Tue Oct 7 00:00:57 UTC 2025 I: starting to build python-bx/unstable/amd64 on jenkins on '2025-10-07 00:00' Tue Oct 7 00:00:57 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_23/74197/console.log Tue Oct 7 00:00:57 UTC 2025 I: Downloading source for unstable/python-bx=0.13.0-2 --2025-10-07 00:00:57-- http://deb.debian.org/debian/pool/main/p/python-bx/python-bx_0.13.0-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1916 (1.9K) [text/prs.lines.tag] Saving to: ‘python-bx_0.13.0-2.dsc’ 0K . 100% 209M=0s 2025-10-07 00:00:58 (209 MB/s) - ‘python-bx_0.13.0-2.dsc’ saved [1916/1916] Tue Oct 7 00:00:58 UTC 2025 I: python-bx_0.13.0-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: python-bx Binary: python3-bx Architecture: any Version: 0.13.0-2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Michael R. Crusoe Homepage: https://github.com/bxlab/bx-python Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/python-bx Vcs-Git: https://salsa.debian.org/med-team/python-bx.git Testsuite: autopkgtest-pkg-pybuild Build-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, python3-numpy-dev, cython3 Package-List: python3-bx deb python optional arch=any Checksums-Sha1: bb4f1db8e7b49d900539bb64d9ab0ad5f4c43d32 1611987 python-bx_0.13.0.orig.tar.gz fd207e8d605acf0e17a4822dffcac9da383a5666 13876 python-bx_0.13.0-2.debian.tar.xz Checksums-Sha256: 90016460f4799758dc2891cf3209fbbbe41c9e7221a49821d958089c47bbbe33 1611987 python-bx_0.13.0.orig.tar.gz d50d95cd6cb3a7a49ad2785ab0b9da74861f555c9003d3b3e2867c17b0949a1a 13876 python-bx_0.13.0-2.debian.tar.xz Files: f1b5b00c996f8a4ff38794ab99b67ccf 1611987 python-bx_0.13.0.orig.tar.gz d12ce573413a6679cb52d9e22d9c60ae 13876 python-bx_0.13.0-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmjj6aEACgkQQc5/C58b izKj7ggAlscTaR2jWg9wQOSAZNRSks/X8f784NmNkMhrZ8AzcMAxdxcEmbX570Ec 1jeH63c0vHNpkoD5og0DNXf3Sr44BngewDh4tg+qig/m7U2CjjhjprspndU63Ezz tUxBvREzceXfazS5RFO6tSbHX98l7KmGStJYFxm0vOTTorFLjMPMxnKeFYcVPZ/N XJRrIPix/oFZCQw5Hx/Sk8ybWcygDIu18VWC5LJVTfk6WOrRcCE5bDUsUYqv9lIF GyH+1e/veXf8KoraCZkwxmX7jQtl8MnJ5dfbc+ZKbkZYfpQjIRM3r69IWE9FDnum rRfa6LsBqvKMsRdx4kdoaTULZ+tUTw== =O7zH -----END PGP SIGNATURE----- Tue Oct 7 00:00:58 UTC 2025 I: Checking whether the package is not for us Tue Oct 7 00:00:58 UTC 2025 I: Starting 1st build on remote node ionos11-amd64.debian.net. Tue Oct 7 00:00:58 UTC 2025 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Tue Oct 7 00:03:51 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Oct 6 12:00:58 -12 2025 I: pbuilder-time-stamp: 1759795258 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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_0.13.0-2.dsc] I: copying [./python-bx_0.13.0.orig.tar.gz] I: copying [./python-bx_0.13.0-2.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./python-bx_0.13.0-2.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_0.13.0-2.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: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/117306/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='153e92c4b2cd43f0877b9ba484712521' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='117306' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/pbuilderrc_LCK7 --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/b1 --logfile b1/build.log python-bx_0.13.0-2.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/117306/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, python3-numpy-dev, 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 ... 19856 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 python3-numpy-dev; however: Package python3-numpy-dev 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} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libjs-sphinxdoc{a} liblapack3{a} liblzo2-2{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{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-jaraco.text{a} python3-lzo{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-packaging{a} python3-pkg-resources{a} python3-pluggy{a} python3-pygments{a} python3-pyparsing{a} python3-pyproject-hooks{a} python3-pytest{a} python3-pytest-cython{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-wheel{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-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 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 86 newly installed, 0 to remove and 0 not upgraded. Need to get 41.5 MB of archives. After unpacking 173 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 python3-numpy-dev amd64 1:2.2.4+ds-1.2 [142 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.1-7 [215 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 15.2.0-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.1-7 [2785 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 python3-numpy amd64 1:2.2.4+ds-1.2 [5224 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.2-3 [98.3 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 cython3 amd64 3.0.11+dfsg-2+b1 [2504 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 42 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.28 [941 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.3-1 [165 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-7 [27.6 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 liblzo2-2 amd64 2.10-3+b1 [55.1 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.13.7-1 [1068 B] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 25.0-1 [56.6 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.46.1-2 [21.7 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-4 [36.2 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20250414 [11.8 kB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.13.7-1 [1048 B] Get: 66 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.13.7-1 [1068 B] Get: 69 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 python3-iniconfig all 1.1.1-2 [6396 B] Get: 75 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 81 http://deb.debian.org/debian unstable/main amd64 python3-lzo amd64 1.15-2+b4 [8812 B] Get: 82 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 1.6.0-1 [27.1 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-2 [836 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 python3-pytest all 8.4.2-1 [266 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 python3-pytest-cython all 0.3.1-1 [8032 B] Fetched 41.5 MB in 4s (10.4 MB/s) Preconfiguring packages ... 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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 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.2-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.6+dfsg-0.1) ... Setting up libdebhelper-perl (13.28) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-2) ... Setting up liblzo2-2:amd64 (2.10-3+b1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 7 00:01:46 UTC 2025. Universal Time is now: Tue Oct 7 00:01:46 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:amd64 (3.12.1-7) ... 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 (2.7.3-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up python3-numpy-dev:amd64 (1:2.2.4+ds-1.2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-7) ... Setting up libgfortran5:amd64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up liblapack3:amd64 (3.12.1-7) ... 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 (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-pygments (2.18.0+dfsg-2) ... Setting up python3-packaging (25.0-1) ... Setting up python3-pyproject-hooks (1.2.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up cython3 (3.0.11+dfsg-2+b1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.2.4+ds-1.2) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-pluggy (1.6.0-1) ... Setting up python3-lzo:amd64 (1.15-2+b4) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-pytest (8.4.2-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up python3-all (3.13.7-1) ... Setting up debhelper (13.28) ... Setting up python3-wheel (0.46.1-2) ... Setting up python3-inflect (7.5.0-1) ... Setting up libpython3-all-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-build (1.2.2-4) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-all-dev (3.13.7-1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-pytest-cython (0.3.1-1) ... Setting up pybuild-plugin-pyproject (6.20250414) ... Processing triggers for libc-bin (2.41-12) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/python-bx-0.13.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-bx_0.13.0-2_source.changes dpkg-buildpackage: info: source package python-bx dpkg-buildpackage: info: source version 0.13.0-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila 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 python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.13_bx-python * Building wheel... /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: MIT License See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running bdist_wheel running build running build_py creating build/lib.linux-x86_64-cpython-313/bx copying lib/bx/__init__.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/seqmapping_tests.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/interval_index_file.