[Bioperl-l] Cvs update tests fail

Lincoln Stein lincoln.stein at gmail.com
Thu Sep 7 16:34:01 EDT 2006


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?
>
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>



-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
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PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT michelse at cshl.edu


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