Hi,
I’m trying to install Samtools 1.3 on a RHEL 6.2 system. I seemed to be able
to install htslib 1.3 but as I try to install samtools 1.3 I encountered the
following error when I type:
./configure (output below for reference)
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 location of HTSlib source tree... htslib-1.3
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... yes
checking for working ncursesw.h... no
checking for working ncurses.h... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
=== configuring in htslib-1.3
(/usr/local/packages/samtools/samtools-1.3/htslib-1.3)
configure: running /bin/sh ./configure --disable-option-checking
'--prefix=/usr/local' --cache-file=/dev/null --srcdir=.
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 how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for sys/param.h... yes
checking for getpagesize... yes
checking for working mmap... yes
checking for gmtime_r... yes
checking for zlib.h... yes
checking for inflate in -lz... yes
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
config.status: config.h is unchanged
make
make[1]: Entering directory
`/usr/local/packages/samtools/samtools-1.3/htslib-1.3'
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
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
make[1]: Leaving directory
`/usr/local/packages/samtools/samtools-1.3/htslib-1.3'
gcc -pthread -rdynamic -o samtools bam_index.o bam_plcmd.o sam_view.o
bam_cat.o bam_md.o bam_reheader.o bam_sort.o bedidx.o kprobaln.o bam_rmdup.o
bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o bam2bcf.o
bam2bcf_indel.o errmod.o sample.o sam_opts.o cut_target.o phase.o bam2depth.o
padding.o bedcov.o bamshuf.o faidx.o dict.o stats.o stats_isize.o bam_flags.o
bam_split.o bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o
bam_quickcheck.o bam_addrprg.o libbam.a htslib-1.3/libhts.a -lncursesw -lm -lz
-ldl
bedidx.o: In function `bed_read':
/usr/local/packages/samtools/samtools-1.3/bedidx.c:170: undefined reference to
`gzopen64'
phase.o: In function `loadpos':
/usr/local/packages/samtools/samtools-1.3/phase.c:506: undefined reference to
`gzopen64'
bedcov.o: In function `main_bedcov':
/usr/local/packages/samtools/samtools-1.3/bedcov.c:118: undefined reference to
`gzopen64'
dict.o: In function `write_dict':
/usr/local/packages/samtools/samtools-1.3/dict.c:50: undefined reference to
`gzopen64'
collect2: ld returned 1 exit status
make: *** [samtools] Error 1
I have the following zlib versions that came with RHEL 6.2
zlib.i686 1.2.3-29.el6 @rhel-6-server-rpms
zlib.x86_64 1.2.3-29.el6 @rhel-6-server-rpms
zlib-devel.i686 1.2.3-29.el6 @rhel-6-server-rpms
zlib-devel.x86_64 1.2.3-29.el6 @rhel-6-server-rpms
Any suggestions to fix the gzopen64 error message would be greatly appreciated.
The same issue seems to affect pysam installation.
Cheers,
Will
William Hsiao
[email protected]
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