Your message dated Wed, 09 Jul 2014 13:03:50 +0000 with message-id <e1x4rxk-0001vb...@franck.debian.org> and subject line Bug#753233: fixed in r-bioc-rsamtools 1.16.1-2 has caused the Debian Bug report #753233, regarding r-bioc-rsamtools: FTBFS: utilities.c:99:5: error: unknown type name 'cachedXVectorList' 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.) -- 753233: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=753233 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: r-bioc-rsamtools Version: 1.14.2-1 Severity: serious Tags: jessie sid User: debian...@lists.debian.org Usertags: qa-ftbfs-20140628 qa-ftbfs Justification: FTBFS on amd64 Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG > -I"/usr/lib/R/site-library/IRanges/include" > -I"/usr/lib/R/site-library/XVector/include" > -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -D_USE_KNETFILE > -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -Dfprintf=_samtools_fprintf > -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools > -I./samtools/bcftools -I./tabix -fpic -g -O2 -fstack-protector > --param=ssp-buffer-size=4 -Wformat -Werror=format-security > -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o > utilities.c: In function '_as_XStringSet': > utilities.c:99:5: error: unknown type name 'cachedXVectorList' > cachedXVectorList cache; > ^ > utilities.c:100:5: error: unknown type name 'cachedCharSeq' > cachedCharSeq dest; > ^ > utilities.c:101:5: warning: implicit declaration of function > 'cache_XVectorList' [-Wimplicit-function-declaration] > cache = cache_XVectorList(ans); > ^ > utilities.c:104:9: warning: implicit declaration of function > 'get_cachedXRawList_elt' [-Wimplicit-function-declaration] > dest = get_cachedXRawList_elt(&cache, i); > ^ > utilities.c:105:46: error: request for member 'length' in something not a > structure or union > Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, (char *) dest.seq, > ^ > utilities.c:105:72: error: request for member 'seq' in something not a > structure or union > Ocopy_bytes_to_i1i2_with_lkup(0, dest.length - 1, (char *) dest.seq, > ^ > utilities.c:106:43: error: request for member 'length' in something not a > structure or union > dest.length, seq, strlen(seq), lkup0, > ^ > make[1]: *** [utilities.o] Error 1 The full build log is available from: http://aws-logs.debian.net/ftbfs-logs/2014/06/28/r-bioc-rsamtools_1.14.2-1_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
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--- Begin Message ---Source: r-bioc-rsamtools Source-Version: 1.16.1-2 We believe that the bug you reported is fixed in the latest version of r-bioc-rsamtools, 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 753...@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-rsamtools 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 Jul 2014 13:38:19 +0200 Source: r-bioc-rsamtools Binary: r-bioc-rsamtools Architecture: source amd64 Version: 1.16.1-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i Closes: 753233 Changes: r-bioc-rsamtools (1.16.1-2) unstable; urgency=medium . * debian/README.test: Fix advise for testing the package * debian/control: Recommends: r-bioc-shortread * Rebuild against recent BioC tools Closes: #753233 Checksums-Sha1: 3c721385c92d7cf38fd968c7ec66a6f3b0d648d2 2216 r-bioc-rsamtools_1.16.1-2.dsc 4ea80cb99a398b8857fb45ce21b36177fea1c022 6328 r-bioc-rsamtools_1.16.1-2.debian.tar.xz 964c44356dcfdbb05c7bbe27ad34a9a78f76cf34 3132034 r-bioc-rsamtools_1.16.1-2_amd64.deb Checksums-Sha256: e13965a06b2aff8016a387f38fa8dfd4b7b7924dee18eade61e0bf2a25ab57a8 2216 r-bioc-rsamtools_1.16.1-2.dsc e68b01eea04d5bd9c56309aa9a8902b925f4cf462492ca414fa0584254c2f4ef 6328 r-bioc-rsamtools_1.16.1-2.debian.tar.xz 77efe4d2bf9e692bacee85057df74d60f48002eeb1385bf0b4290c877a128cd8 3132034 r-bioc-rsamtools_1.16.1-2_amd64.deb Files: d0cba37232bb75c412f6eed36362ce1a 3132034 gnu-r optional r-bioc-rsamtools_1.16.1-2_amd64.deb 9e6abe89f646afb1c0a8f42992f257ae 2216 gnu-r optional r-bioc-rsamtools_1.16.1-2.dsc 40f6737c80094b7c704ef1f14ba0f497 6328 gnu-r optional r-bioc-rsamtools_1.16.1-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJTvTuQAAoJEFeKBJTRxkbRZjAP/2UWl2S+9yFtzj70UWPZqLWP uVl93At5uxDuNdACLPTLy0tLaaA/ZQ0YypRXNtZVzn/tBkrjEI78O4OMexPF8iwI sWObY0HI184REh9ZjHAATiipmkmLxY4sxDqCbYdpMpDltIj/ppuDffu/0Kiu/sNl 8J9a4ntxrR7CmNim+00kOF0HYN5UzI+Ky+4rGQsml2fnzQmz8z5jRXGGvcJFEMVe 7VXFGSyNq2vLN2hf0UdIYWsVNQ9Bif7wj7RQ+bH6Jeq30JXSYM4eQ/99h9W8xtvX QkfbIIEvTuANPZhbmbBaBtxJIFOUqTY/mr99YpL4o3zpU79GaVA7F7JjIV/ZTvWL IHOzDRueWpzIrKS5W61CYcbzgJyf5EbThxnQ9u7jr3xnjUaPa/4RMQ1EJ6bpqna+ evFcr+6BjcjisDh0/sjwfR4ydSnuewmCTJK7gDNjkdeXIB94ZPUreBPNFb41nROF uuS0CHbte+CWig16S8WL9/QZbg1RLp6xmbdBtgLNwHW8lUYUj1VIntwo2QfcRn1E CQOn3O9NVG+Olg0p5HOWHh0SjwVaz7n5U8b4FaQKcbEzoq9ahUELkzVnLaRD9a9m 3yqumys1Qa7K50qrCthgMtd2zwTXHRfATvbDdCMjwnbswDiOYKxNwVNE63UMEryd EQkPEwyXhTyjYEE41ere =esWu -----END PGP SIGNATURE-----
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