Author: ginggs Date: 2017-05-29 13:00:05 +0000 (Mon, 29 May 2017) New Revision: 23769
Added: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/ trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch Removed: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use-debian-packaged-libs.patch trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch Log: Tagged 1.28.0-1 Deleted: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog 2017-05-26 15:55:33 UTC (rev 23767) +++ trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog 2017-05-29 13:00:05 UTC (rev 23769) @@ -1,90 +0,0 @@ -r-bioc-rsamtools (1.26.1-2) unstable; urgency=medium - - * Remove test requiring network connection - * debhelper 10 - * d/watch: version=4 - * drop unused lintian override - - -- Andreas Tille <[email protected]> Sun, 15 Jan 2017 17:25:11 +0100 - -r-bioc-rsamtools (1.26.1-1) unstable; urgency=medium - - * New upstream version - * Convert to dh-r - * Generic BioConductor homepage - - -- Andreas Tille <[email protected]> Wed, 26 Oct 2016 17:15:09 +0200 - -r-bioc-rsamtools (1.24.0-1) unstable; urgency=medium - - * New upstream version - * Fix versioned Dependencies - - -- Andreas Tille <[email protected]> Sun, 08 May 2016 21:06:24 +0200 - -r-bioc-rsamtools (1.22.0-2) unstable; urgency=medium - - * Fix autopkgtest by adding r-cran-runit - * cme fix dpkg-control - - -- Andreas Tille <[email protected]> Wed, 27 Apr 2016 20:29:49 +0200 - -r-bioc-rsamtools (1.22.0-1) unstable; urgency=medium - - * New upstream version - * (Build-)Depends: r-bioc-biocparallel - * Add lintian-override for false positive - - -- Andreas Tille <[email protected]> Fri, 30 Oct 2015 14:05:41 +0100 - -r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium - - * New upstream version - - -- Andreas Tille <[email protected]> Sat, 27 Jun 2015 16:20:16 +0200 - -r-bioc-rsamtools (1.20.1-1) unstable; urgency=medium - - * New upstream version - * Activate autopkgtest - - -- Andreas Tille <[email protected]> Mon, 11 May 2015 11:34:17 +0200 - -r-bioc-rsamtools (1.18.0-1) experimental; urgency=medium - - * New upstream version - * cme fix dpkg-control - - -- Andreas Tille <[email protected]> Mon, 20 Oct 2014 18:30:04 +0200 - -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 - - -- Andreas Tille <[email protected]> Wed, 09 Jul 2014 13:38:19 +0200 - -r-bioc-rsamtools (1.16.1-1) unstable; urgency=medium - - * New upstream version - * cme fix dpkg-control - * debian/README.test: More verbose information how to run the - test suite - - -- Andreas Tille <[email protected]> Mon, 16 Jun 2014 16:28:55 +0200 - -r-bioc-rsamtools (1.14.2-1) unstable; urgency=low - - * New upstream version (adapted patch) - Closes: #730984 - * Build-Depends: r-bioc-xvector - - -- Andreas Tille <[email protected]> Sun, 01 Dec 2013 09:45:58 +0100 - -r-bioc-rsamtools (1.12.4-1) unstable; urgency=low - - * Initial release (closes: #728285) - - -- Andreas Tille <[email protected]> Wed, 04 Sep 2013 11:11:22 +0200 Copied: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog (from rev 23768, trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog) =================================================================== --- trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog (rev 0) +++ trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/changelog 2017-05-29 13:00:05 UTC (rev 23769) @@ -0,0 +1,98 @@ +r-bioc-rsamtools (1.28.0-1) unstable; urgency=medium + + * Team upload + * New upstream version + * Drop unused debian/patches/use-debian-packaged-libs.patch + + -- Graham Inggs <[email protected]> Mon, 29 May 2017 13:43:34 +0200 + +r-bioc-rsamtools (1.26.1-2) unstable; urgency=medium + + * Remove test requiring network connection + * debhelper 10 + * d/watch: version=4 + * drop unused lintian override + + -- Andreas Tille <[email protected]> Sun, 15 Jan 2017 17:25:11 +0100 + +r-bioc-rsamtools (1.26.1-1) unstable; urgency=medium + + * New upstream version + * Convert to dh-r + * Generic BioConductor homepage + + -- Andreas Tille <[email