Sorry John,
The problem was solved for samtools and bcftools under OSX/macports but not for
htslib 1.3 where building still leads to
gcc: error: -compatibility_version only allowed with -dynamiclib
make: *** [libhts.dylib] Error 1
after editing Makefile
...
libhts.dylib: $(LIBHTS_OBJS)
$(CC) -Wl,-export_dynamic -install_name
$(libdir)/libhts.$(LIBHTS_SOVERSION).dylib -current_version $(NUMERIC_VERSION)
-compatibility_version $(LIBHTS_SOVERSION) $(LDFLAGS) -o $@ $(LIBHTS_OBJS) -lz
$(LIBS)
ln -sf $@ libhts.$(LIBHTS_SOVERSION).dylib
…
And I do not find editable parts in config.mk(.in) for dynamic
Any new saving tip?
make
gcc -g -O2 -I. -c -o kfunc.o kfunc.c
gcc -g -O2 -I. -c -o knetfile.o knetfile.c
gcc -g -O2 -I. -c -o kstring.o kstring.c
gcc -g -O2 -I. -c -o bgzf.o bgzf.c
gcc -g -O2 -I. -c -o faidx.o faidx.c
gcc -g -O2 -I. -c -o hfile.o hfile.c
gcc -g -O2 -I. -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3"' > version.h
gcc -g -O2 -I. -c -o hts.o hts.c
gcc -g -O2 -I. -c -o md5.o md5.c
gcc -g -O2 -I. -c -o regidx.o regidx.c
gcc -g -O2 -I. -c -o sam.o sam.c
gcc -g -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -I. -c -o tbx.o tbx.c
gcc -g -O2 -I. -c -o vcf.o vcf.c
gcc -g -O2 -I. -c -o vcfutils.o vcfutils.c
gcc -g -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -I. -c -o cram/files.o cram/files.c
gcc -g -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -I. -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -O2 -I. -c -o cram/vlen.o cram/vlen.c
gcc -g -O2 -I. -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o
hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o
vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o
cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o
cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o
cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gcc -Wl,-export_dynamic -install_name
/Users/splaisan/Downloads/htslib-1.3/lib/libhts.1.dylib -current_version 1.3
-compatibility_version 1 -o libhts.dylib kfunc.o knetfile.o kstring.o bgzf.o
faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o
vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o
cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o
cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o
cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o
cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o -lz
gcc: error: -compatibility_version only allowed with -dynamiclib
make: *** [libhts.dylib] Error 1
I looked for Makefile and
On 16 Feb 2016, at 11:44, Stephane Plaisance <[email protected]>
wrote:
> I get the following on OSX 10.10.5
[...]
>
> gcc: error: unrecognized command line option '-rdynamic'
See https://sourceforge.net/p/samtools/mailman/message/34699333/ ; most GCC
compiler drivers understand this option, but apparently not the MacPorts one
you have on OS X.
We will add to the configure script to detect whether this option will be
accepted, but in the meantime the previous response shows you how to work
around this and build samtools successfully.
John
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