[med-svn] [Git][med-team/abyss][master] 7 commits: Replace python-markdown by markdown
Andreas Tille
gitlab at salsa.debian.org
Sun Dec 15 06:37:07 GMT 2019
Andreas Tille pushed to branch master at Debian Med / abyss
Commits:
6318aea7 by Andreas Tille at 2019-12-14T20:55:07Z
Replace python-markdown by markdown
- - - - -
d4f29a51 by Andreas Tille at 2019-12-14T20:55:33Z
routine-update: Standards-Version: 4.4.1
- - - - -
af46cd7e by Andreas Tille at 2019-12-14T20:55:38Z
Remove patches abyss-32-bit.patch, gtest.patch that are missing from debian/patches/series.
Fixes lintian: patch-file-present-but-not-mentioned-in-series
See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details.
- - - - -
cc6e90d1 by Andreas Tille at 2019-12-14T20:55:43Z
Set upstream metadata fields: Repository, Repository-Browse.
- - - - -
e529ea45 by Andreas Tille at 2019-12-14T20:55:44Z
Remove obsolete fields Contact, Name from debian/upstream/metadata.
- - - - -
e0effa0e by Andreas Tille at 2019-12-14T23:00:33Z
Use libtext-multimarkdown-perl to obtain html documentation
- - - - -
c0bbb786 by Andreas Tille at 2019-12-14T23:11:09Z
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- − debian/patches/abyss-32-bit.patch
- − debian/patches/gtest.patch
- debian/rules
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+abyss (2.2.3-2) unstable; urgency=medium
+
+ * Use libtext-multimarkdown-perl to obtain html documentation
+ Closes: #942908
+ * Standards-Version: 4.4.1
+
+ -- Andreas Tille <tille at debian.org> Sun, 15 Dec 2019 00:00:48 +0100
+
abyss (2.2.3-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -5,7 +5,6 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 12),
- python-markdown,
libboost-graph-dev,
libopenmpi-dev,
libsparsehash-dev,
@@ -13,7 +12,7 @@ Build-Depends: debhelper-compat (= 12),
libsqlite3-dev,
pkg-config,
help2man
-Standards-Version: 4.4.0
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/abyss
Vcs-Git: https://salsa.debian.org/med-team/abyss.git
Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
=====================================
debian/patches/abyss-32-bit.patch deleted
=====================================
@@ -1,34 +0,0 @@
-Author: Graham Inggs <graham at nerve.org.za>
-Last-Update: Thu, 16 Jul 2015 10:44:56 +0200
-Forwarded: https://github.com/bcgsc/abyss/pull/278
-Bug-Debian: http://bugs.debian.org/780409
-Description: Fix FTBFS on 32-bit architectures
- Version 1.5.2-1 of abyss FTBFS on 32-bit architectures (armhf, i386 and
- powerpc). Previous versions built fine on all architectures.
- .
- There were a couple of places in the code that was introduced in version
- 1.5.2 where size_t data type was used instead of a fixed size data type.
- The patch builds on amd64, i386 and armhf with and all unit tests passed.
- .
- Question: is this software useful on a 32-bit system at all?
-
---- a/Common/StringUtil.h
-+++ b/Common/StringUtil.h
-@@ -178,7 +178,7 @@ bool isReadNamePair(const std::string& n
- return false;
- }
-
--static inline size_t SIToBytes(std::istringstream& iss)
-+static inline unsigned long long SIToBytes(std::istringstream& iss)
- {
- double size;
- std::string units;
-@@ -194,7 +194,7 @@ static inline size_t SIToBytes(std::istr
- // no units given; clear fail flag
- // and assume bytes
- iss.clear(std::ios::eofbit);
-- return (size_t)ceil(size);
-+ return (unsigned long long)ceil(size);
- }
-
- if (units.size() > 1) {
=====================================
debian/patches/gtest.patch deleted
=====================================
@@ -1,181 +0,0 @@
-Author: Anthony Raymond <traymond at bcgsc.ca>
-Last-Updated: Wed, 17 Sep 2014 12:17:23 -0700
-Description: Make sure gtest works properly
- I had to follow the instructions on this post to build libgtest.a and libgtest_main.a:
- http://askubuntu.com/questions/145887/why-no-library-files-installed-for-google-test
- .
- Attention: This patch needs heave adaption and is deactivated for the moment
-
---- a/Unittest/Makefile.am
-+++ b/Unittest/Makefile.am
-@@ -1,58 +1,72 @@
-+check_LIBRARIES = libgtest.a libgtest_main.a
-+
-+gtest-all.cc:
-+ cp $(GTEST)/src/gtest-all.cc .
-+
-+gtest_main.cc:
-+ cp $(GTEST)/src/gtest_main.cc .
