[med-svn] [Git][med-team/jellyfish][master] Clean up quilt patches
Andreas Tille
gitlab at salsa.debian.org
Mon Sep 3 07:57:05 BST 2018
Andreas Tille pushed to branch master at Debian Med / jellyfish
Commits:
ea26fa3a by Andreas Tille at 2018-09-03T06:56:52Z
Clean up quilt patches
- - - - -
9 changed files:
- debian/changelog
- − debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
- − debian/patches/add_small_mers.sh.patch
- − debian/patches/drop-rpath
- − debian/patches/gcc-7.patch
- − debian/patches/modern-g++
- − debian/patches/pkg-config-with-name
- debian/patches/series
- − debian/patches/spelling
Changes:
=====================================
debian/changelog
=====================================
@@ -4,10 +4,11 @@ jellyfish (2.2.10-1) UNRELEASED; urgency=medium
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* Adapt watch file to also catch v$VERSION tarball names
+ * Clean up quilt patches
* Try to enable swig Python bindings
TODO: ... but failed
- -- Andreas Tille <tille at debian.org> Thu, 26 Apr 2018 21:19:48 +0200
+ -- Andreas Tille <tille at debian.org> Mon, 03 Sep 2018 08:34:22 +0200
jellyfish (2.2.8-3) unstable; urgency=medium
=====================================
debian/patches/6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch deleted
=====================================
@@ -1,22 +0,0 @@
-From 6dfc57b516249454dc0a708ceb4833623cbf0ffd Mon Sep 17 00:00:00 2001
-From: Guillaume Marcais <gmarcais at cs.cmu.edu>
-Date: Wed, 14 Feb 2018 07:29:54 -0500
-Subject: [PATCH] Fix testing on arm64.
-
----
- jellyfish/fastq2sam.cc | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/jellyfish/fastq2sam.cc b/jellyfish/fastq2sam.cc
-index e152ccf..b0b6b0d 100644
---- a/jellyfish/fastq2sam.cc
-+++ b/jellyfish/fastq2sam.cc
-@@ -25,7 +25,7 @@ int main(int argc, char* argv[]) {
- // os << "@PG\tID:fastq2sam\tPN:fastq2sam\n";
-
- std::string name, seq, quals;
-- char c = is.get();
-+ int c = is.get();
- while(c == '@') {
- std::getline(is, name);
- std::getline(is, seq);
=====================================
debian/patches/add_small_mers.sh.patch deleted
=====================================
@@ -1,27 +0,0 @@
-From 0adb7ea223a6718bad4e82fc9813ae7708b59ee2 Mon Sep 17 00:00:00 2001
-From: Guillaume Marcais <gmarcais at cs.cmu.edu>
-Date: Mon, 12 Feb 2018 14:32:29 -0500
-Subject: [PATCH] Added missing tests/small_mers.sh file.
-
----
- tests/small_mers.sh | 11 +++++++++++
- 1 file changed, 11 insertions(+)
- create mode 100644 tests/small_mers.sh
-
-diff --git a/tests/small_mers.sh b/tests/small_mers.sh
-new file mode 100644
-index 0000000..5eb7db0
---- /dev/null
-+++ b/tests/small_mers.sh
-@@ -0,0 +1,11 @@
-+#! /bin/sh
-+
-+cd tests
-+. ./compat.sh
-+
-+sort -k2,2 > ${pref}.md5sum <<EOF
-+
-+EOF
-+
-+$JF count -t $nCPUs -o ${pref}_m10_10M.jf -s 1M -m 7 -C seq10m.fa
-+$JF histo ${pref}_m10_10M.jf > ${pref}_m10_10M.histo
=====================================
debian/patches/drop-rpath deleted
=====================================
@@ -1,88 +0,0 @@
-Description: Don't compile using an rpath
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- jellyfish.orig/swig/python/setup.py
-+++ jellyfish/swig/python/setup.py
-@@ -25,7 +25,6 @@
-
