Binary files /tmp/tmpcU2PPW/ZiqGY0M_yc/r-bioc-bitseq-1.26.1+dfsg/build/vignette.rds and /tmp/tmpcU2PPW/WXGOrCYk9X/r-bioc-bitseq-1.28.0+dfsg/build/vignette.rds differ diff -Nru r-bioc-bitseq-1.26.1+dfsg/debian/changelog r-bioc-bitseq-1.28.0+dfsg/debian/changelog --- r-bioc-bitseq-1.26.1+dfsg/debian/changelog 2019-01-09 06:50:30.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/debian/changelog 2019-07-19 07:35:31.000000000 +0000 @@ -1,3 +1,11 @@ +r-bioc-bitseq (1.28.0+dfsg-1) unstable; urgency=medium + + * New upstream version + * debhelper 12 + * Standards-Version: 4.4.0 + + -- Andreas Tille Fri, 19 Jul 2019 09:35:31 +0200 + r-bioc-bitseq (1.26.1+dfsg-1) unstable; urgency=medium * Team upload. diff -Nru r-bioc-bitseq-1.26.1+dfsg/debian/compat r-bioc-bitseq-1.28.0+dfsg/debian/compat --- r-bioc-bitseq-1.26.1+dfsg/debian/compat 2019-01-09 06:50:30.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/debian/compat 2019-07-19 07:35:31.000000000 +0000 @@ -1 +1 @@ -11 +12 diff -Nru r-bioc-bitseq-1.26.1+dfsg/debian/control r-bioc-bitseq-1.28.0+dfsg/debian/control --- r-bioc-bitseq-1.26.1+dfsg/debian/control 2019-01-09 06:50:30.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/debian/control 2019-07-19 07:35:31.000000000 +0000 @@ -4,15 +4,15 @@ Section: gnu-r Testsuite: autopkgtest-pkg-r Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper (>= 12~), dh-r, r-base-dev, - r-bioc-rsamtools, - r-bioc-zlibbioc, + r-bioc-rsamtools (>= 1.99.3), r-bioc-s4vectors, r-bioc-iranges, + r-bioc-rhtslib, libboost-dev -Standards-Version: 4.3.0 +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-bioc-bitseq Vcs-Git: https://salsa.debian.org/r-pkg-team/r-bioc-bitseq.git Homepage: https://bioconductor.org/packages/BitSeq/ diff -Nru r-bioc-bitseq-1.26.1+dfsg/DESCRIPTION r-bioc-bitseq-1.28.0+dfsg/DESCRIPTION --- r-bioc-bitseq-1.26.1+dfsg/DESCRIPTION 2019-01-05 00:38:44.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/DESCRIPTION 2019-05-03 00:27:10.000000000 +0000 @@ -1,12 +1,12 @@ Package: BitSeq Type: Package -Depends: Rsamtools, zlibbioc +Depends: Rsamtools (>= 1.99.3) Imports: S4Vectors, IRanges -LinkingTo: Rsamtools (>= 1.19.38), zlibbioc +LinkingTo: Rhtslib (>= 1.15.5) Suggests: edgeR, DESeq, BiocStyle Title: Transcript expression inference and differential expression analysis for RNA-seq data -Version: 1.26.1 +Version: 1.28.0 Date: 2014-10-03 Author: Peter Glaus, Antti Honkela and Magnus Rattray Maintainer: Antti Honkela , Panagiotis Papastamoulis @@ -22,13 +22,13 @@ expression and ranking the transcripts based on the likelihood of differential expression. License: Artistic-2.0 + file LICENSE -Packaged: 2019-01-05 00:38:44 UTC; biocbuild +Packaged: 2019-05-03 00:27:10 UTC; biocbuild biocViews: ImmunoOncology, GeneExpression, DifferentialExpression, Sequencing, RNASeq, Bayesian, AlternativeSplicing, DifferentialSplicing, Transcription git_url: https://git.bioconductor.org/packages/BitSeq -git_branch: RELEASE_3_8 -git_last_commit: 1f44958 -git_last_commit_date: 2019-01-04 -Date/Publication: 2019-01-04 +git_branch: RELEASE_3_9 +git_last_commit: 63856e9 +git_last_commit_date: 2019-05-02 +Date/Publication: 2019-05-02 NeedsCompilation: yes Binary files /tmp/tmpcU2PPW/ZiqGY0M_yc/r-bioc-bitseq-1.26.1+dfsg/inst/doc/BitSeq.pdf and /tmp/tmpcU2PPW/WXGOrCYk9X/r-bioc-bitseq-1.28.0+dfsg/inst/doc/BitSeq.pdf differ diff -Nru r-bioc-bitseq-1.26.1+dfsg/NAMESPACE r-bioc-bitseq-1.28.0+dfsg/NAMESPACE --- r-bioc-bitseq-1.26.1+dfsg/NAMESPACE 2018-10-30 19:39:03.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/NAMESPACE 2019-05-02 20:58:56.000000000 +0000 @@ -1,4 +1,3 @@ -import(zlibbioc) useDynLib("BitSeq") import(S4Vectors) diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/bam_plbuf.c r-bioc-bitseq-1.28.0+dfsg/src/bam_plbuf.c --- r-bioc-bitseq-1.26.1+dfsg/src/bam_plbuf.c 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/bam_plbuf.c 2019-05-02 20:58:56.000000000 +0000 @@ -0,0 +1 @@ +#include diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/Makevars.common r-bioc-bitseq-1.28.0+dfsg/src/Makevars.common --- r-bioc-bitseq-1.26.1+dfsg/src/Makevars.common 2018-10-30 19:39:03.