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/bitset_tests.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/interval_index_file_tests.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/bitset_builders.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/filter.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/gene_reader.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/wiggle_tests.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/binned_array_tests.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/bitset_utils.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/seqmapping.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/binned_array.py -> build/lib.linux-x86_64-cpython-313/bx copying lib/bx/wiggle.py -> build/lib.linux-x86_64-cpython-313/bx creating build/lib.linux-x86_64-cpython-313/bx_extras copying lib/bx_extras/__init__.py -> build/lib.linux-x86_64-cpython-313/bx_extras copying lib/bx_extras/stats.py -> build/lib.linux-x86_64-cpython-313/bx_extras copying lib/bx_extras/fpconst.py -> build/lib.linux-x86_64-cpython-313/bx_extras copying lib/bx_extras/fpconst_tests.py -> build/lib.linux-x86_64-cpython-313/bx_extras copying lib/bx_extras/lrucache.py -> build/lib.linux-x86_64-cpython-313/bx_extras copying lib/bx_extras/pstat.py -> build/lib.linux-x86_64-cpython-313/bx_extras creating build/lib.linux-x86_64-cpython-313/bx/intseq copying lib/bx/intseq/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intseq creating build/lib.linux-x86_64-cpython-313/bx/tabular copying lib/bx/tabular/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/tabular copying lib/bx/tabular/io.py -> build/lib.linux-x86_64-cpython-313/bx/tabular creating build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/maf_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/lav_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/maf.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/lav.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/score_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/axt.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/epo_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/score.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/core.py -> build/lib.linux-x86_64-cpython-313/bx/align copying lib/bx/align/epo.py -> build/lib.linux-x86_64-cpython-313/bx/align creating build/lib.linux-x86_64-cpython-313/bx/bbi copying lib/bx/bbi/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/bbi copying lib/bx/bbi/bigwig_tests.py -> build/lib.linux-x86_64-cpython-313/bx/bbi creating build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/bed_score_aligned_string.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/pwm_tests.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/pwm_score_maf.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/position_weight_matrix.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/pwm_score_motifs.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/pwm_score_positions.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/maf_select_motifs.py -> build/lib.linux-x86_64-cpython-313/bx/pwm copying lib/bx/pwm/bed_score_aligned_pwm.py -> build/lib.linux-x86_64-cpython-313/bx/pwm creating build/lib.linux-x86_64-cpython-313/bx/arrays copying lib/bx/arrays/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/arrays copying lib/bx/arrays/array_tree_tests.py -> build/lib.linux-x86_64-cpython-313/bx/arrays creating build/lib.linux-x86_64-cpython-313/bx/intervals copying lib/bx/intervals/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intervals copying lib/bx/intervals/intersection_tests.py -> build/lib.linux-x86_64-cpython-313/bx/intervals copying lib/bx/intervals/io.py -> build/lib.linux-x86_64-cpython-313/bx/intervals copying lib/bx/intervals/cluster_tests.py -> build/lib.linux-x86_64-cpython-313/bx/intervals copying lib/bx/intervals/random_intervals.py -> build/lib.linux-x86_64-cpython-313/bx/intervals creating build/lib.linux-x86_64-cpython-313/bx/motif copying lib/bx/motif/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif copying lib/bx/motif/pwm_tests.py -> build/lib.linux-x86_64-cpython-313/bx/motif copying lib/bx/motif/pwm.py -> build/lib.linux-x86_64-cpython-313/bx/motif creating build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/twobit.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/nib_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/qdna_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/nib.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/qdna.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/seq.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/core.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/fasta.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/seq_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/twobit_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq copying lib/bx/seq/fasta_tests.py -> build/lib.linux-x86_64-cpython-313/bx/seq creating build/lib.linux-x86_64-cpython-313/bx/phylo copying lib/bx/phylo/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/phylo copying lib/bx/phylo/phast_tests.py -> build/lib.linux-x86_64-cpython-313/bx/phylo copying lib/bx/phylo/phast.py -> build/lib.linux-x86_64-cpython-313/bx/phylo copying lib/bx/phylo/newick_tests.py -> build/lib.linux-x86_64-cpython-313/bx/phylo copying lib/bx/phylo/newick.py -> build/lib.linux-x86_64-cpython-313/bx/phylo creating build/lib.linux-x86_64-cpython-313/bx/cookbook copying lib/bx/cookbook/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook copying lib/bx/cookbook/doc_optparse.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook copying lib/bx/cookbook/attribute.py -> build/lib.linux-x86_64-cpython-313/bx/cookbook creating build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/binary_file.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/cdb_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/filecache.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/bgzf_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/filecache_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/seekbzip2.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/seeklzop.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/cdb.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/seeklzop_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/readlengths.py -> build/lib.linux-x86_64-cpython-313/bx/misc copying lib/bx/misc/seekbzip2_tests.py -> build/lib.linux-x86_64-cpython-313/bx/misc creating build/lib.linux-x86_64-cpython-313/bx/align/sitemask copying lib/bx/align/sitemask/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask copying lib/bx/align/sitemask/cpg.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask copying lib/bx/align/sitemask/quality.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask copying lib/bx/align/sitemask/sitemask_tests.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask copying lib/bx/align/sitemask/core.py -> build/lib.linux-x86_64-cpython-313/bx/align/sitemask creating build/lib.linux-x86_64-cpython-313/bx/align/tools copying lib/bx/align/tools/chop.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools copying lib/bx/align/tools/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools copying lib/bx/align/tools/fuse.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools copying lib/bx/align/tools/tile.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools copying lib/bx/align/tools/thread.py -> build/lib.linux-x86_64-cpython-313/bx/align/tools creating build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/find_clusters.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/base_coverage.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/quicksect.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/concat.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/merge.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/coverage.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/intersect.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/complement.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/join.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations copying lib/bx/intervals/operations/subtract.py -> build/lib.linux-x86_64-cpython-313/bx/intervals/operations creating build/lib.linux-x86_64-cpython-313/bx/motif/io copying lib/bx/motif/io/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io copying lib/bx/motif/io/transfac_tests.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io copying lib/bx/motif/io/transfac.py -> build/lib.linux-x86_64-cpython-313/bx/motif/io creating build/lib.linux-x86_64-cpython-313/bx/motif/logo copying lib/bx/motif/logo/__init__.py -> build/lib.linux-x86_64-cpython-313/bx/motif/logo copying lib/bx/motif/logo/template.ps -> build/lib.linux-x86_64-cpython-313/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-313/lib/bx creating build/temp.linux-x86_64-cpython-313/src creating build/temp.linux-x86_64-cpython-313/src/kent x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/bitset.c -o build/temp.linux-x86_64-cpython-313/lib/bx/bitset.o x86_64-linux-gnu-gcc -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/python3.13 -c src/binBits.c -o build/temp.linux-x86_64-cpython-313/src/binBits.o x86_64-linux-gnu-gcc -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/python3.13 -c src/kent/bits.c -o build/temp.linux-x86_64-cpython-313/src/kent/bits.o x86_64-linux-gnu-gcc -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/python3.13 -c src/kent/common.