecache_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/readlengths.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/bgzf.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/misc/seeklzop.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-312/bx/__init__.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/interval_index_file_tests.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/arrays copying build/lib.linux-x86_64-cpython-312/bx/arrays/bed.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree_tests.py -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-312/bx/arrays/array_tree.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-312/bx/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-312/bx/arrays/wiggle.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-312/bx/binned_array.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/gene_reader.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/binned_array_tests.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/_seqmapping.cpython-312-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-312/bx/seqmapping.py -> build/bdist.linux-x86_64/wheel/./bx running install_egg_info running egg_info creating lib/bx_python.egg-info writing lib/bx_python.egg-info/PKG-INFO writing dependency_links to lib/bx_python.egg-info/dependency_links.txt writing requirements to lib/bx_python.egg-info/requires.txt writing top-level names to lib/bx_python.egg-info/top_level.txt writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest file 'lib/bx_python.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'lib/bx_python.egg-info/SOURCES.txt' Copying lib/bx_python.egg-info to build/bdist.linux-x86_64/wheel/./bx_python-0.13.0.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/wiggle_to_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_thread_for_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/lzop_build_offset_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/axt_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_split_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/find_in_sorted_file.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/pretty_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/aggregate_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/gene_fourfold_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_filter_max_wc.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_rand_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/nib_length.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_chunk.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_bigwig_profile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_coverage.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_print_scores.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_div_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_subtract_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_count_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_gap_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/axt_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/div_snp_table_chr.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/mMK_bitset.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/random_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_count_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_to_concat_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/get_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_shuffle_columns.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_limit_to_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/qv_to_bqv.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_merge_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/interval_count_intersections.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_col_counts_all.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/prefix_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_col_counts.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_diff_basewise_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/ucsc_gene_table_to_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_count.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_extract_chrom_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_coverage_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/axt_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_complement.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_drop_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_percent_columns_matching.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_to_int_seqs.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/one_field_per_line.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/align_print_template.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_species_in_all_files.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/wiggle_to_array_tree.