htslib v1.2.1 compilation error #205
Description
Hi there!
I was trying to compile latest version of htslib (1.2.1) but an error appeared and broke the compilation. Logs for the "configure" and "make" commands are at the end of the post. It also happened with version 1.2.
I'm performing the installation on a CentOS 5.5. I'm compiling with gcc version 4.7.4.
Any help would be really appreciated.
Best,
Santiago
$ ./configure
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for ranlib... ranlib
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
$ 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 "1.2.1"' > version.h
gcc -g -O2 -I. -c -o hts.o hts.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
cram/cram_decode.c: In function ‘cram_dependent_data_series’:
cram/cram_decode.c:670:28: error: ‘SAM_QNAME’ undeclared (first use in this function)
cram/cram_decode.c:670:28: note: each undeclared identifier is reported only once for each function it appears in
cram/cram_decode.c:673:28: error: ‘SAM_FLAG’ undeclared (first use in this function)
cram/cram_decode.c:676:28: error: ‘SAM_RNAME’ undeclared (first use in this function)
cram/cram_decode.c:679:28: error: ‘SAM_POS’ undeclared (first use in this function)
cram/cram_decode.c:682:28: error: ‘SAM_MAPQ’ undeclared (first use in this function)
cram/cram_decode.c:685:28: error: ‘SAM_CIGAR’ undeclared (first use in this function)
cram/cram_decode.c:688:28: error: ‘SAM_RNEXT’ undeclared (first use in this function)
cram/cram_decode.c:691:28: error: ‘SAM_PNEXT’ undeclared (first use in this function)
cram/cram_decode.c:694:28: error: ‘SAM_TLEN’ undeclared (first use in this function)
cram/cram_decode.c:698:28: error: ‘SAM_SEQ’ undeclared (first use in this function)
cram/cram_decode.c:701:30: error: ‘SAM_AUX’ undeclared (first use in this function)
cram/cram_decode.c:705:28: error: ‘SAM_QUAL’ undeclared (first use in this function)
cram/cram_decode.c:711:28: error: ‘SAM_RGAUX’ undeclared (first use in this function)
cram/cram_decode.c: In function ‘cram_decode_slice_xref’:
cram/cram_decode.c:1699:30: error: ‘SAM_RNEXT’ undeclared (first use in this function)
cram/cram_decode.c:1699:42: error: ‘SAM_PNEXT’ undeclared (first use in this function)
cram/cram_decode.c:1699:54: error: ‘SAM_TLEN’ undeclared (first use in this function)
cram/cram_decode.c: In function ‘cram_decode_slice’:
cram/cram_decode.c:1913:32: error: ‘SAM_SEQ’ undeclared (first use in this function)
cram/cram_decode.c:2053:39: error: ‘SAM_TLEN’ undeclared (first use in this function)
cram/cram_decode.c: In function ‘cram_to_bam’:
cram/cram_decode.c:2387:31: error: ‘SAM_QNAME’ undeclared (first use in this function)
cram/cram_decode.c:2418:32: error: ‘SAM_SEQ’ undeclared (first use in this function)
cram/cram_decode.c:2418:42: error: ‘SAM_QUAL’ undeclared (first use in this function)
cram/cram_decode.c: In function ‘cram_next_slice’:
cram/cram_decode.c:2562:30: error: ‘SAM_POS’ undeclared (first use in this function)
make: *** [cram/cram_decode.o] Error 1