[med-svn] [canu] 01/04: Update and refresh patches

[Afif Elghraoui]

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 <afif at debian.org>
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 <afif at debian.org>
 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 <afif at debian.org>
-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);

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