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_gc_content.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_intersect_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_chop.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/out_to_chain.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_mask_cpg.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_print_chroms.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/table_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_region_coverage_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_extract_ranges_indexed.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_build_windows.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/int_seqs_to_char_strings.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_truncate.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/wiggle_to_simple.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/interval_join.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/table_add_column.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/line_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_mean_length_ungapped_piece.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_translate_chars.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/lav_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_tile_2.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_build_index.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bnMapper.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_interval_alignibility.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/nib_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/tfloc_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/mask_quality.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_mapping_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_randomize.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/axt_to_lav.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/bed_extend_to.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_tile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_tile_2bit.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_percent_identity.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/lav_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/wiggle_to_chr_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_covered_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/nib_chrom_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.12/maf_covered_regions.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_binned_array.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_thread_for_species.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lzop_build_offset_table.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_fasta.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_split_by_src.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/find_in_sorted_file.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/pretty_table.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/aggregate_scores_in_intervals.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/gene_fourfold_sites.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter_max_wc.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_rand_intersect.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_length.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chunk.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_bigwig_profile.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_scores.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_div_sites.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_fasta.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_subtract_basewise.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_by_interval.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gap_frequency.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_maf.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/div_snp_table_chr.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mMK_bitset.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_word_frequency.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/random_lines.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_count_overlapping.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_concat_fasta.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/get_scores_in_intervals.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_shuffle_columns.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_limit_to_species.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/qv_to_bqv.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_merge_overlapping.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_count_intersections.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts_all.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/prefix_lines.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_col_counts.