Subject: use debian libs
Description: upstream makes use of embedded libs, use debian ones.
Author: Olivier Sallou <osallou@debian.org>
Last-Update: 2017-01-13
Forwarded: no
Index: bedops/interfaces/src/data/starch/starchFileHelpers.c
===================================================================
--- bedops.orig/interfaces/src/data/starch/starchFileHelpers.c
+++ bedops/interfaces/src/data/starch/starchFileHelpers.c
@@ -194,7 +194,7 @@ STARCH_gzip_deflate(FILE *source, FILE *
     /* deflateInit2 allows creation of archive with gzip header, i.e. a gzip file */
     /* cf. http://www.zlib.net/manual.html */
 #ifdef __cplusplus
-    ret = deflateInit2cpp(&strm, level, Z_DEFLATED, (15+16), 8, Z_DEFAULT_STRATEGY);
+    ret = deflateInit2(&strm, level, Z_DEFLATED, (15+16), 8, Z_DEFAULT_STRATEGY);
 #else
     ret = deflateInit2(&strm, level, Z_DEFLATED, (15+16), 8, Z_DEFAULT_STRATEGY);
 #endif
Index: bedops/system.mk/Makefile.linux
===================================================================
--- bedops.orig/system.mk/Makefile.linux
+++ bedops/system.mk/Makefile.linux
@@ -60,14 +60,14 @@ LIBS = $(addprefix $(PARTY3)/, jansson/l
 
 support: $(LIBS)
 
-${PARTY3}/jansson/lib/libjansson.a: $(WHICHJANSSON).tar.bz2
-	bzcat $^ | tar -x -C ${PARTY3}
-	cd ${PARTY3}/${JANSSONVERSION} && ./configure --prefix=${WDIR}/${PARTY3}/${JANSSONVERSION} && $(MAKE) && $(MAKE) install && cd ${WDIR} && rm -f jansson && ln -sf ${JANSSONVERSION} ${PARTY3}/jansson
+${PARTY3}/jansson/lib/libjansson.a:
+	#bzcat $^ | tar -x -C ${PARTY3}
+	#cd ${PARTY3}/${JANSSONVERSION} && ./configure --prefix=${WDIR}/${PARTY3}/${JANSSONVERSION} && $(MAKE) && $(MAKE) install && cd ${WDIR} && rm -f jansson && ln -sf ${JANSSONVERSION} ${PARTY3}/jansson
 
-$(PARTY3)/bzip2/libbz2.a: $(WHICHBZIP2).tar.bz2
-	bzcat $^ | tar -x -C ${PARTY3}
-	cd ${PARTY3}/${BZIP2VERSION} && $(MAKE) libbz2.a && cd ${WDIR} && rm -f bzip2 && ln -sf ${BZIP2VERSION} ${PARTY3}/bzip2
+$(PARTY3)/bzip2/libbz2.a:
+	#bzcat $^ | tar -x -C ${PARTY3}
+	#cd ${PARTY3}/${BZIP2VERSION} && $(MAKE) libbz2.a && cd ${WDIR} && rm -f bzip2 && ln -sf ${BZIP2VERSION} ${PARTY3}/bzip2
 
-${PARTY3}/zlib/libz.a: $(WHICHZLIB).tar.bz2
-	bzcat $^ | tar -x -C ${PARTY3}
-	cd ${PARTY3}/${ZLIBVERSION} && ./configure --static && $(MAKE) && cd ${WDIR} && rm -f zlib && ln -sf ${ZLIBVERSION} ${PARTY3}/zlib
+${PARTY3}/zlib/libz.a:
+	#bzcat $^ | tar -x -C ${PARTY3}
+	#cd ${PARTY3}/${ZLIBVERSION} && ./configure --static && $(MAKE) && cd ${WDIR} && rm -f zlib && ln -sf ${ZLIBVERSION} ${PARTY3}/zlib
Index: bedops/applications/bed/conversion/src/Makefile
===================================================================
--- bedops.orig/applications/bed/conversion/src/Makefile
+++ bedops/applications/bed/conversion/src/Makefile
@@ -13,7 +13,7 @@ OBJDIR                    = objects${POS
 WRAPPERDIR                = wrappers
 PROG                      = convert2bed
 SOURCE                    = convert2bed.c
-SFLAGS                    = -static
+SFLAGS                    =
 
 all: build
 
Index: bedops/applications/bed/sort-bed/src/Makefile
===================================================================
--- bedops.orig/applications/bed/sort-bed/src/Makefile
+++ bedops/applications/bed/sort-bed/src/Makefile
@@ -4,7 +4,7 @@ LIB1                = $(MAIN)/interfaces
 LIB2                = $(MAIN)/interfaces/src/utility
 LIB3                = $(MAIN)/interfaces/src/data/starch
 THISDIR             = ${shell pwd}
-INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
+INCLUDES            = -iquote$(HEAD)
 