protected]> Wed, 26 Oct 2016 17:15:09 +0200 + +r-bioc-rsamtools (1.24.0-1) unstable; urgency=medium + + * New upstream version + * Fix versioned Dependencies + + -- Andreas Tille <[email protected]> Sun, 08 May 2016 21:06:24 +0200 + +r-bioc-rsamtools (1.22.0-2) unstable; urgency=medium + + * Fix autopkgtest by adding r-cran-runit + * cme fix dpkg-control + + -- Andreas Tille <[email protected]> Wed, 27 Apr 2016 20:29:49 +0200 + +r-bioc-rsamtools (1.22.0-1) unstable; urgency=medium + + * New upstream version + * (Build-)Depends: r-bioc-biocparallel + * Add lintian-override for false positive + + -- Andreas Tille <[email protected]> Fri, 30 Oct 2015 14:05:41 +0100 + +r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium + + * New upstream version + + -- Andreas Tille <[email protected]> Sat, 27 Jun 2015 16:20:16 +0200 + +r-bioc-rsamtools (1.20.1-1) unstable; urgency=medium + + * New upstream version + * Activate autopkgtest + + -- Andreas Tille <[email protected]> Mon, 11 May 2015 11:34:17 +0200 + +r-bioc-rsamtools (1.18.0-1) experimental; urgency=medium + + * New upstream version + * cme fix dpkg-control + + -- Andreas Tille <[email protected]> Mon, 20 Oct 2014 18:30:04 +0200 + +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 + + -- Andreas Tille <[email protected]> Wed, 09 Jul 2014 13:38:19 +0200 + +r-bioc-rsamtools (1.16.1-1) unstable; urgency=medium + + * New upstream version + * cme fix dpkg-control + * debian/README.test: More verbose information how to run the + test suite + + -- Andreas Tille <[email protected]> Mon, 16 Jun 2014 16:28:55 +0200 + +r-bioc-rsamtools (1.14.2-1) unstable; urgency=low + + * New upstream version (adapted patch) + Closes: #730984 + * Build-Depends: r-bioc-xvector + + -- Andreas Tille <[email protected]> Sun, 01 Dec 2013 09:45:58 +0100 + +r-bioc-rsamtools (1.12.4-1) unstable; urgency=low + + * Initial release (closes: #728285) + + -- Andreas Tille <[email protected]> Wed, 04 Sep 2013 11:11:22 +0200 Deleted: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use-debian-packaged-libs.patch =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use-debian-packaged-libs.patch 2017-05-26 15:55:33 UTC (rev 23767) +++ trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use-debian-packaged-libs.patch 2017-05-29 13:00:05 UTC (rev 23769) @@ -1,85 +0,0 @@ -Author: Andreas Tille <[email protected]> -LastChanged: Wed, 04 Sep 2013 11:11:22 +0200 -Description: This does not yet work / patch disabled - The purpose of this patch was to link dynymically against libbam which - is provided by libbam-dev package since the source of Rsamtools contains - a copy of samtools code which should be avoided. Unfortunately this - simple hack does not work because of some magic in the R build process - which is not yet fully understood and needs more investigation most - probably by discussing the issue with upstream. - . - It was verified that this patch does not work by the following method: - R --no-save < tests/Rsamtools_unit_tests.R - which crashed after: - Error in checkIdentical(exp, sapply(obs, length)) : FALSE. - Without the patch the test also runs in some errors - some of them - due to missing modules pasillaBamSubset and ShortRead (see Suggested - Depends in debian/control - these modules are not yet packaged) and - some due to blocked http, but the whole test at least finished with - some summary. - - ---- a/Rsamtools.mk -+++ b/Rsamtools.mk -@@ -2,7 +2,7 @@ SAMTOOLS_PATH=\ - `echo 'cat(system.file("usrlib", .Platform[["r_arch"]],\ - package="Rsamtools", mustWork=TRUE))' |\ - "${R_HOME}/bin/R" --vanilla --slave` --PKG_LIBS+="$(SAMTOOLS_PATH)/libbam.a" "$(SAMTOOLS_PATH)/libbcf.a"\ -+PKG_LIBS+="-lbam" "$(SAMTOOLS_PATH)/libbcf.a"\ - "$(SAMTOOLS_PATH)/libtabix.a" -lz -pthread - PKG_CPPFLAGS+=-D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 \ - -D_LARGEFILE64_SOURCE ---- a/src/Makevars.common -+++ b/src/Makevars.common -@@ -1,13 +1,8 @@ - PATCH_O = samtools_patch.o - KNETFILE_O = knetfile.o --BAMOBJ_0 = \ -- bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ -- bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o \ -- $(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o - BCFOBJ_0 = \ - bcf.o vcf.o bcfutils.o prob1.o kfunc.o index.o fet.o \ - bcf2qcall.o --BAMOBJ=$(BAMOBJ_0:%=samtools/%) $(PATCH_O) - BCFOBJ=$(BCFOBJ_0:%=samtools/bcftools/%) $(PATCH_O) - TABIXOBJ = \ - samtools/bgzf.o samtools/kstring.o samtools/knetfile.o \ -@@ -25,7 +20,7 @@ PKG_CFLAGS += \ - - PKG_LIBS += -pthread \ - $(SHLIB_OPENMP_CFLAGS) \ -- "${R_PACKAGE_DIR}/usrlib${R_ARCH}/libbam.a" \ -+ "-lbam" \ - "${R_PACKAGE_DIR}/usrlib${R_ARCH}/libbcf.a" \ - "${R_PACKAGE_DIR}/usrlib${R_ARCH}/libtabix.a" - -@@ -44,8 +39,8 @@ libs: libs0 - cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \ - "${R_PACKAGE_DIR}/include/tabix/" - mkdir -p "${R_PACKAGE_DIR}/usrlib${R_ARCH}" -- cp libbam.a libbcf.a libtabix.a "${R_PACKAGE_DIR}/usrlib${R_ARCH}" -+ cp libbcf.a libtabix.a "${R_PACKAGE_DIR}/usrlib${R_ARCH}" - - clean: -- rm $(BAMOBJ) $(BCFOBJ) $(TABIXOBJ) *.a *.o *.so *.dll -+ rm $(BCFOBJ) $(TABIXOBJ) *.a *.o *.so *.dll - ---- a/src/Makevars -+++ b/src/Makevars -@@ -2,13 +2,10 @@ include Makevars.common - - PKG_LIBS += -lz - --libs0: libbam.a libbcf.a libtabix.a -+libs0: libbcf.a libtabix.a - mkdir -p "${R_PACKAGE_DIR}/usretc${R_ARCH}" - cp ../Rsamtools.mk "${R_PACKAGE_DIR}/usretc${R_ARCH}" - --libbam.a: $(BAMOBJ) -- $(AR) -crus $@ $(BAMOBJ) -- - libbcf.a: $(BCFOBJ) - $(AR) -crus $@ $(BCFOBJ) - Deleted: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch 2017-05-26 15:55:33 UTC (rev 23767) +++ trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch 2017-05-29 13:00:05 UTC (rev 23769) @@ -1,27 +0,0 @@ -Author: Andreas Tille <[email protected]> -LastChanged: Sun, 01 Dec 2013 09:45:58 +0100 -Description: If the systems includes zlib natively there is no point in - requiring the import of zlibbioc - ---- a/DESCRIPTION -+++ b/DESCRIPTION -@@ -17,7 +17,7 @@ LazyLoad: yes - Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.21.6), - Biostrings (>= 2.37.1) - Imports: utils, BiocGenerics (>= 0.1.3), S4Vectors (>= 0.7.11), IRanges -- (>= 2.3.7), XVector (>= 0.9.1), zlibbioc, bitops, BiocParallel -+ (>= 2.3.7), XVector (>= 0.9.1), bitops, BiocParallel - Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, - TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, - TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, ---- a/NAMESPACE -+++ b/NAMESPACE -@@ -2,8 +2,6 @@ useDynLib(Rsamtools, .registration=TRUE) - - import(methods) - --import(zlibbioc) -- - importFrom(bitops, bitAnd) - - importFrom(utils, read.table) # normalizePath --> base in R-2.13 Copied: trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch (from rev 23768, trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch) =================================================================== --- trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch (rev 0) +++ trunk/packages/R/r-bioc-rsamtools/tags/1.28.0-1/patches/use_debian_packaged_zlib.patch 2017-05-29 13:00:05 UTC (rev 23769) @@ -0,0 +1,27 @@ +Author: Andreas Tille <[email protected]> +LastChanged: Sun, 01 Dec 2013 09:45:58 +0100 +Description: If the systems includes zlib natively there is no point in + requiring the import of zlibbioc + +--- a/DESCRIPTION ++++ b/DESCRIPTION +@@ -17,7 +17,7 @@ + Depends: methods, GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.21.6), + Biostrings (>= 2.37.1) + Imports: utils, BiocGenerics (>= 0.1.3), S4Vectors (>= 0.13.8), IRanges +- (>= 2.3.7), XVector (>= 0.15.1), zlibbioc, bitops, BiocParallel ++ (>= 2.3.7), XVector (>= 0.15.1), bitops, BiocParallel + Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, + TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, + TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, +--- a/NAMESPACE ++++ b/NAMESPACE +@@ -2,8 +2,6 @@ + + import(methods) + +-import(zlibbioc) +- + importFrom(bitops, bitAnd) + + importFrom(utils, read.table) # normalizePath --> base in R-2.13 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
