[med-svn] r23769 - in trunk/packages/R/r-bioc-rsamtools/tags: . 1.28.0-1 1.28.0-1/patches
Graham Inggs
ginggs at moszumanska.debian.org
Mon May 29 13:00:05 UTC 2017
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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Fri, 30 Oct 2015 14:05:41 +0100
-
-r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium
-
- * New upstream version
-
- -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Sun, 01 Dec 2013 09:45:58 +0100
-
-r-bioc-rsamtools (1.12.4-1) unstable; urgency=low
-
- * Initial release (closes: #728285)
-
- -- Andreas Tille <tille at debian.org> 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 <ginggs at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Fri, 30 Oct 2015 14:05:41 +0100
+
+r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> 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 <tille at debian.org> Sun, 01 Dec 2013 09:45:58 +0100
+
+r-bioc-rsamtools (1.12.4-1) unstable; urgency=low
+
+ * Initial release (closes: #728285)
+
+ -- Andreas Tille <tille at debian.org> 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 <tille at debian.org>
-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 <tille at debian.org>
-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 <tille at debian.org>
+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
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