- jf_libs = [re.sub(r'-l', '', x) for x in os.popen("pkg-config --libs-only-l jellyfish-2.0").read().rstrip().split()]
- jf_libdir = [re.sub(r'-L', '', x) for x in os.popen("pkg-config --libs-only-L jellyfish-2.0").read().rstrip().split()]
--jf_rpath = [re.sub(r'^', '-Wl,-rpath,', x) for x in jf_libdir]
- jf_ldflags = os.popen("pkg-config --libs-only-other jellyfish-2.0").read().rstrip().split()
-
-
-@@ -35,7 +34,7 @@
- libraries = jf_libs,
- library_dirs = jf_libdir,
- extra_compile_args = ["-std=c++0x"] + jf_cflags,
-- extra_link_args = jf_ldflags + jf_rpath,
-+ extra_link_args = jf_ldflags,
- language = "c++")
- setup(name = 'dna_jellyfish',
- version = '0.0.1',
---- jellyfish.orig/swig/Tuprules.tup
-+++ jellyfish/swig/Tuprules.tup
-@@ -77,12 +77,6 @@
- JELLYFISH_LIBS = `pkg-config --libs jellyfish-2.0`
- endif
-
--ifdef JELLYFISH_RPATH
-- JELLYFISH_RPATH = @(JELLYFISH_RPATH)
--else
-- JELLYFISH_RPATH = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`
--endif
--
- ifdef RUBY_CFLAGS
- RUBY_CFLAGS = @(RUBY_CFLAGS)
- else
---- jellyfish.orig/swig/perl5/Makefile.PL
-+++ jellyfish/swig/perl5/Makefile.PL
-@@ -9,7 +9,6 @@
-
- my $jf_cflags = `pkg-config --cflags jellyfish-2.0`;
- my $jf_libs = `pkg-config --libs jellyfish-2.0`;
--my $jf_rpath = `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`;
-
- WriteMakefile(NAME => 'jellyfish',
- CC => 'g++-4.4',
---- jellyfish.orig/swig/perl5/Tupfile
-+++ jellyfish/swig/perl5/Tupfile
-@@ -3,7 +3,7 @@
- export PKG_CONFIG_PATH
- SWIGFLAGS = -perl5
- CXXFLAGS += $(JELLYFISH_CFLAGS) $(PERL_CFLAGS) -fPIC
--LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(PERL_LIBS)
-+LDFLAGS += -shared $(JELLYFISH_LIBS) $(PERL_LIBS)
-
- : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx | jellyfish.pm <jf>
- : jellyfish_wrap.cxx |> !cxx |>
---- jellyfish.orig/swig/python/Tupfile
-+++ jellyfish/swig/python/Tupfile
-@@ -3,7 +3,7 @@
- export PKG_CONFIG_PATH
- SWIGFLAGS = -python
- CXXFLAGS += $(JELLYFISH_CFLAGS) $(PYTHON_CFLAGS) -fPIC
--LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(PYTHON_LIBS)
-+LDFLAGS += -shared $(JELLYFISH_LIBS) $(PYTHON_LIBS)
-
- : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx | jellyfish.py <jf>
- : jellyfish_wrap.cxx |> !cxx |>
---- jellyfish.orig/swig/ruby/Tupfile
-+++ jellyfish/swig/ruby/Tupfile
-@@ -3,7 +3,7 @@
- export PKG_CONFIG_PATH
- SWIGFLAGS = -ruby
- CXXFLAGS += $(JELLYFISH_CFLAGS) $(RUBY_CFLAGS) -fPIC
--LDFLAGS += -shared $(JELLYFISH_LIBS) $(JELLYFISH_RPATH) $(RUBY_LIBS)
-+LDFLAGS += -shared $(JELLYFISH_LIBS) $(RUBY_LIBS)
-
- : ../jellyfish.i |> !swigxx |> jellyfish_wrap.cxx
- : jellyfish_wrap.cxx |> !cxx |>
---- jellyfish.orig/swig/ruby/extconf.rb
-+++ jellyfish/swig/ruby/extconf.rb
-@@ -7,6 +7,5 @@
-
- $defs << `pkg-config --cflags jellyfish-2.0`.chomp << '-std=c++0x'
- $libs << `pkg-config --libs jellyfish-2.0`.chomp
--$libs << `pkg-config --libs-only-L jellyfish-2.0 | sed -e 's/-L/-Wl,-rpath,/g'`.chomp
-
- create_makefile('jellyfish')
=====================================
debian/patches/gcc-7.patch deleted
=====================================
@@ -1,15 +0,0 @@
-Description: Don't use -Werror
- The SWIG-generated swig/perl5/swig_wrap.cpp gives warnings with
- gcc 7, don't make these fatal with -Werror.
