[JdeBruin]

This is indeed a RHEL 6.x system

I have not done as suggested with "libbam.a" is this included in the Casava dir?

Thanks

[GenoMax]

This is indeed a RHEL 6.x system

I have not done as suggested with "libbam.a" is this included in the Casava dir?

Thanks

Looking at your original log, is the error being produced during "samtools" build? We built casava-1.8.2 a long time ago so I do not remember if "samtools" was included in the installer or we already had it installed.

The "libbam.a" is part of the samtools and should get built as a part of the samtools package.

[JdeBruin]

Yes I get the error when samtools are being build as part of a Casava installation.
I found libbam.a in opt/samtools-0.1.8/ but I believe due to the fact that the error is produced while samtools are being built, libbam.a should be placed when the build (make command) has been completed succefully...

[GenoMax]

Is samtools being built successfully? Do you see the samtools executable?

[JdeBruin]

Samtools fails to build, the configure pass no problem but the make command fails.

[GenoMax]

Have you installed both "zlib" and "zlib-devel"?

[JdeBruin]

Hi,

Yes I have installed both:
Version : 1.2.3 Vendor: Red Hat, Inc.

[GenoMax]

Would you mind getting the samtools package from here (as an aside) and checking if it compiles? http://sourceforge.net/projects/samtools/files/

[JdeBruin]

Hi will do so

[JdeBruin]

I have done so and I am still unable to "make" succesfully.

Error:

/root/apps/tmp_samtools/samtools-0.1.19/phase.c:475: undefined reference to `gzopen64'
bedcov.o: In function `main_bedcov':
/root/apps/tmp_samtools/samtools-0.1.19/bedcov.c:69: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `__bam_get_lines':
/root/apps/tmp_samtools/samtools-0.1.19/bam_import.c:76: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_open':
/root/apps/tmp_samtools/samtools-0.1.19/bam_import.c:472: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_header_read2':
/root/apps/tmp_samtools/samtools-0.1.19/bam_import.c:126: undefined reference to `gzopen64'
libbam.a(bedidx.o):/root/apps/tmp_samtools/samtools-0.1.19/bedidx.c:107: more undefined references to `gzopen64' follow

What is this gzopen64 ?

[GenoMax]

I have done so and I am still unable to "make" succesfully.

Error:

/root/apps/tmp_samtools/samtools-0.1.19/phase.c:475: undefined reference to `gzopen64'
bedcov.o: In function `main_bedcov':
/root/apps/tmp_samtools/samtools-0.1.19/bedcov.c:69: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `__bam_get_lines':
/root/apps/tmp_samtools/samtools-0.1.19/bam_import.c:76: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_open':
/root/apps/tmp_samtools/samtools-0.1.19/bam_import.c:472: undefined reference to `gzopen64'
libbam.a(bam_import.o): In function `sam_header_read2':
/root/apps/tmp_samtools/samtools-0.1.19/bam_import.c:126: undefined reference to `gzopen64'
libbam.a(bedidx.o):/root/apps/tmp_samtools/samtools-0.1.19/bedidx.c:107: more undefined references to `gzopen64' follow

What is this gzopen64 ?

That means that your zlib is probably not installed correctly. Are you using the RH supplied zlib?

Where exactly is your zlib.h installed?

[JdeBruin]

Hey,

I have used the RH installed zlib I have also downloaded the latest zlib from zlib.org and compiled from source.

Probably have to uninstall all zlib and start over?

[GenoMax]

Hey,

I have used the RH installed zlib I have also downloaded the latest zlib from zlib.org and compiled from source.

Probably have to uninstall all zlib and start over?

I would say remove the zlib you downloaded from zlib.org and try the compile again.