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|
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
--- a/interfaces/src/data/starch/starchFileHelpers.c
+++ b/interfaces/src/data/starch/starchFileHelpers.c
@@ -194,7 +194,7 @@
/* 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
--- a/system.mk/Makefile.linux
+++ b/system.mk/Makefile.linux
@@ -64,14 +64,14 @@
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
--- a/applications/bed/conversion/src/Makefile
+++ b/applications/bed/conversion/src/Makefile
@@ -13,7 +13,7 @@
WRAPPERDIR = wrappers
PROG = convert2bed
SOURCE = convert2bed.c
-SFLAGS = -static
+SFLAGS =
all: build
--- a/applications/bed/sort-bed/src/Makefile
+++ b/applications/bed/sort-bed/src/Makefile
@@ -4,7 +4,7 @@
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 @@
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)))
--- a/applications/bed/starch/src/Makefile
+++ b/applications/bed/starch/src/Makefile
@@ -29,15 +29,15 @@
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 = v2.4.40
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 =
STARCH_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
STARCH_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
STARCH_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 @@
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} ${STARCH_CXXFLAGS} ${MEGAFLAGS} -c $*.c -o $(LOCALOBJDIR)/$*.o ${INCLUDES}
${CXX} ${CXXFLAGS} ${STARCH_CXXFLAGS} ${MEGAFLAGS} $(LOCALOBJDIR)/$*.o -o $@ ${LOCALSTARCHLIB} ${LIBRARIES}
@@ -102,7 +102,7 @@
mkdir -p $(LOCALSTARCHLIBDIR)
${AR} rcs $@ $^
-$(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c $(LIBRARIES)
+$(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c
mkdir -p $(LOCALOBJDIR)
${CXX} ${CXXFLAGS} ${STARCH_CXXFLAGS} ${MEGAFLAGS} -c $< -o $@ ${INCLUDES}
--- a/applications/bed/starch/src/starchcat.c
+++ b/applications/bed/starch/src/starchcat.c
@@ -6178,7 +6178,7 @@
/* 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
--- a/docs/conf.py
+++ b/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 @@
# 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 @@
}
# 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".
--- a/applications/bed/bedops/src/Makefile
+++ b/applications/bed/bedops/src/Makefile
@@ -22,11 +22,11 @@
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)))
--- a/applications/bed/bedextract/src/Makefile
+++ b/applications/bed/bedextract/src/Makefile
@@ -21,11 +21,11 @@
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)))
--- a/applications/bed/bedmap/src/Makefile
+++ b/applications/bed/bedmap/src/Makefile
@@ -20,11 +20,11 @@
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)))
--- a/applications/bed/closestfeats/src/Makefile
+++ b/applications/bed/closestfeats/src/Makefile
@@ -20,11 +20,11 @@
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)))
|
