Your message dated Wed, 27 Nov 2013 07:49:02 +0000 with message-id <e1vlzrq-0007nl...@franck.debian.org> and subject line Bug#730574: fixed in r-bioc-genomicranges 1.14.3-1 has caused the Debian Bug report #730574, regarding r-bioc-genomicranges: FTBFS: error: unknown type name 'cachedCharSeq' 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.) -- 730574: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=730574 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: r-bioc-genomicranges Version: 1.12.4-1 Severity: serious Hi, r-bioc-genomicranges FTBFS like this: ... gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/IRanges/include" -fpic -O3 -pipe -g -c transcript_utils.c -o transcript_utils.o transcript_utils.c:146:1: error: unknown type name 'cachedCharSeq' transcript_utils.c: In function 'copy_exon': transcript_utils.c:154:3: warning: implicit declaration of function 'Orevcopy_bytes_from_i1i2_with_lkup' [-Wimplicit-function-declaration] transcript_utils.c:156:6: error: request for member 'seq' in something not a structure or union transcript_utils.c:156:15: error: request for member 'length' in something not a structure or union transcript_utils.c:159:3: warning: implicit declaration of function 'Ocopy_bytes_from_i1i2_with_lkup' [-Wimplicit-function-declaration] transcript_utils.c:161:6: error: request for member 'seq' in something not a structure or union transcript_utils.c:161:15: error: request for member 'length' in something not a structure or union transcript_utils.c: At top level: transcript_utils.c:167:1: error: unknown type name 'cachedCharSeq' transcript_utils.c: In function 'extract_transcripts': transcript_utils.c:260:2: error: unknown type name 'cachedCharSeq' transcript_utils.c:262:2: error: unknown type name 'cachedXVectorList' transcript_utils.c:266:2: warning: implicit declaration of function 'cache_XRaw' [-Wimplicit-function-declaration] transcript_utils.c:269:2: error: request for member 'length' in something not a structure or union transcript_utils.c:271:2: warning: implicit declaration of function 'alloc_XRawList' [-Wimplicit-function-declaration] transcript_utils.c:271:2: warning: assignment makes pointer from integer without a cast [enabled by default] transcript_utils.c:273:2: warning: implicit declaration of function 'cache_XVectorList' [-Wimplicit-function-declaration] transcript_utils.c:274:2: warning: implicit declaration of function 'get_cachedXVectorList_length' [-Wimplicit-function-declaration] transcript_utils.c:285:3: warning: implicit declaration of function 'get_cachedXRawList_elt' [-Wimplicit-function-declaration] transcript_utils.c:288:29: error: request for member 'seq' in something not a structure or union make[1]: *** [transcript_utils.o] Error 1 make[1]: Leaving directory `/«PKGBUILDDIR»/src' make[1]: Entering directory `/«PKGBUILDDIR»/src' make[1]: Leaving directory `/«PKGBUILDDIR»/src' ERROR: compilation failed for package 'GenomicRanges' * removing '/«PKGBUILDDIR»/debian/r-bioc-genomicranges/usr/lib/R/site-library/GenomicRanges' make: *** [R_any_arch] Error 1 ... Roland -- System Information: Debian Release: 7.0 APT prefers unreleased APT policy: (500, 'unreleased'), (500, 'unstable') Architecture: powerpcspe (ppc) Kernel: Linux 3.9.0-dirty (SMP w/2 CPU cores) Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8) (ignored: LC_ALL set to en_GB.UTF-8) Shell: /bin/sh linked to /bin/dash
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--- Begin Message ---Source: r-bioc-genomicranges Source-Version: 1.14.3-1 We believe that the bug you reported is fixed in the latest version of r-bioc-genomicranges, 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 730...@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-genomicranges 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: SHA1 Format: 1.8 Date: Tue, 26 Nov 2013 19:52:13 +0100 Source: r-bioc-genomicranges Binary: r-bioc-genomicranges Architecture: source amd64 Version: 1.14.3-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: r-bioc-genomicranges - BioConductor representation and manipulation of genomic intervals Closes: 730574 Changes: r-bioc-genomicranges (1.14.3-1) unstable; urgency=low . * New upstream version Closes: #730574 * Build-Depends: r-bioc-xvector Checksums-Sha1: 3189def3b9f7216720b148d6b83de24550ff0715 1564 r-bioc-genomicranges_1.14.3-1.dsc 7e1b3cdd88791f675e50927f55758e8c9be37e13 2238516 r-bioc-genomicranges_1.14.3.orig.tar.gz c325bfb7bba50b1b24a5c1e63a8dac0829cbf13a 4238 r-bioc-genomicranges_1.14.3-1.debian.tar.gz bf0bdb064b705e80df1821907d6ae0f071ecf8eb 2842424 r-bioc-genomicranges_1.14.3-1_amd64.deb Checksums-Sha256: ac12a38f4e14b6705150484e62f380a8d89ba646734f98685c7ebe364b1a5033 1564 r-bioc-genomicranges_1.14.3-1.dsc f537cfd9bc711e8c1a769fcc9dfaceb90a068e78adf14bb126343c901135cf69 2238516 r-bioc-genomicranges_1.14.3.orig.tar.gz 816eb363871b2a92884d3870013e23c1c066df07557995ea5f6da22283edaa1e 4238 r-bioc-genomicranges_1.14.3-1.debian.tar.gz 8d568c10f25f9aa3605a47cf12dca4867b65e2acf258051fc1cea22f7f1d72cc 2842424 r-bioc-genomicranges_1.14.3-1_amd64.deb Files: e6c1312afe13f79b2fc35ba86a1cdf97 1564 gnu-r optional r-bioc-genomicranges_1.14.3-1.dsc c5831b8b65363c18edaafcf9426d455e 2238516 gnu-r optional r-bioc-genomicranges_1.14.3.orig.tar.gz ca6bdb8ed70936e7c774a8f902996746 4238 gnu-r optional r-bioc-genomicranges_1.14.3-1.debian.tar.gz cd6262209bf9f4220f4b53fae3c147e3 2842424 gnu-r optional r-bioc-genomicranges_1.14.3-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) iEYEARECAAYFAlKVovIACgkQYDBbMcCf01ojvgCfUJ9N9ckSSVLO+X1voVmk5r8e LnUAoKtREt19GPVzItqUhi4PCMOOs0aL =YQEA -----END PGP SIGNATURE-----
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