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_diff_basewise_summary.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/ucsc_gene_table_to_intervals.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_count.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_chrom_ranges.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_coverage_by_interval.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_extract_ranges.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_complement.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_drop_overlapping.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_columns_matching.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_int_seqs.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/one_field_per_line.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/align_print_template.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_species_in_all_files.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_array_tree.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_gc_content.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_intersect_basewise.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_chop.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/out_to_chain.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mask_cpg.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_print_chroms.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_filter.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_filter.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_region_coverage_by_src.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_extract_ranges_indexed.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_build_windows.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/int_seqs_to_char_strings.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_truncate.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_simple.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/interval_join.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/table_add_column.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/line_select.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mean_length_ungapped_piece.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_translate_chars.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_to_axt.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_maf.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_build_index.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bnMapper.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_interval_alignibility.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_intervals_to_fasta.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/tfloc_summary.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/mask_quality.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_select.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_mapping_word_frequency.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_randomize.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/axt_to_lav.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/bed_extend_to.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_tile_2bit.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_percent_identity.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/lav_to_axt.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/wiggle_to_chr_binned_array.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_ranges.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/nib_chrom_intervals_to_fasta.py to 755 changing mode of build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts/maf_covered_regions.py to 755 creating build/bdist.linux-x86_64/wheel/bx_python-0.13.0.dist-info/WHEEL creating '/build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/.tmp-xtd2et67/bx_python-0.13.0-cp312-cp312-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'bx/__init__.py' adding 'bx/_seqmapping.cpython-312-x86_64-linux-gnu.so' adding 'bx/binned_array.py' adding 'bx/binned_array_tests.py' adding 'bx/bitset.cpython-312-x86_64-linux-gnu.so' adding 'bx/bitset_builders.py' adding 'bx/bitset_tests.py' adding 'bx/bitset_utils.py' adding 'bx/filter.py' adding 'bx/gene_reader.py' adding 'bx/interval_index_file.py' adding 'bx/interval_index_file_tests.py' adding 'bx/seqmapping.py' adding 'bx/seqmapping_tests.py' adding 'bx/wiggle.py' adding 'bx/wiggle_tests.py' adding 'bx/align/__init__.py' adding 'bx/align/_core.cpython-312-x86_64-linux-gnu.so' adding 'bx/align/_epo.cpython-312-x86_64-linux-gnu.so' adding 'bx/align/axt.py' adding 'bx/align/core.py' adding 'bx/align/epo.py' adding 'bx/align/epo_tests.py' adding 'bx/align/lav.py' adding 'bx/align/lav_tests.py' adding 'bx/align/maf.py' adding 'bx/align/maf_tests.py' adding 'bx/align/score.py' adding 'bx/align/score_tests.py' adding 'bx/align/sitemask/__init__.py' adding 'bx/align/sitemask/_cpg.cpython-312-x86_64-linux-gnu.so' adding 'bx/align/sitemask/core.py' adding 