[BioC] Ruuid had non-zero exit status
Herve Pages
hpages at fhcrc.org
Fri Jun 16 01:01:41 CEST 2006
Zong-Pei,
Just to know wether this is an R/BioC/Ruuid or a Sparc/glib/gcc related pb,
can you please try this:
gcc -I/package/R/2.3.1/lib/R/include -I/package/R/2.3.1/lib/R/include \
-I/usr/local/include -I/ usr/local/include/glib-2.0 \
-I/usr/local/lib/glib-2.0/include -DHAVE_UNISTD_H=1 -fPIC -O2 \
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -c Rinit.c -o Rinit.o
with the Rinit.c file replaced by the following test.c file:
#include <glib.h>
int main() {}
If you do _not_ get this anymore
/usr/local/include/glib-2.0/glib/gtypes.h:41: error: syntax error
before "typedef"
then we will know for sure that it's a Ruuid pb.
If you still get the error, then we'll have to look somewhere else. Then
you could try:
gcc -I/usr/local/include -I/ usr/local/include/glib-2.0
-I/usr/local/lib/glib-2.0/include test.c
and if you still get an error then we will no for sure that this is a
Sparc/glib/gcc related pb.
Cheers,
H.
zph at herald.ox.ac.uk wrote:
> On Tue, 13 Jun 2006, Herve Pages wrote:
> ...
>
>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1
>>
>
> Hi, Herve:
>
> These are for handling large files in R. They work
> well with R pre-2.3
>
> Looks likely that changes in Ruuid 1.8.0 cause
> the problem. I find Ruuid 1.5.3 can be installed
> it doesn't work because R complains its namespace
> is missing.
>
> I hope the BioC developers would consider to
> maintain the packages like Perl modules under
> CPAN. In other words, previous installed CRAN
> packages should be usable for later version
> of R/BioC unless users want to update them.
>
> Regards,
>
> Zong-Pei
>
>
--
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Hervé Pagès
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
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