[BioSQL-l] Help installing BioSQL and its (Perl) dependencies

Hilmar Lapp hlapp at drycafe.net
Wed Jan 13 12:21:13 EST 2010 

Sammy - please always keep the list copied. Links to and documentation  
for downloads are at http://biosql.org. Specifically look for the  
section titled 'Downloads'.

	-hilmar

On Jan 13, 2010, at 12:09 PM, Bolin, Samuel wrote:

> I have not looked at the install file as I am unable to find a  
> biosql package/rpm/tar etc
> Could you point me in the direction of that, I am working off of  
> instructions given to me by amy
>
> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at drycafe.net]
> Sent: Wednesday, January 13, 2010 10:05 AM
> To: Bolin, Samuel
> Cc: Mark A. Jensen; biosql-l
> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl)  
> dependencies
>
> (hit send erroneously ...)
>
> Hi Sammy,
>
> please always direct your questions to the mailing list. There are
> many more people there who can help you out.
>
> Have you looked at the INSTALL file that comes with BioSQL and tried
> to follow the instructions therein? If yes, what did you find not to
> work?
>
> 	-hilmar
>
> 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 :
> ===========================================================
>
>
>
>
>
>

-- 
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :
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