Your message dated Thu, 10 Mar 2016 10:21:55 +0000 with message-id <e1adxj9-0005t7...@franck.debian.org> and subject line Bug#814765: fixed in python-pysam 0.9.0+ds-1 has caused the Debian Bug report #814765, regarding python-pysam: FTBFS: samtools index: "ex2_truncated.bam" is corrupted or unsorted 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 ow...@bugs.debian.org immediately.) -- 814765: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=814765 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: python-pysam Version: 0.8.4+ds-1 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org Dear Maintainer, python-pysam fails to build from source in unstable/amd64: [..] samtools index softclip.bam samtools index tag_bug.bam samtools index ex10.bam samtools index example_empty_header.bam samtools index test_unaligned.bam samtools index ex9_fail.bam samtools index issue100.bam samtools index ex5.bam samtools index ex6.bam samtools index rg_with_tab.bam samtools index ex9_nofail.bam samtools index example_btag.bam samtools index example_unmapped_reads_no_sq.bam samtools index ex4.bam samtools index example_user_header.bam samtools index ex8.bam samtools index ex3.bam samtools view -bC -T ex1.fa ex1.sam > ex1.cram samtools view -bC -T ex1.fa ex2.sam > ex2.cram samtools view -bC -T ex1.fa ex3.sam > ex3.cram samtools index ex1.cram samtools index ex2.cram samtools index ex3.cram cp ex1.bam example_bai.bam samtools index example_bai.bam mv example_bai.bam.bai example_bai.bai head -c 124000 ex2.bam > ex2_truncated.bam samtools index ex2_truncated.bam [W::bam_hdr_read] EOF marker is absent. The input is probably truncated. samtools index: "ex2_truncated.bam" is corrupted or unsorted Makefile:48: recipe for target 'ex2_truncated.bam.bai' failed make[2]: *** [ex2_truncated.bam.bai] Error 1 make[2]: Leaving directory '/home/lamby/temp/cdt.20160215090723.RznKM9ufGc/python-pysam-0.8.4+ds/tests/pysam_data' debian/rules:26: recipe for target 'override_dh_auto_test' failed make[1]: *** [override_dh_auto_test] Error 2 make[1]: Leaving directory '/home/lamby/temp/cdt.20160215090723.RznKM9ufGc/python-pysam-0.8.4+ds' debian/rules:20: recipe for target 'build' failed make: *** [build] Error 2 [..] The full build log is attached. Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-
python-pysam.0.8.4+ds-1.unstable.amd64.log.txt.gz
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--- Begin Message ---Source: python-pysam Source-Version: 0.9.0+ds-1 We believe that the bug you reported is fixed in the latest version of python-pysam, 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 814...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Afif Elghraoui <a...@debian.org> (supplier of updated python-pysam 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 09 Mar 2016 23:43:59 -0800 Source: python-pysam Binary: python-pysam python3-pysam python-pysam-tests Architecture: source Version: 0.9.0+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Afif Elghraoui <a...@debian.org> Description: python-pysam - interface for the SAM/BAM sequence alignment and mapping format ( python-pysam-tests - interface for the SAM/BAM sequence alignment and mapping format ( python3-pysam - interface for the SAM/BAM sequence alignment and mapping format ( Closes: 814765 Changes: python-pysam (0.9.0+ds-1) unstable; urgency=medium . * Add filenamemangle to d/watch and space out content * Imported Upstream version 0.9.0+ds (Closes: #814765) * Bump htslib and samtools minimum versions * Update policy statndards-version to 3.9.7 * Use encrypted protocols for Vcs URLs in d/control * Use readthedocs page as pysam's homepage * Update packaging for external htslib link * Refresh patches * Delete obsolete patch Checksums-Sha1: b0c50f117257b4a4d12ea1e4fc5c761c84f77996 2434 python-pysam_0.9.0+ds-1.dsc 0785911909d818d92b63fe64cea3cdf72e3d74ac 2267692 python-pysam_0.9.0+ds.orig.tar.gz 91f58c4405241e0f6d36bd86f37fbcf57c78dfc6 9284 python-pysam_0.9.0+ds-1.debian.tar.xz Checksums-Sha256: 590d476697b631aeb0ee1c1ff2d2f25daf18f1eaa454f3134c113a37e7533f83 2434 python-pysam_0.9.0+ds-1.dsc 2a35ce4269b34c19a8812711683a9a878c9c2ad633c05ecfb2cb2d8524aac007 2267692 python-pysam_0.9.0+ds.orig.tar.gz fa01aa54229e556e11154942a7bafbb550ab3efe29142127f89f66ac68f53027 9284 python-pysam_0.9.0+ds-1.debian.tar.xz Files: d1acd10e31517e04a54ed996dd516522 2434 python optional python-pysam_0.9.0+ds-1.dsc b15242fff8fc11f2ce184976d022b0d7 2267692 python optional python-pysam_0.9.0+ds.orig.tar.gz 6701648f251b7dae1128445f4356aceb 9284 python optional python-pysam_0.9.0+ds-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJW4Sa0AAoJEM6uatOv6Cb7DZwP/iLyLQWo2c9KiHW3BKOAP1YC uzxG+3czsE16BRMHgpl9eAMLAsD2zDlC79m+CPdspRVYC25FFE5I3o+349JV6vpy xQGmrLM/D8TvRpGbGQie5a1TkGyJTqGtwBQW3kx0PDbKYkIegaueruXPyvmFxOhm jK5hyH1ZmCO+g/r3myjL1MoQ9KzXQJOdwPCnSN611dVf5cL+hrWZJVpaShe+dFIB 54MAQuL7LaRjjlH7X/k1kubgDtIhCnSdwZE1SAkuGKFKqCUnmnLBQI1so6ejh+OA /pVKiGaCV2jS3ynKXvJSzp7Caz3yGAqR7CKPtssUkDlfjf7WH71P9yiGQj1K7ucA vAY/ggP89G5tecX6lYff1JFEmytlDgoCOpWOL9ZNOnDo4IE/RntQ0lvP052uu7at WoV5SKKOJ0AZmwovITne8ZAZv69utiCVkBOMbtlvc/jke4Z3CfuBTHLJ17NDSbBZ ggQFdtQwCP9wE7eGN+sBS2cZUFYm6PjKVrchd72sVoZbqKMkoAwTfqZUjPBSC2vM jcYKwivyR6K3TT/ltftW006XAt816ajj3y3YTqwgJIpkeerftfFAwgQOAasio9w1 pucVQzLeDECVx8tgDRajy/3Odq3GJwJLCENWXb4Fx9JZlp7ZTVkT0TerttxxqHiD L4rieAZZfd6dFkESwC4H =vPVX -----END PGP SIGNATURE-----
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