 PARTY3              = ${THISDIR}/$(MAIN)/third-party
 LIBJANSSON          = libjansson.a
@@ -22,15 +22,15 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
 LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
 LOCALZLIBINCDIR     = ${LOCALZLIBDIR}
 
-LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
-LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+LIBLOCATION         = 
+LIBRARIES           = -ljansson -lz -lbz2
 
 PROG                = sort-bed-${BINARY_TYPE}
 BINDIR              = ../bin
 OBJDIR              = objects-${BINARY_TYPE}
 WARNINGS            = -Wall -Wextra -pedantic
 BLDFLAGS            = ${WARNINGS} -O3 -std=c++11 ${MEGAFLAGS}
-SFLAGS              = -static
+SFLAGS              = 
 
 dependency_names    = starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding SortDetails Sort CheckSort
 dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
Index: bedops/applications/bed/starch/src/Makefile
===================================================================
--- bedops.orig/applications/bed/starch/src/Makefile
+++ bedops/applications/bed/starch/src/Makefile
@@ -29,15 +29,15 @@ LOCALZLIBLIB              = ${LOCALZLIBL
 LOCALZLIBINCDIR           = ${LOCALZLIBDIR}
 OBJDIR                    = ${INTERFACES}/src/data/starch
 LOCALOBJDIR               = objects${POSTFIX}
-INCLUDES                  = -iquote${MAIN} -iquote${HEAD} -iquote${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
-LIBRARIES                 = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES                  = -iquote${MAIN} -iquote${HEAD}
+LIBRARIES                 = -ljansson -lz -lbz2
 ARCH_VERSION              = v2.2
 BIN_VERSION               = v2.4.27
 TEST                      = ../test
 TEST_LINUX_BINDIR         = ${TEST}/binaries/linux/${ARCH_VERSION}/bin
 TEST_OSX_BINDIR           = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
 AR                        = ar
-SFLAGS                    = -static
+SFLAGS                    = 
 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} -DDEBUG=1
 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} -DDEBUG=1 -pg
@@ -65,7 +65,7 @@ starchcluster: $(BINDIR)/starchcluster_g
 starch-diff: $(BINDIR)/starch-diff-$(BINARY_TYPE)
 starchstrip: $(BINDIR)/starchstrip-$(BINARY_TYPE)
 
-$(BINDIR)/%-$(BINARY_TYPE) : %.c $(LOCALSTARCHLIB) $(LIBRARIES)
+$(BINDIR)/%-$(BINARY_TYPE) : %.c $(LOCALSTARCHLIB)
 	mkdir -p $(BINDIR)
 	${CXX} ${CXXFLAGS} ${MEGAFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
 	${CXX} ${CXXFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@ ${LOCALSTARCHLIB} ${LIBRARIES}
@@ -102,7 +102,7 @@ $(LOCALSTARCHLIB) : $(STARCH_OBJECTS)
 	mkdir -p $(LOCALSTARCHLIBDIR)
 	${AR} rcs $@ $^
 
-$(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c $(LIBRARIES)
+$(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c
 	mkdir -p $(LOCALOBJDIR)
 	${CXX} ${CXXFLAGS} ${MEGAFLAGS} -c $< -o $@ ${INCLUDES}
 
Index: bedops/applications/bed/starch/src/starchcat.c
===================================================================
--- bedops.orig/applications/bed/starch/src/starchcat.c
+++ bedops/applications/bed/starch/src/starchcat.c
@@ -6178,7 +6178,7 @@ STARCHCAT2_setupGzipOutputStream(z_strea
 
     /* cf. http://www.zlib.net/manual.html for level information */
 #ifdef __cplusplus
-    zError = deflateInit2cpp(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL, Z_DEFLATED, STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
+    zError = deflateInit2(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL, Z_DEFLATED, STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
 #else
     zError = deflateInit2(zStreamPtr, STARCH_Z_COMPRESSION_LEVEL, Z_DEFLATED, STARCH_Z_WINDOW_BITS, STARCH_Z_MEMORY_LEVEL, Z_DEFAULT_STRATEGY);
 #endif
Index: bedops/docs/conf.py
===================================================================
--- bedops.orig/docs/conf.py
+++ bedops/docs/conf.py
@@ -12,7 +12,6 @@
 # serve to show the default.
 
