Author: ginggs Date: 2017-05-29 12:59:06 +0000 (Mon, 29 May 2017) New Revision: 23768
Removed: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use-debian-packaged-libs.patch Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch Log: New upstream version, refresh patches, upload to unstable Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/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/trunk/debian/changelog 2017-05-29 12:59:06 UTC (rev 23768) @@ -1,3 +1,11 @@ +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 Deleted: trunk/packages/R/r-bioc-rsamtools/trunk/debian/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/trunk/debian/patches/use-debian-packaged-libs.patch 2017-05-29 12:59:06 UTC (rev 23768) @@ -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) - Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/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/trunk/debian/patches/use_debian_packaged_zlib.patch 2017-05-29 12:59:06 UTC (rev 23768) @@ -5,18 +5,18 @@ --- a/DESCRIPTION +++ b/DESCRIPTION -@@ -17,7 +17,7 @@ LazyLoad: yes +@@ -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 (>= 0.7.11), IRanges -- (>= 2.3.7), XVector (>= 0.9.1), zlibbioc, bitops, BiocParallel -+ (>= 2.3.7), XVector (>= 0.9.1), bitops, BiocParallel + 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 @@ useDynLib(Rsamtools, .registration=TRUE) +@@ -2,8 +2,6 @@ import(methods) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