-+
-+libgtest_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)
-+libgtest_a_SOURCES = gtest-all.cc
-+
-+libgtest_main_a_CPPFLAGS = -I$(top_srcdir) -I$(GTEST)
-+libgtest_main_a_SOURCES = gtest_main.cc gtest-all.cc
-+
- UNIT_TESTS = common_stringutil
- check_PROGRAMS = common_stringutil
- common_stringutil_SOURCES = Common/StringUtilTest.cpp
- common_stringutil_CPPFLAGS = -I$(top_srcdir)
--common_stringutil_LDADD = $(GTEST_LIBS)
-+common_stringutil_LDADD = libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += common_histogram
- check_PROGRAMS += common_histogram
- common_histogram_SOURCES = Common/HistogramTest.cpp
- common_histogram_CPPFLAGS = -I$(top_srcdir)
--common_histogram_LDADD = $(GTEST_LIBS)
-+common_histogram_LDADD = libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += common_bitutil
- check_PROGRAMS += common_bitutil
- common_bitutil_SOURCES = Common/BitUtilTest.cpp
- common_bitutil_CPPFLAGS = -I$(top_srcdir)
--common_bitutil_LDADD = $(GTEST_LIBS)
-+common_bitutil_LDADD = libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += common_kmer
- check_PROGRAMS += common_kmer
- common_kmer_SOURCES = Common/KmerTest.cpp
- common_kmer_CPPFLAGS = -I$(top_srcdir)
--common_kmer_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+common_kmer_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += common_sequence
- check_PROGRAMS += common_sequence
- common_sequence_SOURCES = Common/Sequence.cc
- common_sequence_CPPFLAGS = -I$(top_srcdir)
--common_sequence_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+common_sequence_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += common_KmerIterator
- check_PROGRAMS += common_KmerIterator
- common_KmerIterator_SOURCES = Common/KmerIteratorTest.cpp
- common_KmerIterator_CPPFLAGS = -I$(top_srcdir)
--common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+common_KmerIterator_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += common_sam
- check_PROGRAMS += common_sam
- common_sam_SOURCES = Common/SAM.cc
- common_sam_CPPFLAGS = -I$(top_srcdir)
--common_sam_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+common_sam_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += BloomFilter
- check_PROGRAMS += BloomFilter
- BloomFilter_SOURCES = Konnector/BloomFilter.cc
- BloomFilter_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
- BloomFilter_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
--BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+BloomFilter_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += Konnector_DBGBloom
- check_PROGRAMS += Konnector_DBGBloom
- Konnector_DBGBloom_SOURCES = Konnector/DBGBloomTest.cpp
- Konnector_DBGBloom_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
- Konnector_DBGBloom_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
--Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+Konnector_DBGBloom_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += Konnector_DBGBloomAlgorithms
- check_PROGRAMS += Konnector_DBGBloomAlgorithms
-@@ -61,38 +75,38 @@ Konnector_DBGBloomAlgorithms_CPPFLAGS =
- Konnector_DBGBloomAlgorithms_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
- Konnector_DBGBloomAlgorithms_LDADD = \
- $(top_builddir)/Common/libcommon.a \
-- $(GTEST_LIBS)
-+ libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += graph_ConstrainedBFSVisitor
- check_PROGRAMS += graph_ConstrainedBFSVisitor
- graph_ConstrainedBFSVisitor_SOURCES = Graph/ConstrainedBFSVisitorTest.cpp
- graph_ConstrainedBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
--graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+graph_ConstrainedBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += graph_BidirectionalBFS
- check_PROGRAMS += graph_BidirectionalBFS
- graph_BidirectionalBFS_SOURCES = Graph/BidirectionalBFSTest.cpp
- graph_BidirectionalBFS_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
--graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+graph_BidirectionalBFS_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += graph_AllPathsSearch
- check_PROGRAMS += graph_AllPathsSearch
- graph_AllPathsSearch_SOURCES = Graph/AllPathsSearchTest.cpp
- graph_AllPathsSearch_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
--graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+graph_AllPathsSearch_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += graph_HashGraph
