[BioSQL-l] Help installing BioSQL and its (Perl) dependencies
Hilmar Lapp
hlapp at drycafe.net
Wed Jan 13 12:03:06 EST 2010
Hi Sammy,
please always
On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote:
> 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 :
> > ===========================================================
> >
> >
> >
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biosql-l
> >
> >
>
>
>
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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