[Bioperl-l] RE: [BioSQL-l] biosql & bioperl-db on Solaris

[Richard HOLLAND]

Hi,

This may seem a bit basic but it's worth a go.

CPAN looks for "cc" - which on a Sun machine is the Sun compiler. If you
have "gcc" installed then you may need to create a soft-link to it
called "cc" and ensure that softlink appears earlier in your path than
the location of the Sun compiler. You must then export the path or add
it to your profile as CPAN starts new sub-shells internally).

eg. if your gcc binary is /usr/bin/gcc, and assuming a bash-like shell:

	mkdir ~/bin
	ln -s /usr/bin/gcc ~/bin/cc
	PATH=~/bin:$PATH
	export PATH
	
Then run CPAN and see what happens.

Hope it helps.

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biosql-l-bounces at portal.open-bio.org 
> [mailto:biosql-l-bounces at portal.open-bio.org] On Behalf Of 
> Mike Muratet
> Sent: Wednesday, November 16, 2005 3:57 AM
> To: biosql-l at open-bio.org
> Cc: bioperl-l at bioperl.org
> Subject: [BioSQL-l] biosql & bioperl-db on Solaris
> 
> 
> Greetings
> 
> This is not strictly a bioperl or biosql issue, but is 
> related. In the 
> process of trying to install bioperl-db on a Solaris 9 
> system, I had to go 
> back and install the latest bioperl, DBI, AND DBD modules. 
> The DBD install 
> via CPAN is failing for an ELF64 incompatibility when it 
> tries to link to 
> the mysql client libs because I also installed the 
> latest 64bit mysql. According to the mysql docs, 64bit is 4% slower 
> than the 32bit version, but you get more threads and memory 
> (which would 
> seem to be faster in the long run).
> 
> Although I have installed gcc and gnu make, CPAN is picking 
> up the native 
> Sun compiler (and why do they spread things out over so many 
> subdirectories?) and linker.
> 
> Has anyone else come up against this before (I didn't find 
> anything in the 
> archives)? Is the best course to install a 32bit mysql? 
> Should I forgo 
> CPAN and try to do a manual install where I might have some 
> control over 
> Makefile.PL? Has anybody tried biosql on a 64bit system and 
> does it make a 
> difference?
> 
> Thanks
> 
> Mike
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