[med-svn] [bedops] 04/05: fix debian patch for new release

[Olivier Sallou]

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osallou pushed a commit to branch master
in repository bedops.

commit ecd23a92f181ca034ce8277406c8a8cdad09528f
Author: Olivier Sallou <osallou at debian.org>
Date:   Wed Jun 21 12:11:23 2017 +0000

    fix debian patch for new release
---
 debian/patches/use_debian_libs | 21 ++++++---------------
 1 file changed, 6 insertions(+), 15 deletions(-)

diff --git a/debian/patches/use_debian_libs b/debian/patches/use_debian_libs
index 81a68d5..759dc2c 100644
--- a/debian/patches/use_debian_libs
+++ b/debian/patches/use_debian_libs
@@ -77,7 +77,7 @@ Forwarded: no
  dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
 --- a/system.mk/Makefile.linux
 +++ b/system.mk/Makefile.linux
-@@ -154,14 +154,14 @@
+@@ -169,14 +169,14 @@
  
  support: $(LIBS)
  
@@ -181,16 +181,16 @@ Forwarded: no
  CXXFLAGS                  = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O2 -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 ${SFLAGS} -s
  CXXDFLAGS                 = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O0 -g -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS}
  CXXGFLAGS                 = -D__STDC_CONSTANT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE=1 -DUSE_ZLIB -DUSE_BZLIB -O -Wformat -Wall -Wextra -Wswitch-enum -std=c++11 -DDEBUG_VERBOSE=1 ${SFLAGS} -pg
-@@ -60,7 +60,7 @@
- starchcat: $(BINDIR)/starchcat
- starchcluster: $(BINDIR)/starchcluster_gnuParallel $(BINDIR)/starchcluster_sge
+@@ -62,7 +62,7 @@
+ starch-diff: $(BINDIR)/starch-diff
+ starchstrip: $(BINDIR)/starchstrip
  
 -$(BINDIR)/% : %.c $(LOCALSTARCHLIB) $(LIBRARIES)
 +$(BINDIR)/% : %.c $(LOCALSTARCHLIB)
  	mkdir -p $(BINDIR)
  	${CXX} ${CXXFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
  	${CXX} ${CXXFLAGS} $(LOCALOBJDIR)/$*.o -o $@ ${LOCALSTARCHLIB} ${LIBRARIES}
-@@ -85,7 +85,7 @@
+@@ -91,7 +91,7 @@
  	mkdir -p $(LOCALSTARCHLIBDIR)
  	${AR} rcs $@ $^
  
@@ -201,7 +201,7 @@ Forwarded: no
  
 --- a/applications/bed/starch/src/starchcat.c
 +++ b/applications/bed/starch/src/starchcat.c
-@@ -4870,7 +4870,7 @@
+@@ -5319,7 +5319,7 @@
  
      /* cf. http://www.zlib.net/manual.html for level information */
  #ifdef __cplusplus
@@ -220,15 +220,6 @@ Forwarded: no
  
  # If extensions (or modules to document with autodoc) are in another directory,
  # add these directories to sys.path here. If the directory is relative to the
-@@ -26,7 +25,7 @@
- 
- # Add any Sphinx extension module names here, as strings. They can be extensions
- # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
--extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode'] 
-+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.imgmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode']
- #, 'sphinx.ext.mathbase']
- 
- # Add any paths that contain templates here, relative to this directory.
 @@ -96,8 +95,8 @@
  
  # The theme to use for HTML and HTML Help pages.  See the documentation for

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