-Author: Adrian Bunk <bunk at debian.org>
-Last-Update: Tue, 15 Aug 2017 15:56:06 +0300
-Bug-Debian: https://bugs.debian.org/872262
-
---- a/development.mk
-+++ b/development.mk
-@@ -1,4 +1,4 @@
--AM_CXXFLAGS += -Werror
-+#AM_CXXFLAGS += -Werror
-
- # Count lines of code
- .PHONY: cloc cloc_jellyfish
=====================================
debian/patches/modern-g++ deleted
=====================================
@@ -1,15 +0,0 @@
-Description: Use the version of g++ in Debian, not 4.4
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- jellyfish.orig/swig/perl5/Makefile.PL
-+++ jellyfish/swig/perl5/Makefile.PL
-@@ -11,8 +11,8 @@
- my $jf_libs = `pkg-config --libs jellyfish-2.0`;
-
- WriteMakefile(NAME => 'jellyfish',
-- CC => 'g++-4.4',
-- LD => 'g++-4.4',
-+ CC => 'g++',
-+ LD => 'g++',
- CCFLAGS => "-std=c++0x $jf_cflags",
- LIBS => "$jf_libs",
- OBJECT => 'jellyfish_wrap.o',
=====================================
debian/patches/pkg-config-with-name deleted
=====================================
@@ -1,13 +0,0 @@
-Description: pkg-config must be called with package name
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- jellyfish.orig/swig/python/setup.py
-+++ jellyfish/swig/python/setup.py
-@@ -21,7 +21,7 @@
- os.system("swig -c++ -python -o jellyfish_wrap.cxx ../jellyfish.i")
-
- jf_include = [re.sub(r'-I', '', x) for x in os.popen("pkg-config --cflags-only-I jellyfish-2.0").read().rstrip().split()]
--jf_cflags = os.popen("pkg-config --cflags-only-other").read().rstrip().split()
-+jf_cflags = os.popen("pkg-config --cflags-only-other jellyfish-2.0").read().rstrip().split()
-
- jf_libs = [re.sub(r'-l', '', x) for x in os.popen("pkg-config --libs-only-l jellyfish-2.0").read().rstrip().split()]
- jf_libdir = [re.sub(r'-L', '', x) for x in os.popen("pkg-config --libs-only-L jellyfish-2.0").read().rstrip().split()]
=====================================
debian/patches/series
=====================================
@@ -1,10 +1,3 @@
manpage_whatis_entry.patch
-# pkg-config-with-name
-# drop-rpath
-# modern-g++
-# spelling
-# gcc-7.patch
reproducible.patch
portability.patch
-# add_small_mers.sh.patch
-# 6dfc57b516249454dc0a708ceb4833623cbf0ffd.patch
=====================================
debian/patches/spelling deleted
=====================================
@@ -1,13 +0,0 @@
-Description: Spelling fixes
-Author: Michael R. Crusoe <crusoe at ucdavis.edu>
---- jellyfish.orig/doc/jellyfish.tex
-+++ jellyfish/doc/jellyfish.tex
-@@ -140,7 +140,7 @@
- Important: the size of the couting field does NOT change the result,
- it only impacts the amount of memory used. In particular, there is no
- maximum value in the hash. Even if the counting field uses 5 bits, a
--$k$-mer occuring 2 million times will have a value reported of 2
-+$k$-mer occurring 2 million times will have a value reported of 2
- million (i.e., it is not capped at $2^5$).
-
- The \Opt{-c} specify the length (in bits) of the counting field. The
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a
--
View it on GitLab: https://salsa.debian.org/med-team/jellyfish/commit/ea26fa3aa9903765de174c706b905c3c2ac9cc1a
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