'bx/align/sitemask/cpg.py' adding 'bx/align/sitemask/quality.py' adding 'bx/align/sitemask/sitemask_tests.py' adding 'bx/align/tools/__init__.py' adding 'bx/align/tools/chop.py' adding 'bx/align/tools/fuse.py' adding 'bx/align/tools/thread.py' adding 'bx/align/tools/tile.py' adding 'bx/arrays/__init__.py' adding 'bx/arrays/array_tree.cpython-312-x86_64-linux-gnu.so' adding 'bx/arrays/array_tree_tests.py' adding 'bx/arrays/bed.cpython-312-x86_64-linux-gnu.so' adding 'bx/arrays/wiggle.cpython-312-x86_64-linux-gnu.so' adding 'bx/bbi/__init__.py' adding 'bx/bbi/bbi_file.cpython-312-x86_64-linux-gnu.so' adding 'bx/bbi/bigbed_file.cpython-312-x86_64-linux-gnu.so' adding 'bx/bbi/bigwig_file.cpython-312-x86_64-linux-gnu.so' adding 'bx/bbi/bigwig_tests.py' adding 'bx/bbi/bpt_file.cpython-312-x86_64-linux-gnu.so' adding 'bx/bbi/cirtree_file.cpython-312-x86_64-linux-gnu.so' adding 'bx/cookbook/__init__.py' adding 'bx/cookbook/attribute.py' adding 'bx/cookbook/doc_optparse.py' adding 'bx/intervals/__init__.py' adding 'bx/intervals/cluster.cpython-312-x86_64-linux-gnu.so' adding 'bx/intervals/cluster_tests.py' adding 'bx/intervals/intersection.cpython-312-x86_64-linux-gnu.so' adding 'bx/intervals/intersection_tests.py' adding 'bx/intervals/io.py' adding 'bx/intervals/random_intervals.py' adding 'bx/intervals/operations/__init__.py' adding 'bx/intervals/operations/base_coverage.py' adding 'bx/intervals/operations/complement.py' adding 'bx/intervals/operations/concat.py' adding 'bx/intervals/operations/coverage.py' adding 'bx/intervals/operations/find_clusters.py' adding 'bx/intervals/operations/intersect.py' adding 'bx/intervals/operations/join.py' adding 'bx/intervals/operations/merge.py' adding 'bx/intervals/operations/quicksect.py' adding 'bx/intervals/operations/subtract.py' adding 'bx/intseq/__init__.py' adding 'bx/intseq/ngramcount.cpython-312-x86_64-linux-gnu.so' adding 'bx/misc/__init__.py' adding 'bx/misc/_seekbzip2.cpython-312-x86_64-linux-gnu.so' adding 'bx/misc/bgzf.cpython-312-x86_64-linux-gnu.so' adding 'bx/misc/bgzf_tests.py' adding 'bx/misc/binary_file.py' adding 'bx/misc/cdb.py' adding 'bx/misc/cdb_tests.py' adding 'bx/misc/filecache.py' adding 'bx/misc/filecache_tests.py' adding 'bx/misc/readlengths.py' adding 'bx/misc/seekbzip2.py' adding 'bx/misc/seekbzip2_tests.py' adding 'bx/misc/seeklzop.py' adding 'bx/misc/seeklzop_tests.py' adding 'bx/motif/__init__.py' adding 'bx/motif/_pwm.cpython-312-x86_64-linux-gnu.so' adding 'bx/motif/pwm.py' adding 'bx/motif/pwm_tests.py' adding 'bx/motif/io/__init__.py' adding 'bx/motif/io/transfac.py' adding 'bx/motif/io/transfac_tests.py' adding 'bx/motif/logo/__init__.py' adding 'bx/motif/logo/template.ps' adding 'bx/phylo/__init__.py' adding 'bx/phylo/newick.py' adding 'bx/phylo/newick_tests.py' adding 'bx/phylo/phast.py' adding 'bx/phylo/phast_tests.py' adding 'bx/pwm/__init__.py' adding 'bx/pwm/_position_weight_matrix.cpython-312-x86_64-linux-gnu.so' adding 'bx/pwm/bed_score_aligned_pwm.py' adding 'bx/pwm/bed_score_aligned_string.py' adding 'bx/pwm/maf_select_motifs.py' adding 'bx/pwm/position_weight_matrix.py' adding 'bx/pwm/pwm_score_maf.py' adding 'bx/pwm/pwm_score_motifs.py' adding 'bx/pwm/pwm_score_positions.py' adding 'bx/pwm/pwm_tests.py' adding 'bx/seq/__init__.py' adding 'bx/seq/_nib.cpython-312-x86_64-linux-gnu.so' adding 'bx/seq/_twobit.cpython-312-x86_64-linux-gnu.so' adding 'bx/seq/core.py' adding 'bx/seq/fasta.py' adding 'bx/seq/fasta_tests.py' adding 'bx/seq/nib.py' adding 'bx/seq/nib_tests.py' adding 'bx/seq/qdna.py' adding 'bx/seq/qdna_tests.py' adding 'bx/seq/seq.py' adding 'bx/seq/seq_tests.py' adding 'bx/seq/twobit.py' adding 'bx/seq/twobit_tests.py' adding 'bx/tabular/__init__.py' adding 'bx/tabular/io.py' adding 'bx_extras/__init__.py' adding 'bx_extras/fpconst.py' adding 'bx_extras/fpconst_tests.py' adding 'bx_extras/lrucache.py' adding 'bx_extras/pstat.py' adding 'bx_extras/stats.py' adding 'bx_python-0.13.0.data/scripts/aggregate_scores_in_intervals.py' adding 'bx_python-0.13.0.data/scripts/align_print_template.py' adding 'bx_python-0.13.0.data/scripts/axt_extract_ranges.py' adding 'bx_python-0.13.0.data/scripts/axt_to_fasta.py' adding 'bx_python-0.13.0.data/scripts/axt_to_lav.py' adding 'bx_python-0.13.0.data/scripts/axt_to_maf.py' adding 'bx_python-0.13.0.data/scripts/bed_bigwig_profile.py' adding 'bx_python-0.13.0.data/scripts/bed_build_windows.py' adding 'bx_python-0.13.0.data/scripts/bed_complement.py' adding 'bx_python-0.13.0.data/scripts/bed_count_by_interval.py' adding 'bx_python-0.13.0.data/scripts/bed_count_overlapping.py' adding 'bx_python-0.13.0.data/scripts/bed_coverage.py' adding 'bx_python-0.13.0.data/scripts/bed_coverage_by_interval.py' adding 'bx_python-0.13.0.data/scripts/bed_diff_basewise_summary.py' adding 'bx_python-0.13.0.data/scripts/bed_extend_to.py' adding 'bx_python-0.13.0.data/scripts/bed_intersect.py' adding 'bx_python-0.13.0.data/scripts/bed_intersect_basewise.py' adding 