- check_PROGRAMS += graph_HashGraph
- graph_HashGraph_SOURCES = Graph/HashGraphTest.cpp
- graph_HashGraph_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
--graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+graph_HashGraph_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += graph_ConstrainedBidiBFSVisitor
- check_PROGRAMS += graph_ConstrainedBidiBFSVisitor
- graph_ConstrainedBidiBFSVisitor_SOURCES = \
- Graph/ConstrainedBidiBFSVisitorTest.cpp
- graph_ConstrainedBidiBFSVisitor_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/Common
--graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+graph_ConstrainedBidiBFSVisitor_LDADD = $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- UNIT_TESTS += Konnector_konnector
- check_PROGRAMS += Konnector_konnector
-@@ -102,7 +116,7 @@ Konnector_konnector_CPPFLAGS = -I$(top_s
- Konnector_konnector_CXXFLAGS = $(AM_CXXFLAGS) $(OPENMP_CXXFLAGS)
- Konnector_konnector_LDADD = \
- $(top_builddir)/Align/libalign.a \
-- $(top_builddir)/Common/libcommon.a $(GTEST_LIBS)
-+ $(top_builddir)/Common/libcommon.a libgtest_main.a $(GTEST_LIBS)
-
- ##Tests for log kmer counting / Counting bloom filter
-
---- a/configure.ac
-+++ b/configure.ac
-@@ -89,10 +89,12 @@ fi
- # GTest
- AC_ARG_WITH(gtest, AS_HELP_STRING([--with-gtest=PATH],
- [specify prefix directory for the installed gtest library]))
-+gtest_src="/usr/src/gtest"
- if test "$with_gtest" -a -d "$with_gtest"; then
- gtest_cppflags="-I$with_gtest/include"
-- gtest_ldflags="-L$with_gtest/lib"
-+ gtest_src="$with_gtest"
- fi
-+AC_SUBST(GTEST, "$gtest_src")
-
- AC_ARG_ENABLE(mpich, AS_HELP_STRING([--enable-mpich],
- [use MPICH (default is to use Open MPI)]))
-@@ -118,7 +120,7 @@ boost_ver=1.55.0
- boost_ver_dir=boost_1_55_0
- AC_SUBST(CPPFLAGS,
- "-I$my_abs_srcdir $boost_cppflags $mpi_cppflags $gtest_cppflags $CPPFLAGS -isystem$my_abs_srcdir/$boost_ver_dir")
--AC_SUBST(LDFLAGS, "$mpi_ldflags $gtest_ldflags $LDFLAGS")
-+AC_SUBST(LDFLAGS, "$mpi_ldflags $LDFLAGS")
-
- # Check for the MPI parallel computing library.
- libs="$LIBS"
-@@ -194,8 +196,7 @@ fi
- libs="$LIBS"
- AC_CHECK_HEADERS([gtest/gtest.h])
- AC_CHECK_LIB([pthread], [pthread_create])
--AC_CHECK_LIB([gtest_main],[main])
--AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes -a $ac_cv_lib_gtest_main_main = yes])
-+AM_CONDITIONAL([HAVE_GTEST], [test $ac_cv_header_gtest_gtest_h = yes])
- AC_SUBST(GTEST_LIBS, "$LIBS")
- LIBS=$libs
-
=====================================
debian/rules
=====================================
@@ -15,7 +15,7 @@ override_dh_auto_configure:
override_dh_auto_build:
dh_auto_build
- markdown_py -f README.html README.md
+ markdown README.md > README.html
override_dh_auto_install:
dh_auto_install --destdir=debian/tmp
=====================================
debian/upstream/metadata
=====================================
@@ -1,25 +1,25 @@
-Name: ABySS
Reference:
- Author: >
- Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein
- and Steven J.M. Jones and İnanç Birol
- Title: "ABySS: A parallel assembler for short read sequence data"
- Journal: Genome Research
- Year: 2009
- Volume: 19
- Number: 6
- Pages: 1117-23
- PMID: 19251739
- DOI: 10.1101/gr.089532.108
- URL: http://genome.cshlp.org/content/19/6/1117
- eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html
+ Author: >
+ Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein
+ and Steven J.M. Jones and İnanç Birol
+ Title: "ABySS: A parallel assembler for short read sequence data"
+ Journal: Genome Research
+ Year: 2009
+ Volume: 19
+ Number: 6
+ Pages: 1117-23
+ PMID: 19251739
+ DOI: 10.1101/gr.089532.108
+ URL: http://genome.cshlp.org/content/19/6/1117
+ eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html
Registry:
- - Name: bio.tools
- Entry: ABySS
- - Name: OMICtools
- Entry: OMICS_00006
- - Name: SciCrunch
- Entry: SCR_010709
- - Name: conda:bioconda
- Entry: abyss
-Contact: Shaun Jackman <sjackman at gmail.com>
+- Name: bio.tools
+ Entry: ABySS
+- Name: OMICtools
+ Entry: OMICS_00006
+- Name: SciCrunch
+ Entry: SCR_010709
+- Name: conda:bioconda
+ Entry: abyss
+Repository: https://github.com/bcgsc/abyss.git
+Repository-Browse: https://github.com/bcgsc/abyss
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/a5b116c8e98562941d437bd888a0ce0aeb6489f7...c0bbb786701e74a8aa58a5dd63d3c5421bb2bafb
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