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/bitset.o build/temp.linux-x86_64-cpython-313/src/binBits.o build/temp.linux-x86_64-cpython-313/src/kent/bits.o build/temp.linux-x86_64-cpython-313/src/kent/common.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/bitset.cpython-313-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-313/lib/bx/intervals x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/intervals/intersection.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/intervals/intersection.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/intervals/intersection.cpython-313-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-313/lib/bx/align x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/align/_core.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/align/_core.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/align/_core.cpython-313-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-313/lib/bx/seq x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/seq/_nib.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/seq/_nib.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/seq/_nib.cpython-313-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 -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/python3.13 -c lib/bx/seq/_twobit.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/seq/_twobit.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/seq/_twobit.cpython-313-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 -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/python3.13 -c lib/bx/_seqmapping.c -o build/temp.linux-x86_64-cpython-313/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/python3.13/Python.h:39, 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-313/lib/bx/_seqmapping.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/_seqmapping.cpython-313-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-313/lib/bx/misc creating build/temp.linux-x86_64-cpython-313/src/samtools x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/misc/bgzf.c -o build/temp.linux-x86_64-cpython-313/lib/bx/misc/bgzf.o x86_64-linux-gnu-gcc -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/python3.13 -c src/samtools/bgzf.c -o build/temp.linux-x86_64-cpython-313/src/samtools/bgzf.o 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-313/lib/bx/misc/bgzf.o build/temp.linux-x86_64-cpython-313/src/samtools/bgzf.o -L/usr/lib/x86_64-linux-gnu -lz -o build/lib.linux-x86_64-cpython-313/bx/misc/bgzf.cpython-313-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 -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/python3.13 -c lib/bx/intervals/cluster.c -o build/temp.linux-x86_64-cpython-313/lib/bx/intervals/cluster.o x86_64-linux-gnu-gcc -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/python3.13 -c src/cluster.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/intervals/cluster.o build/temp.linux-x86_64-cpython-313/src/cluster.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/intervals/cluster.cpython-313-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-313/lib/bx/pwm x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/pwm/_position_weight_matrix.c -o build/temp.linux-x86_64-cpython-313/lib/bx/pwm/_position_weight_matrix.o x86_64-linux-gnu-gcc -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/python3.13 -c src/pwm_utils.c -o build/temp.linux-x86_64-cpython-313/src/pwm_utils.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-313/lib/bx/pwm/_position_weight_matrix.o build/temp.linux-x86_64-cpython-313/src/pwm_utils.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/pwm/_position_weight_matrix.cpython-313-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-313/lib/bx/motif x86_64-linux-gnu-gcc -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/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c lib/bx/motif/_pwm.c -o build/temp.linux-x86_64-cpython-313/lib/bx/motif/_pwm.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from lib/bx/motif/_pwm.c:1240: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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-313/lib/bx/motif/_pwm.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/motif/_pwm.cpython-313-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-313/lib/bx/arrays x86_64-linux-gnu-gcc -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/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c lib/bx/arrays/array_tree.c -o build/temp.linux-x86_64-cpython-313/lib/bx/arrays/array_tree.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from lib/bx/arrays/array_tree.c:1249: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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-313/lib/bx/arrays/array_tree.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree.cpython-313-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-313/lib/bx/bbi x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/bbi/bpt_file.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/bbi/bpt_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/bbi/bpt_file.cpython-313-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 -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/python3.13 -c lib/bx/bbi/cirtree_file.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/bbi/cirtree_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/bbi/cirtree_file.cpython-313-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 -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/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c lib/bx/bbi/bbi_file.c -o build/temp.linux-x86_64-cpython-313/lib/bx/bbi/bbi_file.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from lib/bx/bbi/bbi_file.c:1249: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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-313/lib/bx/bbi/bbi_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/bbi/bbi_file.cpython-313-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 -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/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c lib/bx/bbi/bigwig_file.c -o build/temp.linux-x86_64-cpython-313/lib/bx/bbi/bigwig_file.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from lib/bx/bbi/bigwig_file.c:1249: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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-313/lib/bx/bbi/bigwig_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_file.cpython-313-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 -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/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c lib/bx/bbi/bigbed_file.c -o build/temp.linux-x86_64-cpython-313/lib/bx/bbi/bigbed_file.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from lib/bx/bbi/bigbed_file.c:1249: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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-313/lib/bx/bbi/bigbed_file.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/bbi/bigbed_file.cpython-313-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 -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/x86_64-linux-gnu/python3-numpy/numpy/_core/include -I/usr/include/python3.13 -c lib/bx/align/_epo.c -o build/temp.linux-x86_64-cpython-313/lib/bx/align/_epo.o In file included from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarraytypes.h:1913, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/ndarrayobject.h:12, from /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/arrayobject.h:5, from lib/bx/align/_epo.c:1249: /usr/lib/x86_64-linux-gnu/python3-numpy/numpy/_core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 17 | #warning "Using deprecated NumPy API, disable it with " \ | ^~~~~~~ x86_64-linux-gnu-gcc -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -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-313/lib/bx/align/_epo.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/align/_epo.cpython-313-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 -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/python3.13 -c lib/bx/arrays/bed.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/arrays/bed.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/arrays/bed.cpython-313-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 -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/python3.13 -c lib/bx/arrays/wiggle.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/arrays/wiggle.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/arrays/wiggle.cpython-313-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-313/lib/bx/align/sitemask x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/align/sitemask/_cpg.c -o build/temp.linux-x86_64-cpython-313/lib/bx/align/sitemask/_cpg.o x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/align/sitemask/find_cpg.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/align/sitemask/_cpg.o build/temp.linux-x86_64-cpython-313/lib/bx/align/sitemask/find_cpg.