Your message dated Sun, 01 Dec 2013 09:20:03 +0000 with message-id <[email protected]> and subject line Bug#730984: fixed in r-bioc-rsamtools 1.14.2-1 has caused the Debian Bug report #730984, regarding r-bioc-rsamtools: FTBFS: fatal error: XVector_defines.h: No such file or directory 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 [email protected] immediately.) -- 730984: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=730984 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: r-bioc-rsamtools Version: 1.12.4-1 Severity: serious Hi, r-bioc-rsamtools FTBFS like this: ... dh_installdirs usr/lib/R/site-library echo "R:Depends=r-base-core (>= 3.0.2-1)" >> debian/r-bioc-rsamtools.substvars if test -f /usr/bin/xvfb-run; then \ xvfb-run -a \ R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean \ . ; \ else \ R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library \ --clean . ;\ fi * installing *source* package 'Rsamtools' ... ** libs make[1]: Entering directory `/«PKGBUILDDIR»/src' gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Biostrings/include" -I"/usr/lib/R/site-library/IRanges/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 -O3 -pipe -g -c Biostrings_stubs.c -o Biostrings_stubs.o In file included from /usr/lib/R/site-library/Biostrings/include/Biostrings_interface.h:114:0, from /usr/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:1, from Biostrings_stubs.c:1: /usr/lib/R/site-library/Biostrings/include/Biostrings_defines.h:19:29: fatal error: XVector_defines.h: No such file or directory compilation terminated. make[1]: *** [Biostrings_stubs.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 'Rsamtools' * removing '/«PKGBUILDDIR»/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools' 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-rsamtools Source-Version: 1.14.2-1 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <[email protected]> (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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Sun, 01 Dec 2013 09:45:58 +0100 Source: r-bioc-rsamtools Binary: r-bioc-rsamtools Architecture: source amd64 Version: 1.14.2-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i Closes: 730984 Changes: r-bioc-rsamtools (1.14.2-1) unstable; urgency=low . * New upstream version (adapted patch) Closes: #730984 * Build-Depends: r-bioc-xvector Checksums-Sha1: 1ceab71d637f215d08b94a4feafa885243da2b84 1588 r-bioc-rsamtools_1.14.2-1.dsc a6c48a9d0f3cdf783d9e197a87bfb75322b0534a 2954830 r-bioc-rsamtools_1.14.2.orig.tar.gz b5093289b50254b7a0ebe3151b2387fa68a57b5e 6548 r-bioc-rsamtools_1.14.2-1.debian.tar.gz dfe2a9b6b65f0efc14c113dc870ee83f0b6e7114 3213350 r-bioc-rsamtools_1.14.2-1_amd64.deb Checksums-Sha256: a71077637d4b82821d4f13d01bcae8f8db5ddbd6603878b566bbeaf84193ff82 1588 r-bioc-rsamtools_1.14.2-1.dsc 4fb6c0e1d7d47bddd7db2462f40b2780240cfd3f61ecada45aa9e9b3b98e471f 2954830 r-bioc-rsamtools_1.14.2.orig.tar.gz 66b4e0287337488cf0e83ea670620b434610f9f39cb4210c2b3f6501eff0496f 6548 r-bioc-rsamtools_1.14.2-1.debian.tar.gz 98ee615b57419e1996871898d5e5222a5bca8d26268d5740fae7a2b33831ebff 3213350 r-bioc-rsamtools_1.14.2-1_amd64.deb Files: 593350f73a4d57386a0a3ec9faaad49d 1588 gnu-r optional r-bioc-rsamtools_1.14.2-1.dsc 83aa5c41214583f83c86bcc90355d59e 2954830 gnu-r optional r-bioc-rsamtools_1.14.2.orig.tar.gz 168279be05272a81bccbc9f1c49185a0 6548 gnu-r optional r-bioc-rsamtools_1.14.2-1.debian.tar.gz a2c7542be77143531317065df6be2996 3213350 gnu-r optional r-bioc-rsamtools_1.14.2-1_amd64.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) iEYEARECAAYFAlKa+pIACgkQYDBbMcCf01o0AQCdHok0j8TUHtMJBmiPYEIjE1dv x8EAn1zuj5vQeWrhSCOQSQJ+K10uY6pT =RFK/ -----END PGP SIGNATURE-----
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