'bx_python-0.13.0.data/scripts/bed_merge_overlapping.py' adding 'bx_python-0.13.0.data/scripts/bed_rand_intersect.py' adding 'bx_python-0.13.0.data/scripts/bed_subtract_basewise.py' adding 'bx_python-0.13.0.data/scripts/bnMapper.py' adding 'bx_python-0.13.0.data/scripts/div_snp_table_chr.py' adding 'bx_python-0.13.0.data/scripts/find_in_sorted_file.py' adding 'bx_python-0.13.0.data/scripts/gene_fourfold_sites.py' adding 'bx_python-0.13.0.data/scripts/get_scores_in_intervals.py' adding 'bx_python-0.13.0.data/scripts/int_seqs_to_char_strings.py' adding 'bx_python-0.13.0.data/scripts/interval_count_intersections.py' adding 'bx_python-0.13.0.data/scripts/interval_join.py' adding 'bx_python-0.13.0.data/scripts/lav_to_axt.py' adding 'bx_python-0.13.0.data/scripts/lav_to_maf.py' adding 'bx_python-0.13.0.data/scripts/line_select.py' adding 'bx_python-0.13.0.data/scripts/lzop_build_offset_table.py' adding 'bx_python-0.13.0.data/scripts/mMK_bitset.py' adding 'bx_python-0.13.0.data/scripts/maf_build_index.py' adding 'bx_python-0.13.0.data/scripts/maf_chop.py' adding 'bx_python-0.13.0.data/scripts/maf_chunk.py' adding 'bx_python-0.13.0.data/scripts/maf_col_counts.py' adding 'bx_python-0.13.0.data/scripts/maf_col_counts_all.py' adding 'bx_python-0.13.0.data/scripts/maf_count.py' adding 'bx_python-0.13.0.data/scripts/maf_covered_ranges.py' adding 'bx_python-0.13.0.data/scripts/maf_covered_regions.py' adding 'bx_python-0.13.0.data/scripts/maf_div_sites.py' adding 'bx_python-0.13.0.data/scripts/maf_drop_overlapping.py' adding 'bx_python-0.13.0.data/scripts/maf_extract_chrom_ranges.py' adding 'bx_python-0.13.0.data/scripts/maf_extract_ranges.py' adding 'bx_python-0.13.0.data/scripts/maf_extract_ranges_indexed.py' adding 'bx_python-0.13.0.data/scripts/maf_filter.py' adding 'bx_python-0.13.0.data/scripts/maf_filter_max_wc.py' adding 'bx_python-0.13.0.data/scripts/maf_gap_frequency.py' adding 'bx_python-0.13.0.data/scripts/maf_gc_content.py' adding 'bx_python-0.13.0.data/scripts/maf_interval_alignibility.py' adding 'bx_python-0.13.0.data/scripts/maf_limit_to_species.py' adding 'bx_python-0.13.0.data/scripts/maf_mapping_word_frequency.py' adding 'bx_python-0.13.0.data/scripts/maf_mask_cpg.py' adding 'bx_python-0.13.0.data/scripts/maf_mean_length_ungapped_piece.py' adding 'bx_python-0.13.0.data/scripts/maf_percent_columns_matching.py' adding 'bx_python-0.13.0.data/scripts/maf_percent_identity.py' adding 'bx_python-0.13.0.data/scripts/maf_print_chroms.py' adding 'bx_python-0.13.0.data/scripts/maf_print_scores.py' adding 'bx_python-0.13.0.data/scripts/maf_randomize.py' adding 'bx_python-0.13.0.data/scripts/maf_region_coverage_by_src.py' adding 'bx_python-0.13.0.data/scripts/maf_select.py' adding 'bx_python-0.13.0.data/scripts/maf_shuffle_columns.py' adding 'bx_python-0.13.0.data/scripts/maf_species_in_all_files.py' adding 'bx_python-0.13.0.data/scripts/maf_split_by_src.py' adding 'bx_python-0.13.0.data/scripts/maf_thread_for_species.py' adding 'bx_python-0.13.0.data/scripts/maf_tile.py' adding 'bx_python-0.13.0.data/scripts/maf_tile_2.py' adding 'bx_python-0.13.0.data/scripts/maf_tile_2bit.py' adding 'bx_python-0.13.0.data/scripts/maf_to_axt.py' adding 'bx_python-0.13.0.data/scripts/maf_to_concat_fasta.py' adding 'bx_python-0.13.0.data/scripts/maf_to_fasta.py' adding 'bx_python-0.13.0.data/scripts/maf_to_int_seqs.py' adding 'bx_python-0.13.0.data/scripts/maf_translate_chars.py' adding 'bx_python-0.13.0.data/scripts/maf_truncate.py' adding 'bx_python-0.13.0.data/scripts/maf_word_frequency.py' adding 'bx_python-0.13.0.data/scripts/mask_quality.py' adding 'bx_python-0.13.0.data/scripts/nib_chrom_intervals_to_fasta.py' adding 'bx_python-0.13.0.data/scripts/nib_intervals_to_fasta.py' adding 'bx_python-0.13.0.data/scripts/nib_length.py' adding 'bx_python-0.13.0.data/scripts/one_field_per_line.py' adding 'bx_python-0.13.0.data/scripts/out_to_chain.py' adding 'bx_python-0.13.0.data/scripts/prefix_lines.py' adding 'bx_python-0.13.0.data/scripts/pretty_table.py' adding 'bx_python-0.13.0.data/scripts/qv_to_bqv.py' adding 'bx_python-0.13.0.data/scripts/random_lines.py' adding 'bx_python-0.13.0.data/scripts/table_add_column.py' adding 'bx_python-0.13.0.data/scripts/table_filter.py' adding 'bx_python-0.13.0.data/scripts/tfloc_summary.py' adding 'bx_python-0.13.0.data/scripts/ucsc_gene_table_to_intervals.py' adding 'bx_python-0.13.0.data/scripts/wiggle_to_array_tree.py' adding 'bx_python-0.13.0.data/scripts/wiggle_to_binned_array.py' adding 'bx_python-0.13.0.data/scripts/wiggle_to_chr_binned_array.py' adding 'bx_python-0.13.0.data/scripts/wiggle_to_simple.py' adding 'bx_python-0.13.0.dist-info/LICENSE' adding 'bx_python-0.13.0.dist-info/METADATA' adding 'bx_python-0.13.0.dist-info/WHEEL' adding 'bx_python-0.13.0.dist-info/top_level.txt' adding 'bx_python-0.13.0.