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/align/sitemask/_cpg.cpython-313-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-313/lib/bx/intseq x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/intseq/ngramcount.c -o build/temp.linux-x86_64-cpython-313/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-313/lib/bx/intseq/ngramcount.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/intseq/ngramcount.cpython-313-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-313/src/bunzip x86_64-linux-gnu-gcc -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/python3.13 -c lib/bx/misc/_seekbzip2.c -o build/temp.linux-x86_64-cpython-313/lib/bx/misc/_seekbzip2.o x86_64-linux-gnu-gcc -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/python3.13 -c src/bunzip/micro-bunzip.c -o build/temp.linux-x86_64-cpython-313/src/bunzip/micro-bunzip.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-313/lib/bx/misc/_seekbzip2.o build/temp.linux-x86_64-cpython-313/src/bunzip/micro-bunzip.o -L/usr/lib/x86_64-linux-gnu -o build/lib.linux-x86_64-cpython-313/bx/misc/_seekbzip2.cpython-313-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.13 copying and adjusting scripts/maf_gc_content.py -> build/scripts-3.13 copying and adjusting scripts/axt_to_lav.py -> build/scripts-3.13 copying and adjusting scripts/bed_complement.py -> build/scripts-3.13 copying and adjusting scripts/bed_coverage_by_interval.py -> build/scripts-3.13 copying and adjusting scripts/maf_limit_to_species.py -> build/scripts-3.13 copying and adjusting scripts/prefix_lines.py -> build/scripts-3.13 copying and adjusting scripts/maf_percent_identity.py -> build/scripts-3.13 copying and adjusting scripts/one_field_per_line.py -> build/scripts-3.13 copying and adjusting scripts/bed_coverage.py -> build/scripts-3.13 copying and adjusting scripts/maf_build_index.py -> build/scripts-3.13 copying and adjusting scripts/table_filter.py -> build/scripts-3.13 copying and adjusting scripts/maf_species_in_all_files.py -> build/scripts-3.13 copying and adjusting scripts/maf_div_sites.py -> build/scripts-3.13 copying and adjusting scripts/lav_to_maf.py -> build/scripts-3.13 copying and adjusting scripts/maf_extract_ranges_indexed.py -> build/scripts-3.13 copying and adjusting scripts/bnMapper.py -> build/scripts-3.13 copying and adjusting scripts/maf_tile_2.py -> build/scripts-3.13 copying and adjusting scripts/axt_extract_ranges.py -> build/scripts-3.13 copying and adjusting scripts/maf_to_fasta.py -> build/scripts-3.13 copying and adjusting scripts/maf_thread_for_species.py -> build/scripts-3.13 copying and adjusting scripts/maf_chunk.py -> build/scripts-3.13 copying and adjusting scripts/int_seqs_to_char_strings.py -> build/scripts-3.13 copying and adjusting scripts/lav_to_axt.py -> build/scripts-3.13 copying and adjusting scripts/bed_count_by_interval.py -> build/scripts-3.13 copying and adjusting scripts/tfloc_summary.py -> build/scripts-3.13 copying and adjusting scripts/wiggle_to_chr_binned_array.py -> build/scripts-3.13 copying and adjusting scripts/bed_merge_overlapping.py -> build/scripts-3.13 copying and adjusting scripts/bed_bigwig_profile.py -> build/scripts-3.13 copying and adjusting scripts/bed_extend_to.py -> build/scripts-3.13 copying and adjusting scripts/maf_tile.py -> build/scripts-3.13 copying and adjusting scripts/maf_translate_chars.py -> build/scripts-3.13 copying and adjusting scripts/lzop_build_offset_table.py -> build/scripts-3.13 copying and adjusting scripts/maf_covered_ranges.py -> build/scripts-3.13 copying and adjusting scripts/gene_fourfold_sites.py -> build/scripts-3.13 copying and adjusting scripts/maf_percent_columns_matching.py -> build/scripts-3.13 copying and adjusting scripts/line_select.py -> build/scripts-3.13 copying and adjusting scripts/maf_count.py -> build/scripts-3.13 copying and adjusting scripts/maf_word_frequency.py -> build/scripts-3.13 copying and adjusting scripts/aggregate_scores_in_intervals.py -> build/scripts-3.13 copying and adjusting scripts/maf_mapping_word_frequency.py -> build/scripts-3.13 copying and adjusting scripts/axt_to_maf.py -> build/scripts-3.13 copying and adjusting scripts/maf_to_int_seqs.py -> build/scripts-3.13 copying and adjusting scripts/bed_intersect_basewise.py -> build/scripts-3.13 copying and adjusting scripts/bed_rand_intersect.py -> build/scripts-3.13 copying and adjusting scripts/maf_extract_ranges.py -> build/scripts-3.13 copying and adjusting scripts/get_scores_in_intervals.py -> build/scripts-3.13 copying and adjusting scripts/nib_chrom_intervals_to_fasta.py -> build/scripts-3.13 copying and adjusting scripts/find_in_sorted_file.py -> build/scripts-3.13 copying and adjusting scripts/table_add_column.py -> build/scripts-3.13 copying and adjusting scripts/maf_drop_overlapping.py -> build/scripts-3.13 copying and adjusting scripts/out_to_chain.py -> build/scripts-3.13 copying and adjusting scripts/maf_split_by_src.py -> build/scripts-3.13 copying and adjusting scripts/maf_to_axt.py -> build/scripts-3.13 copying and adjusting scripts/bed_intersect.py -> build/scripts-3.13 copying and adjusting scripts/ucsc_gene_table_to_intervals.py -> build/scripts-3.13 copying and adjusting scripts/maf_print_chroms.py -> build/scripts-3.13 copying and adjusting scripts/bed_diff_basewise_summary.py -> build/scripts-3.13 copying and adjusting scripts/wiggle_to_binned_array.py -> build/scripts-3.13 copying and adjusting scripts/div_snp_table_chr.py -> build/scripts-3.13 copying and adjusting scripts/maf_mean_length_ungapped_piece.py -> build/scripts-3.13 copying and adjusting scripts/maf_mask_cpg.py -> build/scripts-3.13 copying and adjusting scripts/axt_to_fasta.py -> build/scripts-3.13 copying and adjusting scripts/maf_extract_chrom_ranges.py -> build/scripts-3.13 copying and adjusting scripts/maf_col_counts_all.py -> build/scripts-3.13 copying and adjusting scripts/maf_tile_2bit.py -> build/scripts-3.13 copying and adjusting scripts/nib_length.py -> build/scripts-3.13 copying and adjusting scripts/bed_count_overlapping.py -> build/scripts-3.13 copying and adjusting scripts/pretty_table.py -> build/scripts-3.13 copying and adjusting scripts/qv_to_bqv.py -> build/scripts-3.13 copying and adjusting scripts/maf_print_scores.py -> build/scripts-3.13 copying and adjusting scripts/bed_build_windows.py -> build/scripts-3.13 copying and adjusting scripts/maf_chop.py -> build/scripts-3.13 copying and adjusting scripts/nib_intervals_to_fasta.py -> build/scripts-3.13 copying and adjusting scripts/bed_subtract_basewise.py -> build/scripts-3.13 copying and adjusting scripts/maf_randomize.py -> build/scripts-3.13 copying and adjusting scripts/maf_shuffle_columns.py -> build/scripts-3.13 copying and adjusting scripts/mask_quality.py -> build/scripts-3.13 copying and adjusting scripts/maf_region_coverage_by_src.py -> build/scripts-3.13 copying and adjusting scripts/maf_gap_frequency.py -> build/scripts-3.13 copying and adjusting scripts/maf_interval_alignibility.py -> build/scripts-3.13 copying and adjusting scripts/wiggle_to_simple.py -> build/scripts-3.13 copying and adjusting scripts/interval_join.py -> build/scripts-3.13 copying and adjusting scripts/mMK_bitset.py -> build/scripts-3.13 copying and adjusting scripts/maf_to_concat_fasta.py -> build/scripts-3.13 copying and adjusting scripts/maf_select.py -> build/scripts-3.13 copying and adjusting scripts/maf_col_counts.py -> build/scripts-3.13 copying and adjusting scripts/interval_count_intersections.py -> build/scripts-3.13 copying and adjusting scripts/random_lines.py -> build/scripts-3.13 copying and adjusting scripts/wiggle_to_array_tree.py -> build/scripts-3.13 copying and adjusting scripts/align_print_template.py -> build/scripts-3.13 copying and adjusting scripts/maf_filter.py -> build/scripts-3.13 copying and adjusting scripts/maf_truncate.py -> build/scripts-3.13 copying and adjusting scripts/maf_filter_max_wc.py -> build/scripts-3.13 copying and adjusting scripts/maf_covered_regions.py -> build/scripts-3.13 changing mode of build/scripts-3.13/maf_gc_content.py from 644 to 755 changing mode of build/scripts-3.13/axt_to_lav.py from 644 to 755 changing mode of build/scripts-3.13/bed_complement.py from 644 to 755 changing mode of build/scripts-3.13/bed_coverage_by_interval.py from 644 to 755 changing mode of build/scripts-3.13/maf_limit_to_species.py from 644 to 755 changing mode of build/scripts-3.13/prefix_lines.py from 644 to 755 changing mode of build/scripts-3.13/maf_percent_identity.py from 644 to 755 changing mode of build/scripts-3.13/one_field_per_line.py from 644 to 755 changing mode of build/scripts-3.13/bed_coverage.py from 644 to 755 changing mode of build/scripts-3.13/maf_build_index.py from 644 to 755 changing mode of build/scripts-3.13/table_filter.py from 644 to 755 changing mode of build/scripts-3.13/maf_species_in_all_files.py from 644 to 755 changing mode of build/scripts-3.13/maf_div_sites.py from 644 to 755 changing mode of build/scripts-3.13/lav_to_maf.py from 644 to 755 changing mode of build/scripts-3.13/maf_extract_ranges_indexed.py from 644 to 755 changing mode of build/scripts-3.13/bnMapper.py from 644 to 755 changing mode of build/scripts-3.13/maf_tile_2.py from 644 to 755 changing mode of