[Bioperl-l] Cvs update tests fail

Chris Fields cjfields at uiuc.edu
Thu Sep 7 16:35:49 EDT 2006


Make sure you run 'make clean; perl Makefile.PL; make;' before you run 'make
test' or 'make install'.  If that doesn't fix it, what I do (when I run into
issues like this) is delete the old bioperl-live directory and checkout a
fresh copy, then run 'perl Makefile.PL; make; make test;' from that copy.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Ryan Golhar
> Sent: Thursday, September 07, 2006 2:55 PM
> To: 'bioperl-l'
> Subject: [Bioperl-l] Cvs update tests fail
> 
> 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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