 import sys, os
-from better import better_theme_path
 
 # 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
@@ -96,8 +95,8 @@ pygments_style = 'sphinx'
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#html_theme = 'default'
-html_theme = 'better'
+html_theme = 'default'
+#html_theme = 'better'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -110,8 +109,8 @@ html_theme_options = {
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
-html_theme_path = [better_theme_path]
+html_theme_path = []
+#html_theme_path = [better_theme_path]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
Index: bedops/applications/bed/bedops/src/Makefile
===================================================================
--- bedops.orig/applications/bed/bedops/src/Makefile
+++ bedops/applications/bed/bedops/src/Makefile
@@ -22,11 +22,11 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
 LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
 LOCALZLIBINCDIR     = ${LOCALZLIBDIR}
 OBJDIR              = objects_${BINARY_TYPE}
-INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
-LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
-LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES            = -iquote$(HEAD)
+LIBLOCATION         = 
+LIBRARIES           = -ljansson -lz -lbz2
 BLDFLAGS            = -Wall -pedantic -O3 -std=c++11
-SFLAGS              = -static
+SFLAGS              = 
 
 dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
 dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
Index: bedops/applications/bed/bedextract/src/Makefile
===================================================================
--- bedops.orig/applications/bed/bedextract/src/Makefile
+++ bedops/applications/bed/bedextract/src/Makefile
@@ -21,11 +21,11 @@ LOCALBZIP2INCDIR        = ${LOCALBZIP2DI
 LOCALZLIBDIR            = ${PARTY3}/zlib
 LOCALZLIBLIB            = ${LOCALZLIBDIR}/${LIBZLIB}
 LOCALZLIBINCDIR         = ${LOCALZLIBDIR}
-INCLUDES                = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
-LIBLOCATION             = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
-LIBRARIES               = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES                = -iquote$(HEAD)
+LIBLOCATION             = 
+LIBRARIES               = -ljansson -lz -lbz2
 BLDFLAGS                = -Wall -pedantic -O3 -std=c++11
-SFLAGS                  = -static ${MEGAFLAGS}
+SFLAGS                  = ${MEGAFLAGS}
 
 dependency_names        = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
 dependencies            = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
Index: bedops/applications/bed/bedmap/src/Makefile
===================================================================
--- bedops.orig/applications/bed/bedmap/src/Makefile
+++ bedops/applications/bed/bedmap/src/Makefile
@@ -20,11 +20,11 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
 LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
 LOCALZLIBINCDIR     = ${LOCALZLIBDIR}
 OBJDIR              = objects_${BINARY_TYPE}
-INCLUDES            = -iquote${HEAD} -I${PARTY3} -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
-LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
-LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES            = -iquote${HEAD}
+LIBLOCATION         = 
+LIBRARIES           = -ljansson -lz -lbz2
 BLDFLAGS            = -Wall -pedantic -O3 -std=c++11 
-SFLAGS              = -static
+SFLAGS              =
 
 dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
 dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
Index: bedops/applications/bed/closestfeats/src/Makefile
===================================================================
--- bedops.orig/applications/bed/closestfeats/src/Makefile
+++ bedops/applications/bed/closestfeats/src/Makefile
@@ -20,11 +20,11 @@ LOCALZLIBDIR        = ${PARTY3}/zlib
 LOCALZLIBLIB        = ${LOCALZLIBDIR}/${LIBZLIB}
 LOCALZLIBINCDIR     = ${LOCALZLIBDIR}
 OBJDIR              = objects_${BINARY_TYPE}
-INCLUDES            = -iquote$(HEAD) -I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
-LIBLOCATION         = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR} -L${LOCALZLIBDIR}
-LIBRARIES           = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES            = -iquote$(HEAD)
+LIBLOCATION         = 
+LIBRARIES           = -ljansson -lz -lbz2
 BLDFLAGS            = -Wall -pedantic -O3 -std=c++11
-SFLAGS              = -static
+SFLAGS              = 
 
 dependency_names    = NaN starchConstants starchFileHelpers starchHelpers starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
 dependencies        = $(addprefix $(OBJDIR)/, $(addsuffix .o, $(dependency_names)))