build/scripts-3.13/axt_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.13/maf_to_fasta.py from 644 to 755 changing mode of build/scripts-3.13/maf_thread_for_species.py from 644 to 755 changing mode of build/scripts-3.13/maf_chunk.py from 644 to 755 changing mode of build/scripts-3.13/int_seqs_to_char_strings.py from 644 to 755 changing mode of build/scripts-3.13/lav_to_axt.py from 644 to 755 changing mode of build/scripts-3.13/bed_count_by_interval.py from 644 to 755 changing mode of build/scripts-3.13/tfloc_summary.py from 644 to 755 changing mode of build/scripts-3.13/wiggle_to_chr_binned_array.py from 644 to 755 changing mode of build/scripts-3.13/bed_merge_overlapping.py from 644 to 755 changing mode of build/scripts-3.13/bed_bigwig_profile.py from 644 to 755 changing mode of build/scripts-3.13/bed_extend_to.py from 644 to 755 changing mode of build/scripts-3.13/maf_tile.py from 644 to 755 changing mode of build/scripts-3.13/maf_translate_chars.py from 644 to 755 changing mode of build/scripts-3.13/lzop_build_offset_table.py from 644 to 755 changing mode of build/scripts-3.13/maf_covered_ranges.py from 644 to 755 changing mode of build/scripts-3.13/gene_fourfold_sites.py from 644 to 755 changing mode of build/scripts-3.13/maf_percent_columns_matching.py from 644 to 755 changing mode of build/scripts-3.13/line_select.py from 644 to 755 changing mode of build/scripts-3.13/maf_count.py from 644 to 755 changing mode of build/scripts-3.13/maf_word_frequency.py from 644 to 755 changing mode of build/scripts-3.13/aggregate_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.13/maf_mapping_word_frequency.py from 644 to 755 changing mode of build/scripts-3.13/axt_to_maf.py from 644 to 755 changing mode of build/scripts-3.13/maf_to_int_seqs.py from 644 to 755 changing mode of build/scripts-3.13/bed_intersect_basewise.py from 644 to 755 changing mode of build/scripts-3.13/bed_rand_intersect.py from 644 to 755 changing mode of build/scripts-3.13/maf_extract_ranges.py from 644 to 755 changing mode of build/scripts-3.13/get_scores_in_intervals.py from 644 to 755 changing mode of build/scripts-3.13/nib_chrom_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.13/find_in_sorted_file.py from 644 to 755 changing mode of build/scripts-3.13/table_add_column.py from 644 to 755 changing mode of build/scripts-3.13/maf_drop_overlapping.py from 644 to 755 changing mode of build/scripts-3.13/out_to_chain.py from 644 to 755 changing mode of build/scripts-3.13/maf_split_by_src.py from 644 to 755 changing mode of build/scripts-3.13/maf_to_axt.py from 644 to 755 changing mode of build/scripts-3.13/bed_intersect.py from 644 to 755 changing mode of build/scripts-3.13/ucsc_gene_table_to_intervals.py from 644 to 755 changing mode of build/scripts-3.13/maf_print_chroms.py from 644 to 755 changing mode of build/scripts-3.13/bed_diff_basewise_summary.py from 644 to 755 changing mode of build/scripts-3.13/wiggle_to_binned_array.py from 644 to 755 changing mode of build/scripts-3.13/div_snp_table_chr.py from 644 to 755 changing mode of build/scripts-3.13/maf_mean_length_ungapped_piece.py from 644 to 755 changing mode of build/scripts-3.13/maf_mask_cpg.py from 644 to 755 changing mode of build/scripts-3.13/axt_to_fasta.py from 644 to 755 changing mode of build/scripts-3.13/maf_extract_chrom_ranges.py from 644 to 755 changing mode of build/scripts-3.13/maf_col_counts_all.py from 644 to 755 changing mode of build/scripts-3.13/maf_tile_2bit.py from 644 to 755 changing mode of build/scripts-3.13/nib_length.py from 644 to 755 changing mode of build/scripts-3.13/bed_count_overlapping.py from 644 to 755 changing mode of build/scripts-3.13/pretty_table.py from 644 to 755 changing mode of build/scripts-3.13/qv_to_bqv.py from 644 to 755 changing mode of build/scripts-3.13/maf_print_scores.py from 644 to 755 changing mode of build/scripts-3.13/bed_build_windows.py from 644 to 755 changing mode of build/scripts-3.13/maf_chop.py from 644 to 755 changing mode of build/scripts-3.13/nib_intervals_to_fasta.py from 644 to 755 changing mode of build/scripts-3.13/bed_subtract_basewise.py from 644 to 755 changing mode of build/scripts-3.13/maf_randomize.py from 644 to 755 changing mode of build/scripts-3.13/maf_shuffle_columns.py from 644 to 755 changing mode of build/scripts-3.13/mask_quality.py from 644 to 755 changing mode of build/scripts-3.13/maf_region_coverage_by_src.py from 644 to 755 changing mode of build/scripts-3.13/maf_gap_frequency.py from 644 to 755 changing mode of build/scripts-3.13/maf_interval_alignibility.py from 644 to 755 changing mode of build/scripts-3.13/wiggle_to_simple.py from 644 to 755 changing mode of build/scripts-3.13/interval_join.py from 644 to 755 changing mode of build/scripts-3.13/mMK_bitset.py from 644 to 755 changing mode of build/scripts-3.13/maf_to_concat_fasta.py from 644 to 755 changing mode of build/scripts-3.13/maf_select.py from 644 to 755 changing mode of build/scripts-3.13/maf_col_counts.py from 644 to 755 changing mode of build/scripts-3.13/interval_count_intersections.py from 644 to 755 changing mode of build/scripts-3.13/random_lines.py from 644 to 755 changing mode of build/scripts-3.13/wiggle_to_array_tree.py from 644 to 755 changing mode of build/scripts-3.13/align_print_template.py from 644 to 755 changing mode of build/scripts-3.13/maf_filter.py from 644 to 755 changing mode of build/scripts-3.13/maf_truncate.py from 644 to 755 changing mode of build/scripts-3.13/maf_filter_max_wc.py from 644 to 755 changing mode of build/scripts-3.13/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/wheel creating build/bdist.linux-x86_64/wheel/bx creating build/bdist.linux-x86_64/wheel/bx/intseq copying build/lib.linux-x86_64-cpython-313/bx/intseq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intseq copying build/lib.linux-x86_64-cpython-313/bx/intseq/ngramcount.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intseq copying build/lib.linux-x86_64-cpython-313/bx/__init__.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/seqmapping_tests.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/interval_index_file.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/bitset_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-313/bx/tabular/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/tabular copying build/lib.linux-x86_64-cpython-313/bx/tabular/io.py -> build/bdist.linux-x86_64/wheel/./bx/tabular creating build/bdist.linux-x86_64/wheel/bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/maf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/lav_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/maf.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/lav.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-313/bx/align/sitemask/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/_cpg.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/cpg.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/quality.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/sitemask_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-313/bx/align/sitemask/core.py -> build/bdist.linux-x86_64/wheel/./bx/align/sitemask copying build/lib.linux-x86_64-cpython-313/bx/align/score_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/axt.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/epo_tests.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/score.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/_epo.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/core.py -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/_core.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/align copying build/lib.linux-x86_64-cpython-313/bx/align/epo.py -> 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-313/bx/align/tools/chop.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-313/bx/align/tools/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-313/bx/align/tools/fuse.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-313/bx/align/tools/tile.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-313/bx/align/tools/thread.py -> build/bdist.linux-x86_64/wheel/./bx/align/tools copying build/lib.linux-x86_64-cpython-313/bx/interval_index_file_tests.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/bitset_builders.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/cirtree_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/bbi_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/bpt_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_tests.py -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigwig_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/bbi/bigbed_file.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/bbi copying build/lib.linux-x86_64-cpython-313/bx/filter.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/bed_score_aligned_string.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_maf.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/position_weight_matrix.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/_position_weight_matrix.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/pwm_score_positions.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/maf_select_motifs.