Does gbrowse2 really require Ace.pm and MOBY/Client/Central.pm

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Does gbrowse2 really require Ace.pm and MOBY/Client/Central.pm

Wes Barris
I am doing a CVS update of GBrowse2 (going from revision 23376 to 23589).
The latest CVS download fails the tests and the errors seem to imply
that I need to install AcePerl and some MOBY module.  I don't use either
of these so I don't know why GBrowse2 all of a sudden is requiring them.
Here is a transcript of my test:

wes@bioweb> ./Build test
NOTE: Run ./Build reconfig to change existing configuration.
t/00.compile.t ............ 55/?
#   Failed test 'bin/process_wormbase.pl compiled ok'
#   at t/00.compile.t line 45.
# stdout:
# stderr: Can't locate Ace.pm in @INC (@INC contains: /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/lib /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/arch
/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/install_util /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl .) at
bin/process_wormbase.pl line 5.
# BEGIN failed--compilation aborted at bin/process_wormbase.pl line 5.

#   Failed test 'bin/register_moby_services.pl compiled ok'
#   at t/00.compile.t line 45.
# stdout:
# stderr: Can't locate MOBY/Client/Central.pm in @INC (@INC contains: /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/lib
/usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/arch /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/install_util /usr/lib/perl5/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl .) at bin/register_moby_services.pl line 17.
# BEGIN failed--compilation aborted at bin/register_moby_services.pl line 17.
t/00.compile.t ............ 86/? # Looks like you failed 2 tests of 88.
t/00.compile.t ............ Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/88 subtests
         (less 2 skipped subtests: 84 okay)
t/01yeast.t ............... ok
t/02.rearchitecture.t ..... ok
t/03.render.t ............. 108/138 Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
  at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
t/03.render.t ............. ok
t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
t/04.remoteserver.t ....... ok
t/05.deferredrendering.t .. ok
t/06.featuresearch.t ...... ok
t/07.karyotype.t .......... ok
t/08.calign.t ............. ok

Test Summary Report
-------------------
t/00.compile.t          (Wstat: 512 Tests: 88 Failed: 2)
   Failed tests:  70, 72
   Non-zero exit status: 2
Files=9, Tests=420, 107 wallclock secs ( 0.21 usr  0.04 sys + 34.91 cusr  5.93 csys = 41.09 CPU)
Result: FAIL
Failed 1/9 test programs. 2/420 subtests failed.
wes@bioweb>

--
Wes Barris

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Re: Does gbrowse2 really require Ace.pm and MOBY/Client/Central.pm

Robert Buels
Hi Wes,

It's not really something to be concerned about, I added a new test, and
it's pointing out some minor things that have been broken for a while.
These particular failures point out some missing deps that should
probably be 'recommends'.

I added those in, but you might still see a test failure or two, there
are still a couple of scripts in bin/ the test is finding that don't
compile, but don't really affect the main functionality of gbrowse.

Those will probably be fixed or removed relatively soon.

Rob

=== appendix ==

The 00.compile test was a recent addition after the das cgi script was
checked in with a syntax error and sat there like that for a while.  It
goes over all the scripts in cgi-bin and bin and checks that they
compile, or if they don't compile it's for an acceptable reason (like a
missing 'recommends' dependency).


Wes Barris wrote:

> I am doing a CVS update of GBrowse2 (going from revision 23376 to 23589).
> The latest CVS download fails the tests and the errors seem to imply
> that I need to install AcePerl and some MOBY module.  I don't use either
> of these so I don't know why GBrowse2 all of a sudden is requiring them.
> Here is a transcript of my test:
>
> wes@bioweb> ./Build test
> NOTE: Run ./Build reconfig to change existing configuration.
> t/00.compile.t ............ 55/?
> #   Failed test 'bin/process_wormbase.pl compiled ok'
> #   at t/00.compile.t line 45.
> # stdout:
> # stderr: Can't locate Ace.pm in @INC (@INC contains: /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/lib /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/arch
> /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/install_util /usr/lib/perl5/5.8.5/i386-linux-thread-multi /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi
> /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl .) at
> bin/process_wormbase.pl line 5.
> # BEGIN failed--compilation aborted at bin/process_wormbase.pl line 5.
>
> #   Failed test 'bin/register_moby_services.pl compiled ok'
> #   at t/00.compile.t line 45.
> # stdout:
> # stderr: Can't locate MOBY/Client/Central.pm in @INC (@INC contains: /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/lib
> /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/blib/arch /usr/local/src/bioinformatics/gbrowse2/Generic-Genome-Browser/install_util /usr/lib/perl5/5.8.5/i386-linux-thread-multi
> /usr/lib/perl5/5.8.5 /usr/lib/perl5/site_perl/5.8.5/i386-linux-thread-multi /usr/lib/perl5/site_perl/5.8.5 /usr/lib/perl5/site_perl /usr/lib/perl5/vendor_perl/5.8.5/i386-linux-thread-multi
> /usr/lib/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl .) at bin/register_moby_services.pl line 17.
> # BEGIN failed--compilation aborted at bin/register_moby_services.pl line 17.
> t/00.compile.t ............ 86/? # Looks like you failed 2 tests of 88.
> t/00.compile.t ............ Dubious, test returned 2 (wstat 512, 0x200)
> Failed 2/88 subtests
>          (less 2 skipped subtests: 84 okay)
> t/01yeast.t ............... ok
> t/02.rearchitecture.t ..... ok
> t/03.render.t ............. 108/138 Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_BINARY redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
>   at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_CREAT redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
>   at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_EXCL redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
>   at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_LARGEFILE redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
>   at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_NOFOLLOW redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
>   at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> Subroutine Bio::DB::SeqFeature::Store::berkeleydb::O_RDWR redefined at /usr/lib/perl5/5.8.5/Exporter.pm line 65.
>   at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 10
> t/03.render.t ............. ok
> t/04.remoteserver.t ....... Sometimes this test gets 'stuck'. If this happens, kill the test and Build test again.
> t/04.remoteserver.t ....... ok
> t/05.deferredrendering.t .. ok
> t/06.featuresearch.t ...... ok
> t/07.karyotype.t .......... ok
> t/08.calign.t ............. ok
>
> Test Summary Report
> -------------------
> t/00.compile.t          (Wstat: 512 Tests: 88 Failed: 2)
>    Failed tests:  70, 72
>    Non-zero exit status: 2
> Files=9, Tests=420, 107 wallclock secs ( 0.21 usr  0.04 sys + 34.91 cusr  5.93 csys = 41.09 CPU)
> Result: FAIL
> Failed 1/9 test programs. 2/420 subtests failed.
> wes@bioweb>
>


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