[Bioperl-l] Cvs update tests fail

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Thu Sep 7 20:14:29 EDT 2006


In a similar way, the -P option removes directories that are empty after 
running the update:

  cvs up -dP

Mauricio.

Lincoln Stein wrote:
> When you run "cvs update" be sure to use the -d option in order to create
> new directories. You probably don't have a Bio/DB/SeqFeature directory at
> all!
> 
>  cvs update -d
> 
> Lincoln
> 
> On 9/7/06, Ryan Golhar <golharam at umdnj.edu> wrote:
>> So I've updated my installation of bioperl from cvs using 'cvs update'.
>> I reran 'perl Makefile.PL' followed by 'make; make test'.
>>
>> I see the following errors from 'make test':
>>
>> t/BioDBSeqFeature............Can't locate Bio/DB/SeqFeature/Store.pm in
>> @INC (@INC contains: /users/golharam/cvswork/bioperl-live/ . ..
>> ./blib/lib t /users/golharam/bioperl/bioperl-live/blib/lib
>> /users/golharam/bioperl/bioperl-live/blib/arch
>> /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl) at
>> t/BioDBSeqFeature.t line 30.
>> BEGIN failed--compilation aborted at t/BioDBSeqFeature.t line 30.
>> t/BioDBSeqFeature............dubious
>>
>>         Test returned status 2 (wstat 512, 0x200)
>> Scalar found where operator expected at (eval 152) line 1, near "'int'
>> $__val"
>>         (Missing operator before   $__val?)
>> DIED. FAILED tests 1-43
>>         Failed 43/43 tests, 0.00% okay
>> t/BioDBSeqFeature_BDB........Can't locate Bio/DB/SeqFeature/Store.pm in
>> @INC (@INC contains: /users/golharam/cvswork/bioperl-live/ . ..
>> ./blib/lib t /users/golharam/bioperl/bioperl-live/blib/lib
>> /users/golharam/bioperl/bioperl-live/blib/arch
>> /usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>> /usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>> /usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>> /usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>> /usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl) at
>> t/BioDBSeqFeature.t line 30.
>> BEGIN failed--compilation aborted at t/BioDBSeqFeature.t line 30.
>> t/BioDBSeqFeature_BDB........FAILED tests 1-43
>>
>>         Failed 43/43 tests, 0.00% okay
>>
>> Any ideas?
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 
> 
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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