Hi John,
Thanks for your help. Below is the output you requested. Btw, I was able to
get Samtools to compile by issuing "sudo make LDFLAGS="-L/usr/local/lib”, where
a newer version of zlib (libz.so.1.2.8) is available. Could it be that the
version that came with RHEL 6.2 just doesn't have the gzopen64 defined?
I still have trouble getting pysam to recognize the new version of libz and as
a result, I still get a gzopen64 error when pysam is invoked. If you have any
suggestion for this problem
(https://github.com/pysam-developers/pysam/issues/235
<https://github.com/pysam-developers/pysam/issues/235>), I would greatly
appreciate it as well.
Thanks.
Cheers,
Will
sudo make htsfile
gcc -g -O2 -I. -c -o htsfile.o htsfile.c
gcc -pthread -L/usr/local/lib -o htsfile htsfile.o libhts.a -lz
sudo gcc -H -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I.
-Ihtslib-1.3 -c -o bedidx.o bedidx.c
. /usr/include/stdlib.h
.. /usr/include/features.h
... /usr/include/sys/cdefs.h
.... /usr/include/bits/wordsize.h
... /usr/include/gnu/stubs.h
.... /usr/include/bits/wordsize.h
.... /usr/include/gnu/stubs-64.h
.. /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
.. /usr/include/bits/waitflags.h
.. /usr/include/bits/waitstatus.h
... /usr/include/endian.h
.... /usr/include/bits/endian.h
.... /usr/include/bits/byteswap.h
..... /usr/include/bits/wordsize.h
.. /usr/include/sys/types.h
... /usr/include/bits/types.h
.... /usr/include/bits/wordsize.h
.... /usr/include/bits/typesizes.h
... /usr/include/time.h
... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
... /usr/include/sys/select.h
.... /usr/include/bits/select.h
..... /usr/include/bits/wordsize.h
.... /usr/include/bits/sigset.h
.... /usr/include/time.h
.... /usr/include/bits/time.h
... /usr/include/sys/sysmacros.h
... /usr/include/bits/pthreadtypes.h
.... /usr/include/bits/wordsize.h
.. /usr/include/alloca.h
... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
. /usr/include/stdint.h
.. /usr/include/bits/wchar.h
.. /usr/include/bits/wordsize.h
. /usr/include/string.h
.. /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
.. /usr/include/xlocale.h
.. /usr/include/bits/string.h
.. /usr/include/bits/string2.h
. /usr/include/stdio.h
.. /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
.. /usr/include/libio.h
... /usr/include/_G_config.h
.... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
.... /usr/include/wchar.h
... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h
.. /usr/include/bits/stdio_lim.h
.. /usr/include/bits/sys_errlist.h
.. /usr/include/bits/stdio.h
. /usr/include/errno.h
.. /usr/include/bits/errno.h
... /usr/include/linux/errno.h
.... /usr/include/asm/errno.h
..... /usr/include/asm-generic/errno.h
...... /usr/include/asm-generic/errno-base.h
. /usr/local/include/zlib.h
.. /usr/local/include/zconf.h
... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h
.... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h
..... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h
...... /usr/include/limits.h
....... /usr/include/bits/posix1_lim.h
........ /usr/include/bits/local_lim.h
......... /usr/include/linux/limits.h
....... /usr/include/bits/posix2_lim.h
... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h
... /usr/include/unistd.h
.... /usr/include/bits/posix_opt.h
.... /usr/include/bits/environments.h
..... /usr/include/bits/wordsize.h
.... /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h
.... /usr/include/bits/confname.h
.... /usr/include/getopt.h
. htslib-1.3/htslib/ksort.h
. htslib-1.3/htslib/kseq.h
.. /usr/include/ctype.h
. htslib-1.3/htslib/khash.h
.. /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h
Multiple include guards may be useful for:
/usr/include/asm/errno.h
/usr/include/bits/byteswap.h
/usr/include/bits/confname.h
/usr/include/bits/endian.h
/usr/include/bits/environments.h
/usr/include/bits/errno.h
/usr/include/bits/local_lim.h
/usr/include/bits/select.h
/usr/include/bits/sigset.h
/usr/include/bits/stdio.h
/usr/include/bits/stdio_lim.h
/usr/include/bits/string.h
/usr/include/bits/string2.h
/usr/include/bits/sys_errlist.h
/usr/include/bits/time.h
/usr/include/bits/typesizes.h
/usr/include/bits/waitflags.h
/usr/include/bits/waitstatus.h
/usr/include/errno.h
/usr/include/gnu/stubs-64.h
/usr/include/gnu/stubs.h
/usr/include/limits.h
/usr/include/wchar.h
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h
> On Feb 22, 2016, at 12:19 AM, John Marshall <[email protected]> wrote:
>
> On 22 Feb 2016, at 01:05, William Hsiao <[email protected]> wrote:
>>
>> 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:
>
> This gzopen64() problem seems to be a long-standing problem on RHEL that we
> have never been able to reproduce elsewhere.
>
>> make[1]: Entering directory
>> `/usr/local/packages/samtools/samtools-1.3/htslib-1.3'
>
> Please also cd into this .../htslib-1.3 directory and type "make htsfile".
> It will be instructive to see whether this htslib-only executable also fails
> to link in the same way.
>
>> bedidx.o: In function `bed_read':
>> /usr/local/packages/samtools/samtools-1.3/bedidx.c:170: undefined reference
>> to `gzopen64'
>
> Please post (or email to me) the output from
>
> gcc -H -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I.
> -Ihtslib-1.3 -c -o bedidx.o bedidx.c
>
> (i.e., adding -H to the gcc command from your make trace that built bedidx.o.)
>
> Hopefully with your help we can get to the bottom of this problem this time
> around!
>
> John
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
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