[med-svn] r23768 - in trunk/packages/R/r-bioc-rsamtools/trunk/debian: . patches

Graham Inggs ginggs at moszumanska.debian.org
Mon May 29 12:59:06 UTC 2017 

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 <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

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 <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)
- 

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)

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