[Bioperl-l] Bioperl 1.0.1 Released
Jason Stajich
jason@cgt.mc.duke.edu
Fri, 14 Jun 2002 09:19:36 -0400 (EDT)
<plea>
I don't ever use windows as a platform for my work, and I don't have
regular access to a windows machine. It would be really great if someone
who was a windows user could volunteer to help out here. This would mean
looking at the warnings and tinkering with the module code or tests to see
what fixes the problems. Until someone is able to provide this
support we probably won't be able to track down the problems very
effectively. </plea>
A quick note - are you sure you have the latest DB_File installed - the
one that shipped with the default ActiveState seems to be more
problematic. This is likely the cause of many of the errors - we can't do
anything if the windows implemenation of DB_File doesn't work. The
warnings about not having the proper modules installed to run the tests is
exactly what you are supposed to see. To test out an individual
test you need to run it by hand.
% perl -I. -w t/testname.t
The consed test does not run consed it tests output files from consed.
On Fri, 14 Jun 2002, Peter Kos wrote:
> Jason,
>
> you have requested notes on Win installation.
> It seems pretty satisfactory for me, but you should know if there are
> serious problems among the failed tests or not.
> I include here for your reference the failed tests' output lines as
> the whole stuff is long and the all other tests were OK.
> Clustalw and TCoffee are not installed so the error is OK. If you are
> interested why StandAloneBlast gave the same messages, I may play
> with the directories and other settings, otherwise I do not care, as
> I run these things under UNIX.
> I do not understand that regex problem though. And the Index thing.
>
> Please let me know if you want me to check out details.
> Specs: Win2000Pro, Perl 5.6.1
>
> 1.)
> t\BlastIndex........FAILED test 3
> Failed 1/13 tests, 92.31% okay
> (I don't know what this means)
> 2.)
> t\Clustalw..........ok 1/10Trailing \ in regex m/^\/ at
> c:/Perl/BIOPER~1.1/blib/lib/Bio/Root/IO.pm line 426.
> (I don't know what this means)
> 3.)
> t\Clustalw..........dubious
> Test returned status 2 (wstat 512, 0x200)
> after all the subtests completed successfully
> (It is OK, I do not have Clustalw installed
> on this machine)
> 4.)
> t\consed............FAILED tests 12, 14
> Failed 2/15 tests, 86.67% okay
> (I don't know what this means, as I know
> consed does not run on Win, so I do not see the whole point in it,
> but you should know)
> 5.)
> t\flat..............DB_File not loaded. This means flat.t test cannot
> be executed. Skipping
> t\flat..............ok 7/7No root path(s) specified
> at c:/Perl/BIOPER~1.1/blib/lib/Bio/Root/IO.pm line 613
> (How can I load DB_File? The same error
> occurred on the SUN. Does it mean that it is not [properly]
> installed?)
> 6.)
> t\game..............XML::Parser::PerlSAX not loaded. This means game
> test cannot be execut...
> (I may not have it installed, I think)
> 7.)
> t\Index.............------------- EXCEPTION -------------
> MSG: This index file is from version [0.1] - You need to rebuild it
> to use module version [0.2]
> STACK Bio::Index::Abstract::_type_and_version
> c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/Abstract.pm:486
> STACK Bio::Index::Abstract::open_dbm
> c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/Abstract.pm:407
> STACK Bio::Index::Abstract::new
> c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/Abstract.pm:151
> STACK Bio::Index::AbstractSeq::new
> c:/Perl/BIOPER~1.1/blib/lib/Bio/Index/AbstractSeq.pm:91
> STACK toplevel t\Index.t:30
>
> --------------------------------------
> t\Index.............dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-12
> Failed 12/12 tests, 0.00% okay
> (NOW what on Earth is this??? I also had this
> on the SUN)
> 8.)
> t\SearchIO..........XML::Parser::PerlSAX not loaded. This means
> SearchIO::blastxml test
> (As above. Perhaps not installed.)
> 9.)
> t\StandAloneBlast...ok 1/10Trailing \ in regex m/^\/ at c:/Perl/BI
> OPER~1.1/blib/lib/Bio/Root/IO.pm line 426.
> t\StandAloneBlast...dubious
> Test returned status 2 (wstat 512, 0x200)
> after all the subtests completed successfully
> (I don't know... Blastall is installed.
> Perhaps setenv problem or such)
> 10.)
> t\TCoffee...........ok 4/16Trailing \ in regex m/^\/ at
> c:/Perl/BIOPER~1.1/blib/lib/Bio/Root/IO.pm line 426.
> t\TCoffee...........dubious
> Test returned status 2 (wstat 512, 0x200)
> after all the subtests completed successfully
> (It is OK, I do not have TCoffee installed on
> this machine)
> 11.)
> t\Variation_IO......ok 10/25
> The XML-format conversion requires the CPAN modules XML::Twig,
> XML::Writer, and IO::String to be installed on your syste
> Skipping these tests.
> 12.)
> t\XEMBL_DB..........SOAP::Lite and/or XML::DOM not installed. This
> means that Bio::DB::XEMBL module is not usable. Skipp
>
> Failed Test Status Wstat Total Fail Failed List of Failed
> ------------------------------------------------------------------
> --------------
> t\BlastIndex.t 13 1 7.69% 3
> t\Clustalw.t 2 512 10 0 0.00% ??
> t\Index.t 255 65280 12 12 100.00% 1-12
> t\StandAloneBlast.t 2 512 10 0 0.00% ??
> t\TCoffee.t 2 512 16 0 0.00% ??
> t\consed.t 15 2 13.33% 12, 14
> 4 subtests skipped.
> Failed 6/93 test scripts, 93.55% okay. 15/3245 subtests failed,
> 99.54% okay.
> NMAKE : fatal error U1077: 'C:\Perl\bin\Perl.exe' : return code
> '0xff'
> Stop.
>
> best regards
> Peter
>
> On Tuesday, June 11, 2002 11:28 PM, Jason Stajich
> [SMTP:jason@cgt.mc.duke.edu] wrote:
> >
> > 11 June 2002
> >
> > I am happy to announce the release of Bioperl 1.0.1 - bugfix
> > release.
> ....
>
> > Note that I did not have access to a windows machine so I couldn't
> > test
> > this myself, please let me know if you have any problems.
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu