Your message dated Tue, 28 Jul 2020 07:03:51 +0000 with message-id <e1k0jer-000abl...@fasolo.debian.org> and subject line Bug#966236: fixed in r-bioc-rsubread 2.2.5-1 has caused the Debian Bug report #966236, regarding r-bioc-rsubread FTBFS with gcc 10 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.) -- 966236: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966236 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: r-bioc-rsubread Version: 2.2.2-1 Severity: serious Tags: ftbfs fixed-upstream https://buildd.debian.org/status/package.php?p=r-bioc-rsubread ... gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsubread.so HelperFunctions.o LRMbase-index.o LRMchro-event.o LRMfile-io.o LRMhashtable.o LRMhelper.o LRMseek-zlib.o LRMsorted-hashtable.o R_wrapper.o RsimReads.o SNPCalling.o aligner.o atgcContent.o build-sam-index.o core-bigtable.o core-indel.o core-interface-aligner.o core-interface-subjunc.o core-junction.o core.o detection-calls.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align-indel.o exon-align.o flattenAnnotations.o fullscan.o fusion-align.o gen_rand_reads.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-blc.o input-files.o interval_merge.o long-hashtable.o longread-mapping.o mergeVCF.o processExons.o propmapped.o qualityScores.o read-repair.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o seek-zlib.o sorted-hashtable.o sublog.o tx-unique.o -lz -lpthread -DMAKE_FOR_EXON -L/usr/lib/R/lib -lR /usr/bin/ld: detectionCallAnnotation.o:/<<PKGBUILDDIR>>/src/detectionCallAnnotation.c:54: multiple definition of `chr_num'; detectionCall.o:/<<PKGBUILDDIR>>/src/detectionCall.c:88: first defined here /usr/bin/ld: detectionCallAnnotation.o:/<<PKGBUILDDIR>>/src/detectionCallAnnotation.c:51: multiple definition of `exon'; detectionCall.o:/<<PKGBUILDDIR>>/src/detectionCall.c:85: first defined here /usr/bin/ld: detectionCallAnnotation.o:/<<PKGBUILDDIR>>/src/detectionCallAnnotation.c:52: multiple definition of `ir'; detectionCall.o:/<<PKGBUILDDIR>>/src/detectionCall.c:86: first defined here /usr/bin/ld: detectionCallAnnotation.o:/<<PKGBUILDDIR>>/src/detectionCallAnnotation.c:55: multiple definition of `current_chr_id'; detectionCall.o:/<<PKGBUILDDIR>>/src/detectionCall.c:89: first defined here /usr/bin/ld: processExons.o:/<<PKGBUILDDIR>>/src/processExons.c:62: multiple definition of `exon_file'; detectionCallAnnotation.o:/<<PKGBUILDDIR>>/src/detectionCallAnnotation.c:58: first defined here collect2: error: ld returned 1 exit status make[1]: *** [/usr/share/R/share/make/shlib.mk:6: Rsubread.so] Error 1 Upstream git says: 24 July 2020 - 2.2.5 (1) Fix errors reported by gcc-10.
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--- Begin Message ---Source: r-bioc-rsubread Source-Version: 2.2.5-1 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of r-bioc-rsubread, 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 966...@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 r-bioc-rsubread 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: Mon, 27 Jul 2020 11:44:20 +0200 Source: r-bioc-rsubread Architecture: source Version: 2.2.5-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net> Changed-By: Andreas Tille <ti...@debian.org> Closes: 966236 Changes: r-bioc-rsubread (2.2.5-1) unstable; urgency=medium . * Team upload. * New upstream version Closes: #966236 * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/copyright (routine-update) * Trim trailing whitespace. Checksums-Sha1: 60e95cfdefa07f7d9555a2669969cea7d2df29c1 2090 r-bioc-rsubread_2.2.5-1.dsc 933da69572d980307b8a7d25a60a30a74c733814 10826597 r-bioc-rsubread_2.2.5.orig.tar.gz 094fbefc8c83a0650901d5adc0cbe4dd0262ca79 3432 r-bioc-rsubread_2.2.5-1.debian.tar.xz e7d68ecc695f0c9d48b356032b718355b403bb17 8903 r-bioc-rsubread_2.2.5-1_amd64.buildinfo Checksums-Sha256: 27836f84f8c7d3b1ee9a89a38306a41a7b1d2c60bedd7e2136647ceb6873c45e 2090 r-bioc-rsubread_2.2.5-1.dsc c4791391c471dec2222a94dffbdd6d9982a1fa57ead724605d4198215870c52d 10826597 r-bioc-rsubread_2.2.5.orig.tar.gz 0fdf01f4404acf7419f2163c03df76794adf1bd8edfe15be0d2f87e3aa219ef2 3432 r-bioc-rsubread_2.2.5-1.debian.tar.xz e516fdb56801cec50441eea02930fef5beb11671e7fcce45f230610847c730ec 8903 r-bioc-rsubread_2.2.5-1_amd64.buildinfo Files: b064db1648c16ac521e193bca835f671 2090 gnu-r optional r-bioc-rsubread_2.2.5-1.dsc a1367ffdb0f4cc71f22e4de45fa21e8b 10826597 gnu-r optional r-bioc-rsubread_2.2.5.orig.tar.gz bd2e1a141357187e6268530277e20cd3 3432 gnu-r optional r-bioc-rsubread_2.2.5-1.debian.tar.xz c000401b8e6e8099982913f3c6eb82e8 8903 gnu-r optional r-bioc-rsubread_2.2.5-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl8fx1YRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE21A//S+cWmqCTMVqH2AQLwAZtEdJYou4/A9xG 9OFmxki4BgR+jDAxw8a5qzdYKHZqR0y93vN6+oWkUdjGGvk9sqG7TB9dFf2ddpWN QIpi8Sm+ze6rKeQGyIFQ+XfcsmNhukmztXjPMBOijHVXVxPKcNYuCqjjc9HiU2zR CUtkrl++N+lnDSw0zTfRhRVpK0LVrWx9xkRjqjdDN07BgzUyLNCmZNI5QbY6I8ls etZ0UN92rsB/IdptsUDqUfQkS4EwkYBpnMlYEl1Qe0kSXoYKlNzgkTXkJ35Flxvr jN6j0pje83nVRmBKrHXJfEqDknqU8n+oRwqFJlUlvRC7McSZK7ZVhIIyv2/eo7yx RQ4iq41WHDQckBMlK7DZ1HRfl/FzeO28IqBjll2RhjABU5KL07AzN+luTdMz4gbv iipqFBpZu0yrPUrZZl0tUKM03dcgfv3igDFaydN5D3pma9SUjQpcZdhVZiL0qr79 icmc94XVSf+AEdrOSaFZCa7z0Zmz7EabLyiGKjXHsUL0SAOGAPiqbRc1g55fC7AY /jsoBv+Vn8MskBA43g6BFkHiZyNv17g4p0Sm6NWMBMmAt7ICj60UmcsPXxtzeKSK 3Ma4t/woO4QvWz1IEPIf5s5SccoOgVQR6naN6w21fs+LrzApuqTq5zBuBdyjuVy7 IulHypyV6TU= =AwuF -----END PGP SIGNATURE-----
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