Source: bedops
Version: 2.4.20+dfsg-1
Severity: wishlist
Hi maintainer
Please consider applying the attached diff against
debian/patches/use_debian_libs.
It adds -ljansson -lz -lbz2 to LIBRARIES instead of SFLAGS to avoid
underlinking when bedops is linked with --as-needed, as is the default
in Ubuntu.
Regards
Graham
--- a/debian/patches/use_debian_libs
+++ b/debian/patches/use_debian_libs
@@ -14,10 +14,10 @@
-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES = -iquote$(HEAD)
+LIBLOCATION =
-+LIBRARIES =
++LIBRARIES = -ljansson -lz -lbz2
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-SFLAGS = -static
-+SFLAGS = -ljansson -lz -lbz2
++SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
@@ -43,10 +43,10 @@
-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES = -iquote$(HEAD)
+LIBLOCATION =
-+LIBRARIES =
++LIBRARIES = -ljansson -lz -lbz2
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-SFLAGS = -static
-+SFLAGS = -ljansson -lz -lbz2
++SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
@@ -68,10 +68,10 @@
-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES = -iquote${HEAD}
+LIBLOCATION =
-+LIBRARIES =
++LIBRARIES = -ljansson -lz -lbz2
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-SFLAGS = -static
-+SFLAGS = -ljansson -lz -lbz2
++SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
@@ -112,10 +112,10 @@
-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+INCLUDES = -iquote$(HEAD)
+LIBLOCATION =
-+LIBRARIES =
++LIBRARIES = -ljansson -lz -lbz2
BLDFLAGS = -Wall -pedantic -O3 -std=c++11
-SFLAGS = -static
-+SFLAGS = -ljansson -lz -lbz2
++SFLAGS =
dependency_names = NaN starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
@@ -148,7 +148,7 @@
-LIBLOCATION = -L${LOCALJANSSONLIBDIR} -L${LOCALBZIP2LIBDIR}
-L${LOCALZLIBDIR}
-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB} ${LOCALZLIBLIB}
+LIBLOCATION =
-+LIBRARIES =
++LIBRARIES = -ljansson -lz -lbz2
PROG = sort-bed
BINDIR = ../bin
@@ -156,7 +156,7 @@
WARNINGS = -Wall -Wextra -pedantic
BLDFLAGS = ${WARNINGS} -O3 -std=c++11
-SFLAGS = -static
-+SFLAGS = -ljansson -lz -lbz2
++SFLAGS =
dependency_names = starchConstants starchFileHelpers starchHelpers
starchMetadataHelpers unstarchHelpers starchSha1Digest starchBase64Coding
SortDetails Sort CheckSort
dependencies = $(addprefix $(OBJDIR)/, $(addsuffix .o,
$(dependency_names)))
@@ -169,7 +169,7 @@
-INCLUDES = -iquote${MAIN} -iquote${HEAD} -iquote${PARTY3}
-I${LOCALJANSSONINCDIR} -I${LOCALBZIP2INCDIR} -I${LOCALZLIBINCDIR}
-LIBRARIES = ${LOCALJANSSONLIB} ${LOCALBZIP2LIB}
${LOCALZLIBLIB}
+INCLUDES = -iquote${MAIN} -iquote${HEAD}
-+LIBRARIES =
++LIBRARIES = -ljansson -lz -lbz2
ARCH_VERSION = v2.1
BIN_VERSION = v2.4.16
TEST = ../test
@@ -177,10 +177,28 @@
TEST_OSX_BINDIR = ${TEST}/binaries/osx/${ARCH_VERSION}/bin
AR = ar
-SFLAGS = -static
-+SFLAGS = -ljansson -lz -lbz2
++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}
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 $(BINDIR)/starchcluster_sge
+
+-$(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 @@
+ mkdir -p $(LOCALSTARCHLIBDIR)
+ ${AR} rcs $@ $^
+
+-$(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c $(LIBRARIES)
++$(LOCALOBJDIR)/%.o : $(OBJDIR)/%.c
+ mkdir -p $(LOCALOBJDIR)
+ ${CXX} ${CXXFLAGS} -c $< -o $@ ${INCLUDES}
+
--- a/applications/bed/starch/src/starchcat.c
+++ b/applications/bed/starch/src/starchcat.c
@@ -4870,7 +4870,7 @@
