[Bioperl-l] Windows Testing
Lincoln Stein
lstein@cshl.org
Fri, 13 Dec 2002 19:17:00 -0500
I've fixed the warnings. Those two tests are expected to be skipped on
Windows platforms, unless you happen to have mysql or oracle installed, as
well as the appropriate DBI interfaces.
Lincoln
On Tuesday 10 December 2002 03:50 pm, Paul Boutros wrote:
> Hi Lincoln,
>
> Yup, all tests pass, although I should note that I get:
>
> ok 99 # fetch_feature_by_gid() not implemented by this adaptor
> ok 100 # fetch_feature_by_gid() not implemented by this adaptor
>
> on all windows boxes I've tested.
> Paul
>
> On Tue, 10 Dec 2002, Lincoln Stein wrote:
> > Hi Paul,
> >
> > Warnings aside (which I'll fix), do the DBGFF tests pass?
> >
> > Lincoln
> >
> > > BioDBGFF.t
> > > ==========
> > > ok 2
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 1.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 1.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 2.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 3.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 4.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 5.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 9.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 9.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 10.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 10.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 76, <> line 11.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 11.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 12.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 13.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 14.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 15.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/DB/GFF/Adaptor/memory.pm line 77, <> line 16.
> > > <and many more>
> > >
> > > game.t
> > > ======
> > > ok 19
> > > ok 20
> > > Use of uninitialized value in pattern match (m//) at
> > > C:/Perl/site/lib/XML/Writer.pm line 307.
> > > Use of uninitialized value in print at C:/Perl/lib/IO/Handle.pm line
> > > 394. ok 21
> > > ok 22
> > >
> > > Eponine.t
> > > =========
> > > Note: I don't have the software installed, just ran the test to see how
> > > it handled the problem. The "old java version" statement isn't
> > > accurate.
> > >
> > > 1..5
> > > Use of uninitialized value in numeric lt (<) at t\Eponine.t line 52,
> > > <PIPE> line
> > > 2.
> > > You need at least version 1.2 of JDK to run eponine
> > > ok 1 # Skipping due to old java version
> > >
> > > Pise.t
> > > ======
> > > Note: I don't have the software installed, just ran the test to see how
> > > it handled me.
> > >
> > > 1..10
> > > Subroutine stdout redefined at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 53
> > > 4.
> > > Subroutine stderr redefined at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 56
> > > 3.
> > > defined(%hash) is deprecated at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 9
> > > 83.
> > > (Maybe you should just omit the defined()?)
> > > ok 1
> > > ok 2
> > > ok 3
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 844.
> > > Use of uninitialized value in concatenation (.) or string at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 1019.
> > > Use of uninitialized value in concatenation (.) or string at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 1100.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125.
> > > Use of uninitialized value in hash element at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
> > > Use of uninitialized value in hash element at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 131.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125.
> > > Use of uninitialized value in hash element at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125.
> > > Use of uninitialized value in hash element at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 128.
> > > ok 4
> > > ok 5
> > > ok 6
> > > ok 7
> > > ok 8
> > > Odd number of elements in hash assignment at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 982, <GEN8> line 290.
> > > Use of uninitialized value in concatenation (.) or string at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJob.pm line 1100, <GEN8> line 290.
> > > Use of uninitialized value in string eq at
> > > C:/Perl/site/lib/Bio/Tools/Run/PiseJobParser.pm line 125, <GEN8> line
> > > 290. <many times>
> > >
> > >
> > >
> > >
> > > _______________________________________________
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> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> > --
> > ========================================================================
> > Lincoln D. Stein Cold Spring Harbor Laboratory
> > lstein@cshl.org Cold Spring Harbor, NY
> > ========================================================================
--
Lincoln Stein
lstein@cshl.org