This is an automated email from the git hooks/post-receive script. afif pushed a commit to branch master in repository canu.
commit 01c6107b746e7920548647a0db67527bfa58533f Author: Afif Elghraoui <[email protected]> Date: Thu May 18 01:35:01 2017 -0400 Update and refresh patches --- debian/patches/external-deps.patch | 2 +- debian/patches/fix-build-system.patch | 32 ------------------------- debian/patches/relative-paths.patch | 4 ++-- debian/patches/series | 1 - debian/patches/use-debian-mhap-at-runtime.patch | 16 ++++++------- 5 files changed, 11 insertions(+), 44 deletions(-) diff --git a/debian/patches/external-deps.patch b/debian/patches/external-deps.patch index 516daf8..9f82882 100644 --- a/debian/patches/external-deps.patch +++ b/debian/patches/external-deps.patch @@ -3,7 +3,7 @@ Author: Afif Elghraoui <[email protected]> Forwarded: not-needed --- canu.orig/src/main.mk +++ canu/src/main.mk -@@ -157,7 +157,6 @@ +@@ -194,7 +194,6 @@ \ overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.mk \ \ diff --git a/debian/patches/fix-build-system.patch b/debian/patches/fix-build-system.patch deleted file mode 100644 index b2eb7b6..0000000 --- a/debian/patches/fix-build-system.patch +++ /dev/null @@ -1,32 +0,0 @@ -Description: Adjust build system to honor user-provided compiler flags -Author: Afif Elghraoui <[email protected]> -Forwarded: no ---- canu.orig/src/Makefile -+++ canu/src/Makefile -@@ -372,8 +372,8 @@ - ifeq (${OSTYPE}, Linux) - CC ?= gcc - CXX ?= g++ -- CXXFLAGS := -pthread -fPIC -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare # -Wformat -Wall -Wextra -- LDFLAGS := -pthread -lm -+ CXXFLAGS += -pthread -fPIC -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare # -Wformat -Wall -Wextra -+ LDFLAGS += -pthread -lm - - CXXFLAGS += -D_GLIBCXX_PARALLEL -fopenmp - LDFLAGS += -fopenmp -@@ -406,11 +406,11 @@ - CC ?= gcc - CXX ?= g++ - ifeq ($(CLANG), 0) -- CXXFLAGS := -pthread -fopenmp -fPIC -m64 -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -- LDFLAGS := -pthread -fopenmp -lm -+ CXXFLAGS += -pthread -fopenmp -fPIC -m64 -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -+ LDFLAGS += -pthread -fopenmp -lm - else -- CXXFLAGS := -DBROKEN_CLANG_OpenMP -pthread -fPIC -m64 -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -- LDFLAGS := -pthread -lm -+ CXXFLAGS += -DBROKEN_CLANG_OpenMP -pthread -fPIC -m64 -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -+ LDFLAGS += -pthread -lm - endif - - ifeq ($(BUILDPROFILE), 1) diff --git a/debian/patches/relative-paths.patch b/debian/patches/relative-paths.patch index 49d6a04..774e71b 100644 --- a/debian/patches/relative-paths.patch +++ b/debian/patches/relative-paths.patch @@ -6,7 +6,7 @@ Forwarded: not-needed +++ canu/src/pipelines/canu.pl @@ -41,9 +41,9 @@ use FindBin; - use Cwd; + use Cwd qw(getcwd abs_path); -use lib "$FindBin::RealBin/lib"; -use lib "$FindBin::RealBin/lib/canu/lib/perl5"; @@ -15,5 +15,5 @@ Forwarded: not-needed +use lib "$FindBin::RealBin/../lib/canu/lib/perl5"; +use lib "$FindBin::RealBin/../lib/canu/lib64/perl5"; - use File::Path qw(make_path remove_tree); + use File::Path 2.08 qw(make_path remove_tree); diff --git a/debian/patches/series b/debian/patches/series index 65a74bb..033f46d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,3 @@ external-deps.patch -fix-build-system.patch relative-paths.patch use-debian-mhap-at-runtime.patch diff --git a/debian/patches/use-debian-mhap-at-runtime.patch b/debian/patches/use-debian-mhap-at-runtime.patch index f71079a..f96d1e2 100644 --- a/debian/patches/use-debian-mhap-at-runtime.patch +++ b/debian/patches/use-debian-mhap-at-runtime.patch @@ -4,21 +4,21 @@ Forwarded: not-needed Last-Update: 2016-03-20 --- canu.orig/src/pipelines/canu/OverlapMhap.pm +++ canu/src/pipelines/canu/OverlapMhap.pm -@@ -350,7 +350,7 @@ - print F "cd $path/blocks\n"; +@@ -378,7 +378,7 @@ + print F "cd ./blocks\n"; print F "\n"; print F "$javaPath -d64 -server -Xmx", $javaMemory, "m \\\n"; -- print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "\$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; -+ print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "/usr/share/java/mhap.jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; +- print F " -jar $cygA \$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n"; ++ print F " -jar $cygA \$bin/mhap.jar $cygB \\\n"; print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n"; print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1); print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1); -@@ -421,7 +421,7 @@ +@@ -477,7 +477,7 @@ print F "\n"; - print F "if [ ! -e \"$path/results/\$qry.mhap\" ] ; then\n"; + print F "if [ ! -e ./results/\$qry.mhap ] ; then\n"; print F " $javaPath -d64 -server -Xmx", $javaMemory, "m \\\n"; -- print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "\$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; -+ print F " -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "/usr/share/java//mhap.jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n"; +- print F " -jar $cygA \$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n"; ++ print F " -jar $cygA \$bin/mhap.jar $cygB \\\n"; print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n"; print F " --supress-noise 2 \\\n" if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1); print F " --no-tf \\\n" if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1); -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/canu.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
