Your message dated Tue, 31 Jul 2018 08:57:11 +0000 with message-id <e1fkqst-0001fy...@fasolo.debian.org> and subject line Bug#904735: fixed in samtools-legacy 0.1.19-4 has caused the Debian Bug report #904735, regarding libbam-dev: no longer built with -fPIC 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.) -- 904735: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=904735 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: libbio-samtools-perl Version: 1.43-1 Severity: serious Tags: ftbfs Control: block 902557 with -1 This package fails to build on sid/amd64: x86_64-linux-gnu-gcc -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -shared -L/usr/local/lib -fstack-protector-strong -o blib/arch/auto/Bio/DB/Sam/Sam.so lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o -L/usr/lib -lbam -lpthread -lz /usr/bin/ld: /usr/lib/libbam.a(bam_aux.o): relocation R_X86_64_PC32 against symbol `bam_verbose' can not be used when making a shared object; recompile with -fPIC /usr/bin/ld: final link failed: bad value collect2: error: ld returned 1 exit status error building blib/arch/auto/Bio/DB/Sam/Sam.so from lib/Bio/DB/Sam.o c_bin/bam2bedgraph.o at /usr/share/perl/5.26/ExtUtils/CBuilder/Base.pm line 321. dh_auto_build: perl Build returned exit code 2 make: *** [debian/rules:4: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 It seems to have built OK on test.reproducible-builds.org on 2018-07-12, so could be a binutils regression rather than libbam-dev? -- Niko Tyni nt...@debian.org
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--- Begin Message ---Source: samtools-legacy Source-Version: 0.1.19-4 We believe that the bug you reported is fixed in the latest version of samtools-legacy, 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 904...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated samtools-legacy 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: Tue, 31 Jul 2018 09:50:13 +0200 Source: samtools-legacy Binary: libbam-dev Architecture: source Version: 0.1.19-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: libbam-dev - manipulates nucleotide sequence alignments in BAM or SAM format Closes: 904735 Changes: samtools-legacy (0.1.19-4) unstable; urgency=medium . * Team upload. * Vcs-Browser points to correct branch * Standards-Version: 4.1.5 * Make sure it is build with -fPIC Closes: #904735 Checksums-Sha1: 612cb7bd00c64d426117ba0ebcc775373a78f14d 2039 samtools-legacy_0.1.19-4.dsc d261e5ed88949ffebd0259a79f8f2f3e518c91f4 8160 samtools-legacy_0.1.19-4.debian.tar.xz Checksums-Sha256: e6bf1fcc459c5a72045bc285fcef57a1cbf21bdd178f0ac95411c5ebd78274e3 2039 samtools-legacy_0.1.19-4.dsc daf23be151a527189c49138b82a6848d978402fa1b0fda101cf8a609119fcd94 8160 samtools-legacy_0.1.19-4.debian.tar.xz Files: 994e97b6ac6663a84b19810b7912a2bd 2039 science optional samtools-legacy_0.1.19-4.dsc 32e831d9b7119e259dfb37e735767f03 8160 science optional samtools-legacy_0.1.19-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAltgFq0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFaTA/+NduZ+v4rTpXDsELOw5qDlOlDvvjPSYan KBVm4rBR0KA9kS4ukCRA5Ri6hhexaijjiSNsQH3RnUDWEOmf40lggyxYtbXrIsjp k9wailFpSp4BtDXhVZhwHpvFb5Y3XOlBaFRQvyrvFmir39fK9HuNkcMmKsU1bq0G lxGBexyrgpbu5WALKVQMy1LdbNr4G0MwZQ64nOnbqQaFUzpd+CNCX3um9BVffUqN B76pn113pvg3TO+jZuFsnE3oKGHrJm6Hg3383ZAfGHcSDdMIch4GDHgx78QKLNTR aO1ZC1xepJpXF37uzNr1FA4VR0Fgwa6nDjnLht5mGcOtlg5e1nw/K6dKkVPVSg08 wsVNPWQBQN+cDgUQhCrHdZSQtdaguz/5XoDVEYt+y7NHpCjBXrz+6EYXPKIc3uOx RxxBEY4M1mpqf0KmvVL9fzZ8YF4Q01iQvzIWTlT9qeYkM8WyaECOONQ8KmeP97Ny clGb/6534g72thGNUQnRPcqvDFOmNnNcl2Wv8Zc79855ZEsGG2aibFl6VjIH2YHA nq1ouy81AsQrRdyfVSLSpIrIb1BEvL+hwK0v+ZY/6qdZHJ9a7X05n8+KwZSJkkM3 +Y/Aleh79ApQBIZ5mW8a2xPC9/x/74ImqkngnQDbYtqUg6ffeCQUPqr2ctpXSONs WlVgM++UCjg= =U7ch -----END PGP SIGNATURE-----
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