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/Makevars.common 2019-05-02 20:58:56.000000000 +0000 @@ -1,4 +1,6 @@ OBJECTS= \ + sam.o \ + bam_plbuf.o \ ArgumentParser.o \ CollapsedSampler.o \ common.o \ diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/Makevars.in r-bioc-bitseq-1.28.0+dfsg/src/Makevars.in --- r-bioc-bitseq-1.26.1+dfsg/src/Makevars.in 2019-01-05 00:38:44.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/Makevars.in 2019-05-02 20:58:56.000000000 +0000 @@ -1,14 +1,10 @@ -SAMTOOLS_PATH=\ - `echo 'cat(system.file("usrlib", .Platform[["r_arch"]], \ - package="Rsamtools", mustWork=TRUE))' |\ - "${R_HOME}/bin/R" --vanilla --slave` -SAMTOOLS_LIBS="$(SAMTOOLS_PATH)/libbam.a" "$(SAMTOOLS_PATH)/libbcf.a"\ - "$(SAMTOOLS_PATH)/libtabix.a" -lz -pthread -SAMTOOLS_CPPFLAGS=-D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 \ - -D_LARGEFILE64_SOURCE +RHTSLIB_LIBS=`echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\ + "${R_HOME}/bin/R" --vanilla --slave` +RHTSLIB_CPPFLAGS=`echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\ + "${R_HOME}/bin/R" --vanilla --slave` -PKG_LIBS=$(SAMTOOLS_LIBS) @OPENMP_CXXFLAGS@ -PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS) @DEFS@ +PKG_LIBS=$(RHTSLIB_LIBS) @OPENMP_CXXFLAGS@ +PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS) @DEFS@ PKG_CXXFLAGS=-I. @OPENMP_CXXFLAGS@ include Makevars.common diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/Makevars.win r-bioc-bitseq-1.28.0+dfsg/src/Makevars.win --- r-bioc-bitseq-1.26.1+dfsg/src/Makevars.win 2019-01-05 00:38:44.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/Makevars.win 2019-05-03 00:25:30.000000000 +0000 @@ -1,15 +1,12 @@ -# This should set SAM_INCLUDE to point to location Rsamtools.mk e.g.: -# SAM_INCLUDE=F:/PROGRA~1/R/R-2.14.2/library/Rsamtools/usretc/i386/Rsamtools.mk - -SAMVARS=$(shell echo 'cat(system.file("usretc", .Platform[["r_arch"]],\ - "Rsamtools.mk", package="Rsamtools", mustWork=TRUE))' |\ +RHTSLIB_LIBS=$(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\ + "${R_HOME}/bin/R" --vanilla --slave) +RHTSLIB_CPPFLAGS=$(shell echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\ "${R_HOME}/bin/R" --vanilla --slave) -include $(SAMVARS) -PKG_LIBS=$(SAMTOOLS_LIBS) -PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS) +PKG_LIBS=$(RHTSLIB_LIBS) +PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS) -PKG_CPPFLAGS+=-DBS_VERSION=\"1.26.1\" -DBIOC_BUILD -I. +PKG_CPPFLAGS+=-DBS_VERSION=\"1.28.0\" -DBIOC_BUILD -I. include Makevars.common diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/Makevars.win.in r-bioc-bitseq-1.28.0+dfsg/src/Makevars.win.in --- r-bioc-bitseq-1.26.1+dfsg/src/Makevars.win.in 2018-10-30 19:39:03.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/Makevars.win.in 2019-05-02 20:58:56.000000000 +0000 @@ -1,13 +1,10 @@ -# This should set SAM_INCLUDE to point to location Rsamtools.mk e.g.: -# SAM_INCLUDE=F:/PROGRA~1/R/R-2.14.2/library/Rsamtools/usretc/i386/Rsamtools.mk - -SAMVARS=$(shell echo 'cat(system.file("usretc", .Platform[["r_arch"]],\ - "Rsamtools.mk", package="Rsamtools", mustWork=TRUE))' |\ +RHTSLIB_LIBS=$(shell echo 'Rhtslib::pkgconfig("PKG_LIBS")'|\ + "${R_HOME}/bin/R" --vanilla --slave) +RHTSLIB_CPPFLAGS=$(shell echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'|\ "${R_HOME}/bin/R" --vanilla --slave) -include $(SAMVARS) -PKG_LIBS=$(SAMTOOLS_LIBS) -PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS) +PKG_LIBS=$(RHTSLIB_LIBS) +PKG_CPPFLAGS=$(RHTSLIB_CPPFLAGS) PKG_CPPFLAGS+=@DEF_VERSION@ -DBIOC_BUILD -I. diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/ReadDistribution.h r-bioc-bitseq-1.28.0+dfsg/src/ReadDistribution.h --- r-bioc-bitseq-1.26.1+dfsg/src/ReadDistribution.h 2019-01-05 00:38:44.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/ReadDistribution.h 2019-05-02 20:58:56.000000000 +0000 @@ -10,8 +10,8 @@ #include "TranscriptExpression.h" #include "TranscriptSequence.h" -#include "samtools/bam.h" -#include "samtools/sam.h" +#include "bam.h" +#include "sam.h" namespace ns_rD { diff -Nru r-bioc-bitseq-1.26.1+dfsg/src/sam.c r-bioc-bitseq-1.28.0+dfsg/src/sam.c --- r-bioc-bitseq-1.26.1+dfsg/src/sam.c 1970-01-01 00:00:00.000000000 +0000 +++ r-bioc-bitseq-1.28.0+dfsg/src/sam.c 2019-05-02 20:58:56.000000000 +0000 @@ -0,0 +1 @@ +#include