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/pwm/bed_score_aligned_pwm.py -> build/bdist.linux-x86_64/wheel/./bx/pwm copying build/lib.linux-x86_64-cpython-313/bx/gene_reader.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/arrays copying build/lib.linux-x86_64-cpython-313/bx/arrays/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-313/bx/arrays/wiggle.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree_tests.py -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-313/bx/arrays/bed.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays copying build/lib.linux-x86_64-cpython-313/bx/arrays/array_tree.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/arrays creating build/bdist.linux-x86_64/wheel/bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/intersection.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/intersection_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/cluster.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/io.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/cluster_tests.py -> build/bdist.linux-x86_64/wheel/./bx/intervals copying build/lib.linux-x86_64-cpython-313/bx/intervals/random_intervals.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-313/bx/intervals/operations/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/find_clusters.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/base_coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/quicksect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/concat.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/merge.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/coverage.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/intersect.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/complement.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/join.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/intervals/operations/subtract.py -> build/bdist.linux-x86_64/wheel/./bx/intervals/operations copying build/lib.linux-x86_64-cpython-313/bx/wiggle_tests.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/motif copying build/lib.linux-x86_64-cpython-313/bx/motif/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif copying build/lib.linux-x86_64-cpython-313/bx/motif/pwm_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif creating build/bdist.linux-x86_64/wheel/bx/motif/io copying build/lib.linux-x86_64-cpython-313/bx/motif/io/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io copying build/lib.linux-x86_64-cpython-313/bx/motif/io/transfac_tests.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io copying build/lib.linux-x86_64-cpython-313/bx/motif/io/transfac.py -> build/bdist.linux-x86_64/wheel/./bx/motif/io copying build/lib.linux-x86_64-cpython-313/bx/motif/_pwm.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/motif copying build/lib.linux-x86_64-cpython-313/bx/motif/pwm.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-313/bx/motif/logo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/motif/logo copying build/lib.linux-x86_64-cpython-313/bx/motif/logo/template.ps -> build/bdist.linux-x86_64/wheel/./bx/motif/logo copying build/lib.linux-x86_64-cpython-313/bx/_seqmapping.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/bitset.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/binned_array_tests.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/twobit.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/nib_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/_nib.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/qdna_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/nib.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/qdna.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/seq.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/core.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/fasta.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/seq_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/twobit_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/_twobit.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/seq/fasta_tests.py -> build/bdist.linux-x86_64/wheel/./bx/seq copying build/lib.linux-x86_64-cpython-313/bx/bitset_utils.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/seqmapping.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/phylo copying build/lib.linux-x86_64-cpython-313/bx/phylo/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-313/bx/phylo/phast_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-313/bx/phylo/phast.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-313/bx/phylo/newick_tests.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-313/bx/phylo/newick.py -> build/bdist.linux-x86_64/wheel/./bx/phylo copying build/lib.linux-x86_64-cpython-313/bx/binned_array.py -> build/bdist.linux-x86_64/wheel/./bx copying build/lib.linux-x86_64-cpython-313/bx/wiggle.py -> build/bdist.linux-x86_64/wheel/./bx creating build/bdist.linux-x86_64/wheel/bx/cookbook copying build/lib.linux-x86_64-cpython-313/bx/cookbook/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook copying build/lib.linux-x86_64-cpython-313/bx/cookbook/doc_optparse.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook copying build/lib.linux-x86_64-cpython-313/bx/cookbook/attribute.py -> build/bdist.linux-x86_64/wheel/./bx/cookbook creating build/bdist.linux-x86_64/wheel/bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/binary_file.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/__init__.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/cdb_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/filecache.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/bgzf_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/filecache_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/_seekbzip2.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/seekbzip2.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/seeklzop.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/cdb.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/seeklzop_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/readlengths.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/seekbzip2_tests.py -> build/bdist.linux-x86_64/wheel/./bx/misc copying build/lib.linux-x86_64-cpython-313/bx/misc/bgzf.cpython-313-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel/./bx/misc creating build/bdist.linux-x86_64/wheel/bx_extras copying build/lib.linux-x86_64-cpython-313/bx_extras/__init__.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-313/bx_extras/stats.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-313/bx_extras/fpconst.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-313/bx_extras/fpconst_tests.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-313/bx_extras/lrucache.py -> build/bdist.linux-x86_64/wheel/./bx_extras copying build/lib.linux-x86_64-cpython-313/bx_extras/pstat.py -> build/bdist.linux-x86_64/wheel/./bx_extras 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/scripts copying build/scripts-3.13/maf_gc_content.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/axt_to_lav.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_complement.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_coverage_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_limit_to_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/prefix_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_percent_identity.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/one_field_per_line.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_coverage.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_build_index.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/table_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_species_in_all_files.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_div_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/lav_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_extract_ranges_indexed.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bnMapper.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_tile_2.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/axt_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_thread_for_species.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_chunk.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/int_seqs_to_char_strings.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/lav_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_count_by_interval.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/tfloc_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/wiggle_to_chr_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_merge_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_bigwig_profile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_extend_to.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_tile.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_translate_chars.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/lzop_build_offset_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_covered_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/gene_fourfold_sites.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_percent_columns_matching.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/line_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_count.