[BioSQL-l] Help installing BioSQL and its (Perl) dependencies
Bolin, Samuel
sabolin at sandia.gov
Wed Jan 13 16:22:03 UTC 2010
Mark and Hilmar
I am working with Amy Powell on getting BioSQL up and running
Decided to take a different tact and am now using Fedora
Was able to get MySQL BioPerl installed along with getting past the
DBD and DBI issues
However I have read thru the documentation and have been unable to
figure out how BioSQL ties in must less get it installed
Any guidance?
Sammy
From: Powell Phd, Amy Jo
Sent: Thursday, January 07, 2010 10:29 AM
To: Mark A. Jensen; Hilmar Lapp
Cc: biosql-l; Bolin, Samuel
Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl)
dependencies
Hi there-
Thanks very much for your suggestion. We’ll give it a try and see
what happens. Sincerely, AJP
On 1/7/10 9:08 AM, "Mark A. Jensen" <maj at fortinbras.us> wrote:
This portion
> Running install for module 'DBD::mysql'
> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz
> Has already been unwrapped into directory
> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL
> Has already been made
> Running make test
> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
> t/00base.t .................. 1/6
> # Failed test 'use DBD::mysql;'
> # at t/00base.t line 21.
> # Tried to use 'DBD::mysql'.
> # Error: Can't load
suggests that, though DBD::mysql was made, the module can't be
found by perl (is not in @INC). You could try installing from scratch
again
cpan> fforce install DBD::mysql
The other issue may be that your mysql installation can't be found or
encounters
an error when
DBD::mysql is loaded. Try at the command line
$ perl -MDBD::mysql -e 1
and see if any more helpful errors ensue.
MAJ
----- Original Message -----
From: "Hilmar Lapp" <hlapp at drycafe.net>
To: "Powell Phd, Amy Jo" <ajpowel at sandia.gov>
Cc: "biosql-l" <biosql-l at lists.open-bio.org>; "Bolin,Samuel"
<sabolin at sandia.gov>
Sent: Thursday, January 07, 2010 10:49 AM
Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl)
dependencies
> Hi Amy,
>
> this looks like a problem with installing DBD::mysql, not BioSQL.
I don't
> know how you built DBD::mysql and DBI, and I haven't encountered
this error
> (but maybe someone else on the BioSQL list has come across this?),
so your
> best avenue for getting help is probably the DBD::mysql mailing
list.
>
> Cheers,
>
> -hilmar
>
> On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote:
>
>> Dear Hilmar,
>>
>> Happy New Year! I hope you had enjoyable holidays. So, my sys
admin
>> colleague and I are trying to get BioSQL (with a BioPerl language
binding)
>> up and running ASAP.
>>
>> We have successfully installed MySQL and BioPerl. We are having
trouble,
>> however, getting the DBD::mysql module installed (on a Macbook
Pro running
>> OS X 10.6.1) to finish the last steps of BioSQL installation.
The error
>> message for our attempt is pasted below. We have also attempted
a manual
>> install, and get the same result (i.e., croaking at the make test
>> step)-failed installation.
>>
>> Would you please guide us through the necessary final steps in
getting
>> BioSQL up and running? Any help you can provide would be greatly
>> appreciated. Thanks very much and I look forward to hearing from
you.
>> Sincerely, AJP
>>
>>
>> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION]
>>
>> cpan[1]> install Bundle::DBD::mysql
>> CPAN: Storable loaded ok (v2.21)
>> Going to read '/var/root/.cpan/Metadata'
>> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT
>> CPAN: YAML loaded ok (v0.70)
>> Going to read 52 yaml files from /var/root/.cpan/build/
>> CPAN: Time::HiRes loaded ok (v1.9711)
>> DONE
>> Restored the state of none (in 1.1851 secs)
>> Has already been unwrapped into directory
>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL
>> DBI is up to date (1.609).
>> Running install for module 'DBD::mysql'
>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz
>> Has already been unwrapped into directory
>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL
>> Has already been made
>> Running make test
>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
>> t/00base.t .................. 1/6
>> # Failed test 'use DBD::mysql;'
>> # at t/00base.t line 21.
>> # Tried to use 'DBD::mysql'.
>> # Error: Can't load
>> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/
auto/ DBD/mys
>> ql/mysql.bundle' for module DBD::mysql:
>> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/
arch/auto/D
>> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix
>> # Referenced from:
>> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/
auto/ DBD/mysq
>> l/mysql.bundle
>> # Expected in: flat namespace
>> # in
>> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/
auto/ DBD/mysq
>> l/mysql.bundle at
>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/
DynaLoader.pm line
>> 207.
>> # at (eval 7) line 2
>> # Compilation failed in require at (eval 7) line 2.
>> # BEGIN failed--compilation aborted at (eval 7) line 2.
>> Bailout called. Further testing stopped: Unable to load DBD::mysql
>> FAILED--Further testing stopped: Unable to load DBD::mysql
>> make: *** [test_dynamic] Error 255
>> CAPTTOFU/DBD-mysql-4.013.tar.gz
>> make test -- NOT OK
>> //hint// to see the cpan-testers results for installing this
module, try:
>> reports CAPTTOFU/DBD-mysql-4.013.tar.gz
>> Running make install
>> make test had returned bad status, won't install without force
>> Failed during this command:
>> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO
>>
>>
>
> --
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
> ===========================================================
>
>
>
>
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