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

Hilmar Lapp hlapp at gnf.org
Tue Nov 15 21:21:45 EST 2005

I believe the DBI docs make a pretty strong statement about perl, your 
database client library, and DBI/DBD having to be compiled by the same 
compiler using the same settings.

This may be a bit too strong of a statement, but I'd definitely make 
sure that if you want 64bit in the DBD driver perl is also 64-bit 
compiled, and that they are all compiled by the same brand of compiler.

I.e., you may have to compile perl and the mysql client lib yourself, 
using either the Sun native compiler, or gcc, for all of them 
consistently. Also, I'd definitely forgo CPAN for DBI and DBD::mysql; 
building and installing manually is fairly easy if you don't have 
dependencies (perl Makefile.PL; make; make test; make install), and the 
INSTALL or README document will tell you how to control the choice of 
compiler (often it's like 'make CC=gcc' or some such).


On Nov 15, 2005, at 5:47 PM, Richard HOLLAND wrote:

> 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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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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