Your message dated Sun, 01 Jan 2023 12:53:29 +0000 with message-id <[email protected]> and subject line Bug#1027335: fixed in pairtools 1.0.2-1 has caused the Debian Bug report #1027335, regarding pairtools -- current repo in salsa FTBFS to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 1027335: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1027335 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Source: pairtools Version: 0.3.0-3.2 Severity: serious Pairtools FTBFS with pysam related error. Looks like something is off. dh_auto_clean I: pybuild base:240: python3.11 setup.py clean Traceback (most recent call last): File "/<<PKGBUILDDIR>>/setup.py", line 130, in <module> ext_modules=get_ext_modules(), ^^^^^^^^^^^^^^^^^ File "/<<PKGBUILDDIR>>/setup.py", line 81, in get_ext_modules extra_link_args=pysam.get_libraries(), ^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in get_libraries return [os.path.join(dirname, x + so) for x in pysam_libs] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 100, in <listcomp> return [os.path.join(dirname, x + so) for x in pysam_libs] ~~^~~~ TypeError: can only concatenate str (not "NoneType") to str Thanks, Nilesh -- System Information: Debian Release: bookworm/sid APT prefers testing APT policy: (990, 'testing') Architecture: amd64 (x86_64) Kernel: Linux 6.0.0-6-amd64 (SMP w/8 CPU threads; PREEMPT) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
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--- Begin Message ---Source: pairtools Source-Version: 1.0.2-1 Done: Nilesh Patra <[email protected]> We believe that the bug you reported is fixed in the latest version of pairtools, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nilesh Patra <[email protected]> (supplier of updated pairtools package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Sun, 01 Jan 2023 17:51:23 +0530 Source: pairtools Architecture: source Version: 1.0.2-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Nilesh Patra <[email protected]> Closes: 1027232 1027335 Changes: pairtools (1.0.2-1) unstable; urgency=medium . [ Nilesh Patra ] * Team Upload. * Add patch to fix FTBFS with numpy 1.24 (Closes: #1027232) * Bump Standards-Version to 4.6.2 (no changes needed) * New upstream version 1.0.2 * Add patch for missing bam_dup1 declaration (Closes: #1027335) * Versioned Build dep against pysam * Build depend on python3-bioframe * Skip building docs, as manpages are not rendered the same way anymore * Get rid of B-D on sphinx-click * Move doc/examples/* installation to dedicated examples package * Add patch to not run coverage tests. It makes no sense to run them downstream. * Add patch to take python3 interpreter as different during testing, if CURPY var is set at runtime; helps run build time tests for all supported pyvers . [ Andreas Tille] * Fix clean target * Build-Depends: python3-pandas, python3-pysam, python3-scipy, libhts-dev, python3-yaml <!nocheck> Checksums-Sha1: 7cc8c2fab98560c912141b1def12250cf97bf624 1715 pairtools_1.0.2-1.dsc 09385e835484939f911315dbaf5f3aaa756bae3f 941541 pairtools_1.0.2.orig.tar.gz 5724830af24d92947bf41e66bd2216be9b4d6fff 6916 pairtools_1.0.2-1.debian.tar.xz d8bc03873abddb6c1c53391bb711893f5d0f5285 10945 pairtools_1.0.2-1_amd64.buildinfo Checksums-Sha256: 6d1cfc2104976c284b9b6a59d45b95e6101dc39becc9892a01c4c341272ab64e 1715 pairtools_1.0.2-1.dsc b0224263370d2c2847f383afcc7e2745715d51a2d444b3b7232da089bbd7ace1 941541 pairtools_1.0.2.orig.tar.gz af3abed92b5de81d67acb4660837cf9b7f7e00c4bd93e6a0843f9ec5f5ec7593 6916 pairtools_1.0.2-1.debian.tar.xz 5a78ae9e4a6494417ec1a2d2f6d36c70b32cc4bc0ffeadd73db6bb12cd83926f 10945 pairtools_1.0.2-1_amd64.buildinfo Files: 3ba4ece6dce9d31af666922a28f856d3 1715 python optional pairtools_1.0.2-1.dsc 797fb66f331793395ca92665e00b7fc6 941541 python optional pairtools_1.0.2.orig.tar.gz 6583c7f10e4f9120821f216f2e964f2a 6916 python optional pairtools_1.0.2-1.debian.tar.xz 823a41009021157aad8eb9ed564b5e34 10945 python optional pairtools_1.0.2-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iHUEARYIAB0WIQSglbZu4JAkvuai8HIqJ5BL1yQ+2gUCY7F+BAAKCRAqJ5BL1yQ+ 2qBMAQCYKLSH6kDisVHvdeikLAGU2lfYeJIGBp58R+QZ2D/HzgEA0EVtul7g4vou yR8h6/LNcr7S3QUgkIzvFYGUVbXvuQE= =xfgl -----END PGP SIGNATURE-----
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