Compilation fails in 0.2.0-rc11 and rc12, but rc10 OK

[winni2k]

I am using gcc version 4.7.2 on fedora 18. On 0.2.0-rc11 if I run make, then the command

gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c

gives me a whole string of "conflicting type" errors like these ones:

gcc -g -Wall -O2 -I. -DSAMTOOLS=1 -c -o hts.o hts.c
In file included from /homes/kretzsch/include/htslib/sam.h:5:0,
                 from ./cram/cram_samtools.h:61,
                 from cram/cram.h:47,
                 from hts.c:11:
/homes/kretzsch/include/htslib/hts.h:58:3: error: conflicting types for ‘htsFile’
In file included from hts.c:10:0:
htslib/hts.h:58:3: note: previous declaration of ‘htsFile’ was here
In file included from /homes/kretzsch/include/htslib/sam.h:5:0,
                 from ./cram/cram_samtools.h:61,
                 from cram/cram.h:47,
                 from hts.c:11:

0.2.0-rc10 is fine. Is this happening to anybody else?

[jmarshall]

The problem is that you have the rc10 htslib headers installed in ~/include, which is being picked up before the rc11 headers in the development directory (presumably you are using $CPATH or $C_INCLUDE_PATH?). So you can work around this by uninstalling the previous headers.

That said, building htslib itself should use its own headers within itself in preference to other installed htslib headers. I'll check in a fix for that soon.

[winni2k]

I do use $C_INCLUDE_PATH and deleting all files in ~/include/htslib/ does
the trick. Thanks for the help.

On Tue, Aug 12, 2014 at 9:37 PM, John Marshall notifications@github.com
wrote:

The problem is that you have the rc10 htslib headers installed in
~/include, which is being picked up before the rc11 headers in the
development directory (presumably you are using $CPATH or
$C_INCLUDE_PATH?). So you can work around this by uninstalling the previous
headers.

That said, building htslib itself should use its own headers within itself
in preference to other installed htslib headers. I'll check in a fix for
that soon.

—
Reply to this email directly or view it on GitHub
#117 (comment).

[jmarshall]

What value do you have $C_INCLUDE_PATH set to?

[winni2k]

The value of $C_INCLUDE PATH is /homes/kretzsch/include:/opt/cuda-5.5/include:/homes/kretzsch/include:/opt/cuda-5.5/include:, where /homes/kretzsch is my home directory.