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/aggregate_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_mapping_word_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/axt_to_maf.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_to_int_seqs.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_intersect_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_rand_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_extract_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/get_scores_in_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/nib_chrom_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/find_in_sorted_file.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/table_add_column.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_drop_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/out_to_chain.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_split_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_to_axt.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_intersect.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/ucsc_gene_table_to_intervals.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_print_chroms.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_diff_basewise_summary.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/wiggle_to_binned_array.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/div_snp_table_chr.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_mean_length_ungapped_piece.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_mask_cpg.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/axt_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_extract_chrom_ranges.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_col_counts_all.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_tile_2bit.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/nib_length.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_count_overlapping.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/pretty_table.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/qv_to_bqv.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_print_scores.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_build_windows.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_chop.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/nib_intervals_to_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/bed_subtract_basewise.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_randomize.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_shuffle_columns.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/mask_quality.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_region_coverage_by_src.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_gap_frequency.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_interval_alignibility.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/wiggle_to_simple.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/interval_join.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/mMK_bitset.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_to_concat_fasta.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_select.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_col_counts.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/interval_count_intersections.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/random_lines.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/wiggle_to_array_tree.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/align_print_template.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_filter.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_truncate.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/maf_filter_max_wc.py -> build/bdist.linux-x86_64/wheel/bx_python-0.13.0.data/scripts copying build/scripts-3.13/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/maf_gc_content.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_complement.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/maf_limit_to_species.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_percent_identity.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/bed_coverage.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/table_filter.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/maf_div_sites.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_extract_ranges_indexed.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_tile_2.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_to_fasta.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/maf_chunk.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/lav_to_axt.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/tfloc_summary.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/bed_merge_overlapping.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_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_translate_chars.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/maf_covered_ranges.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_percent_columns_matching.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_count.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/aggregate_scores_in_intervals.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/axt_to_maf.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/bed_intersect_basewise.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/maf_extract_ranges.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/nib_chrom_intervals_to_fasta.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/table_add_column.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/out_to_chain.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/maf_to_axt.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/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_print_chroms.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/wiggle_to_binned_array.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/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_mask_cpg.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_extract_chrom_ranges.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/maf_tile_2bit.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/bed_count_overlapping.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/qv_to_bqv.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/bed_build_windows.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/nib_intervals_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/maf_randomize.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/mask_quality.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_gap_frequency.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/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/mMK_bitset.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/maf_select.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/interval_count_intersections.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/wiggle_to_array_tree.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_filter.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/maf_filter_max_wc.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_3.13_bx-python/.tmp-lux00kae/bx_python-0.13.0-cp313-cp313-linux_x86_64.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'bx/__init__.py' adding 'bx/_seqmapping.cpython-313-x86_64-linux-gnu.so' adding 'bx/binned_array.py' adding 'bx/binned_array_tests.py' adding 'bx/bitset.cpython-313-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-313-x86_64-linux-gnu.so' adding 'bx/align/_epo.cpython-313-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-313-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-313-x86_64-linux-gnu.so' adding 'bx/arrays/array_tree_tests.py' adding 'bx/arrays/bed.cpython-313-x86_64-linux-gnu.so' adding 'bx/arrays/wiggle.cpython-313-x86_64-linux-gnu.so' adding 'bx/bbi/__init__.py' adding 'bx/bbi/bbi_file.cpython-313-x86_64-linux-gnu.so' adding 'bx/bbi/bigbed_file.cpython-313-x86_64-linux-gnu.so' adding 'bx/bbi/bigwig_file.cpython-313-x86_64-linux-gnu.so' adding 'bx/bbi/bigwig_tests.py' adding 'bx/bbi/bpt_file.cpython-313-x86_64-linux-gnu.so' adding 'bx/bbi/cirtree_file.cpython-313-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-313-x86_64-linux-gnu.so' adding 'bx/intervals/cluster_tests.py' adding 'bx/intervals/intersection.cpython-313-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-313-x86_64-linux-gnu.so' adding 'bx/misc/__init__.py' adding 'bx/misc/_seekbzip2.cpython-313-x86_64-linux-gnu.so' adding 'bx/misc/bgzf.cpython-313-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-313-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-313-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-313-x86_64-linux-gnu.so' adding 'bx/seq/_twobit.cpython-313-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/licenses/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-cp313-cp313-linux_x86_64.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.13_bx-python/build; python3.13 -m pytest ============================= test session starts ============================== platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 rootdir: /build/reproducible-path/python-bx-0.13.0/.pybuild/cpython3_3.13_bx-python/build configfile: pytest.ini plugins: cython-0.3.1, typeguard-4.4.4 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:1533 /usr/lib/python3/dist-packages/_pytest/config/__init__.py:1533: 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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dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/axt_extract_ranges.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_to_fasta.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_thread_for_species.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_chunk.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/int_seqs_to_char_strings.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/lav_to_axt.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_count_by_interval.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/tfloc_summary.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_chr_binned_array.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_merge_overlapping.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_bigwig_profile.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_extend_to.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_tile.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_translate_chars.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/lzop_build_offset_table.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_covered_ranges.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/gene_fourfold_sites.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_percent_columns_matching.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/line_select.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_count.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_word_frequency.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/aggregate_scores_in_intervals.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_mapping_word_frequency.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/axt_to_maf.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_to_int_seqs.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_intersect_basewise.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_rand_intersect.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_extract_ranges.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/get_scores_in_intervals.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/nib_chrom_intervals_to_fasta.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/find_in_sorted_file.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/table_add_column.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_drop_overlapping.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/out_to_chain.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_split_by_src.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_to_axt.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_intersect.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/ucsc_gene_table_to_intervals.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_print_chroms.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_diff_basewise_summary.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_binned_array.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/div_snp_table_chr.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_mean_length_ungapped_piece.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_mask_cpg.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/axt_to_fasta.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_extract_chrom_ranges.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_col_counts_all.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_tile_2bit.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/nib_length.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_count_overlapping.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/pretty_table.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/qv_to_bqv.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_print_scores.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_build_windows.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_chop.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/nib_intervals_to_fasta.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/bed_subtract_basewise.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_randomize.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_shuffle_columns.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/mask_quality.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_region_coverage_by_src.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_gap_frequency.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_interval_alignibility.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_simple.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/interval_join.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/mMK_bitset.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_to_concat_fasta.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_select.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_col_counts.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/interval_count_intersections.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/random_lines.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/wiggle_to_array_tree.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/align_print_template.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_filter.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_truncate.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_filter_max_wc.py I: dh_python3 tools:114: replacing shebang in debian/python3-bx/usr/bin/maf_covered_regions.py dh_numpy3 Possible precedence issue with control flow operator (return) at /usr/bin/dh_numpy3 line 57. make[1]: Leaving directory '/build/reproducible-path/python-bx-0.13.0' dh_installsystemduser -O--buildsystem=pybuild dh_lintian -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-bx' in '../python3-bx_0.13.0-2_amd64.deb'. dpkg-deb: building package 'python3-bx-dbgsym' in '../python3-bx-dbgsym_0.13.0-2_amd64.deb'. dpkg-genbuildinfo --build=binary -O../python-bx_0.13.0-2_amd64.buildinfo dpkg-genchanges --build=binary -O../python-bx_0.13.0-2_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: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/117306 and its subdirectories I: Current time: Mon Oct 6 12:03:51 -12 2025 I: pbuilder-time-stamp: 1759795431 Tue Oct 7 00:03:51 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Oct 7 00:03:51 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Oct 7 00:16:22 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Oct 7 00:16:22 UTC 2025 I: python-bx_0.13.0-2_amd64.changes: Format: 1.8 Date: Mon, 06 Oct 2025 16:40:00 +0200 Source: python-bx Binary: python3-bx python3-bx-dbgsym Architecture: amd64 Version: 0.13.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Santiago Vila Description: python3-bx - library to manage genomic data and its alignment Closes: 1116850 Changes: python-bx (0.13.0-2) unstable; urgency=medium . * Team upload. * Drop from python3-numpy in BD. Closes: #1116850. * d/control: Add build-dependency on python3-numpy-dev (lintian error). * d/control: Drop "Rules-Requires-Root: no", it's the default. * d/control: Drop "Priority: optional", it's the default. * d/control: Update standards-version. Checksums-Sha1: e1233966191c4786a722c48cb50c2dcbce187448 6638 python-bx_0.13.0-2_amd64.buildinfo 3abf789d0878c7b189041b2863a894ce8165140d 3811136 python3-bx-dbgsym_0.13.0-2_amd64.deb 2d810d8233d9decd586b24f15d2b69eb519c54ad 725628 python3-bx_0.13.0-2_amd64.deb Checksums-Sha256: 2bf4089c8eca6817e54c910b13132ac002daf757f31c4a8655594391526d6c25 6638 python-bx_0.13.0-2_amd64.buildinfo 325d81edd313d6cf1b56939513064b2397a7e9c7197781bd6e723b5203e8dd97 3811136 python3-bx-dbgsym_0.13.0-2_amd64.deb 06699810bf904d22e3cda8d06cfc1a8f1bc936c30d0413ea5d591b276d85a183 725628 python3-bx_0.13.0-2_amd64.deb Files: d8c669075dad4fb32572a771825d136a 6638 python optional python-bx_0.13.0-2_amd64.buildinfo 561c61c4ca2177a049b814a24bebe88c 3811136 debug optional python3-bx-dbgsym_0.13.0-2_amd64.deb 9d9a673912f5fb84bc5a6145841f0602 725628 python optional python3-bx_0.13.0-2_amd64.deb Tue Oct 7 00:16:23 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_23-74197.service; invocation ID: 84b90ae48c5049ce9ac8ee6d1d0bc00f # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/python-bx_0.13.0-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/python-bx_0.13.0-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/python-bx_0.13.0-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/b1/python-bx_0.13.0-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.nNpA1jCw/b2/python-bx_0.13.0-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 206ms CPU time consumed: 177ms Memory peak: 17.2M (swap: 0B) Tue Oct 7 00:16:24 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 7 00:16:24 UTC 2025 I: python-bx from unstable built successfully and reproducibly on amd64. Tue Oct 7 00:16:24 UTC 2025 I: Removing signed python-bx_0.13.0-2_amd64.buildinfo.asc files: removed './b1/python-bx_0.13.0-2_amd64.buildinfo.asc' removed './b2/python-bx_0.13.0-2_amd64.buildinfo.asc'