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built bx_python-0.13.0-cp312-cp312-linux_x86_64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/build; python3.12 -m pytest ============================= test session starts ============================== platform linux -- Python 3.12.6, pytest-8.3.3, pluggy-1.5.0 rootdir: /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/build configfile: pytest.ini plugins: cython-0.1.1, typeguard-4.3.0 collected 139 items bx/align/epo_tests.py ..... [ 3%] bx/align/lav_tests.py . [ 4%] bx/align/maf_tests.py ........ [ 10%] bx/align/score_tests.py ..... [ 13%] bx/align/sitemask/sitemask_tests.py ... [ 15%] bx/align/tools/fuse.py . [ 16%] bx/align/tools/thread.py . [ 17%] bx/arrays/array_tree_tests.py ...... [ 21%] bx/bbi/bigwig_tests.py ........................... [ 41%] bx/binned_array_tests.py .... [ 43%] bx/bitset_tests.py .................. [ 56%] bx/interval_index_file_tests.py ... [ 58%] bx/intervals/cluster_tests.py ............. [ 68%] bx/intervals/intersection_tests.py ............. [ 77%] bx/intervals/io.py .. [ 79%] bx/misc/bgzf_tests.py . [ 79%] bx/misc/cdb_tests.py . [ 80%] bx/motif/io/transfac_tests.py . [ 81%] bx/motif/pwm_tests.py ... [ 83%] bx/phylo/newick_tests.py ........ [ 89%] bx/phylo/phast_tests.py . [ 89%] bx/pwm/pwm_tests.py . [ 90%] bx/seq/fasta_tests.py . [ 91%] bx/seq/nib_tests.py . [ 92%] bx/seq/qdna_tests.py . [ 92%] bx/seq/seq_tests.py .... [ 95%] bx/seq/twobit_tests.py ... [ 97%] bx/wiggle_tests.py .. [ 99%] bx_extras/fpconst_tests.py . [100%] =============================== warnings summary =============================== ../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead. self.args, self.args_source = self._decide_args( bx/bbi/bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 12000 10 mean n/a n/a n/a n/a -0.164968 -0.194169 -0.0533029 0.00390226 -0.00226906 -0.0365958\n] bx/bbi/bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 20000 100 mean n/a n/a n/a n/a n/a n/a n/a n/a n/a -0.163546 -0.272118 -0.127111 -0.116169 0.0202627 -0.0243522 0.0349913 -0.0054408 -0.00101548 -0.0307148 -0.0374406 -0.0024669 -0.034042 -0.0343892 -0.0199075 -0.0406878 -0.0322236 -0.080479 -0.235991 -0.0897865 -0.041593 0.019942 -0.0608448 0.0144338 -0.0348468 0.0195101 -0.0555526 -0.0892809 0.011672 -0.173894 -0.0849444 0.0718796 0.0608432 0.0313183 0.0439315 -0.0242363 0.03288 0.0318241 0.122005 0.0879138 0.00102565 0.0334753 -0.00263047 -0.103023 -0.0275437 0.0958326 0.0147229 -0.0629772 0.00541821 0.062474 0.069069 -0.0389339 0.0206174 0.0278476 -0.0182009 0.00568736 0.000397305 0.13104 0.105984 -0.00662042 0.143469 0.111045 0.0322849 0.11452 0.0865186 0.055436 0.141388 0.103004 -0.00350213 0.053879 0.10582 0.0983312 -0.0351239 0.10085 0.110439 0.0451646 -0.00949231 0.0487825 0.042197 -0.00328549 -0.00851082 -0.0437525 0.0618735 -0.0315407 -0.00756448 -0.0523631 0.0432315 0.0228745 0.106009 0.0299314 0.0473805\n] bx/bbi/bigwig_tests.py::TestBigWig::test_summary_from_file[chr1 10000 12000 100 mean n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a 0.0508425 0.0508425 -0.0768488 -0.189129 -0.439008 -0.182524 -0.304712 -0.197935 -0.462124 -0.194633 -0.2882 -0.0570346 -0.0724456 -0.301409 0.0508425 -0.0702441 -0.182524 0.0508425 0.0508425 -0.55459 0.0508425 0.0508425 0.0508425 0.0508425 0.00460946 -0.0152047 -0.0152047 -0.095562 -0.0570346 0.0695559 0.127898 0.000206554 -0.013003 0.0167182 -0.0559341 0.0508425 0.0904709 0.101479 -0.155005 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0.094874 0.11689 0.11689 0.105882 0.105882 -0.697695 0.094874 0.094874 0.105882 0.094874 0.105882 0.11689 -0.829788 0.094874 0.105882 -0.906843 0.105882 0.105882 0.105882 0.094874 0.105882 0.105882 0.094874 0.094874 0.11689 0.105882 0.105882 -0.829788 0.094874 0.105882 0.11689 -0.71971 0.105882 0.103756 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 -0.835144 0.090622 0.090622 -0.901269 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 0.090622 -0.818609 0.090622 0.090622 0.090622\n] /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.12_bx-python/build/bx/bbi/bigwig_tests.py:109: RuntimeWarning: invalid value encountered in divide assert allclose(sd.sum_data / sd.valid_count, values) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ======================= 139 passed, 6 warnings in 4.94s ======================== create-stamp debian/debhelper-build-stamp dh_testroot 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dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-bx-dbgsym' in '../python3-bx-dbgsym_0.13.0-1_amd64.deb'. dpkg-deb: building package 'python3-bx' in '../python3-bx_0.13.0-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../python-bx_0.13.0-1_amd64.buildinfo dpkg-genchanges --build=binary -O../python-bx_0.13.0-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2863652/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2863652/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/2863652 and its subdirectories I: Current time: Sun Nov 23 21:56:38 +14 2025 I: pbuilder-time-stamp: 1763884598