[Bioperl-l] make test!!
Nathan Haigh
nathanhaigh at ukonline.co.uk
Mon Oct 25 03:06:55 EDT 2004
Success!!!!
These files seem to do the trick, what did you change - I overwrote the original .t and .pm files?
However, (and I don't use this module, so don't know how likely this is to happen) the only time I can see something failing, is
when using the module for real, the ini file might not be found by _get_ini_files because $home not being set on windows messes
things up in that sub. I assume this could happen on Unix because there is a fall back to retrieve the ini file from the web. This
would fail on windows due to the absence of $home and trying to create and open the ini file from $home/.bioinformatics (which would
become just /.bioinformatics on windows - not a valid windows path).
FYI:
Windows natively uses backslashes ( \ ) as dir delimiters, however in my experience using forward slashes ( / ) in perl has no
adverse effect, and saves time escaping the backslashes.
The only problems I usually encounter in making Unix/windows compatible scripts are:
1) When paths contain spaces
2) When the complete path is used on Unix (from root) as /blah_blah is not valid on windows you need to start with './' 'or ../' or
<drive_letter>:/ It's actually surprisingly compatible with windows.
3) When sripts use /dev/null as this isn't compatible with windows
Thanks for your help!
Nathan
> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: 24 October 2004 22:41
> To: nathanhaigh at ukonline.co.uk
> Subject: RE: [Bioperl-l] make test!!
>
> Nathan,
>
> Let's try again! Please use the attached Registry.pm and Registry.t, same
> test (minor change in Registry.pm, based on our discussion). If this doesn't
> work then we probably have a "/" versus "\" problem.
>
> BIO
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Nathan Haigh
> Sent: Saturday, October 23, 2004 4:23 PM
> To: 'Brian Osborne'; 'Bioperl'
> Subject: RE: [Bioperl-l] make test!!
>
> I get the following error:
>
>
> perl -w -I. t\Registry.t
> 1..12
> ok 1
> ok 2
> ok 3
> This Perl doesn't implement function getpwuid(). Skipping...
>
> -------------------- WARNING ---------------------
> MSG: No seqdatabase.ini file found in ~/.bioinformatics/
> nor in /etc/bioinformatics/ nor in directory specified by
> t/data/registry/flat;t/data/registry/bdb. Using web to get database registry
> from
> http://www.open-bio.org/registry/seqdatabase.ini
> ---------------------------------------------------
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: can't connect: IO::Socket::INET: Bad hostname 'www.open-bio.org'
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:328
> STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:207
> STACK: Bio::DB::Registry::_load_registry Bio/DB/Registry.pm:128
> STACK: Bio::DB::Registry::new Bio/DB/Registry.pm:97
> STACK: t\Registry.t:57
> -----------------------------------------------------------
>
> Nathan
>
> > -----Original Message-----
> > From: Brian Osborne [mailto:brian_osborne at cognia.com]
> > Sent: 22 October 2004 22:12
> > To: nathanhaigh at ukonline.co.uk; 'Bioperl'
> > Subject: RE: [Bioperl-l] make test!!
> >
> > Nathan,
> >
> > Please replace your t/Registry.t with the attached Registry.t file and
> tell
> > me what happens after:
> >
> > >perl -w -I. t/Registry.t
> >
> > Brian O.
> >
> > -----Original Message-----
> > From: Nathan Haigh [mailto:nathanhaigh at ukonline.co.uk]
> > Sent: Thursday, October 21, 2004 7:59 AM
> > To: 'Brian Osborne'; 'Bioperl'
> > Subject: RE: [Bioperl-l] make test!!
> >
> > Ok, I've done some more testing (with the latest CVS 9am GMT) and here is
> > what I've found! I've run "namke test" with and without
> > BIOPERLDEBUG, and running individual tests using " perl -I. -w
> > t/test_name.t".
> >
> > Attached are 3 files with details of errors:
> > Errors.txt - summary and details of failed tests, and other
> > tests with peculiar warnings etc
> > Errors_debug.txt - same as errors.txt but with BIOPERLDEBUG set
> > Perl_test.txt - individual tests run with BIOPERLDEBUG set,
> using
> > "perl -I. -w t/test_name.t"
> >
> > My System:
> > WinXP Pro
> > ActiveState Perl 5.8.0
> > Nmake 6.00.8168.0
> >
> > My Summary:
> > ESEfinder.t - causes perl to crash on test 2 during "nmake test", but
> ok
> > in other tests!
> > Biblio_biofetch.t - throws warning and exception when using
> > BIOPERLDEBUG, but doesn't appear in summary!
> > Index.t - fails get_Seq_by_id ('AI129902') on lines 118 and 124
> > ProtPsm.t - needs "plan tests" in test file changing to 5. When
> > running the individual test can't locate
> > Bio::Matrix::PSM::ProtMatrix
> > Registry.t - several error including "No seqdatabase.ini file found",
> "
> > No database with name testflat in Registry"
> > Primaryqual.t - Test returned status 255. and 'Can't locate object
> method
> > "header"' in individual test
> > seqread_fail.t - gives an exception, is this supposed to happen?
> >
> > Hope this help to iron out bugs when running BioPerl on Windows!
> > Nathan
> >
> >
> > > -----Original Message-----
> > > From: Brian Osborne [mailto:brian_osborne at cognia.com]
> > > Sent: 20 October 2004 19:04
> > > To: nathanhaigh at ukonline.co.uk; 'Bioperl'
> > > Subject: RE: [Bioperl-l] make test!!
> > >
> > > Nathan,
> > >
> > > I noticed most of the Registry tests failing. I know what part of the
> > > problem is (getpwuid() not implemented in Windows/Activestate Perl) and
> I
> > > think I've fixed at least that part. Can you install the most recent
> > > Bio/DB/Registry.pm from bioperl-live and run t/Registry.t again?
> > >
> > > >perl -w -I. t/Registry.t
> > >
> > >
> > > Brian O.
> > >
> > > -----Original Message-----
> > > From: bioperl-l-bounces at portal.open-bio.org
> > > [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Nathan Haigh
> > > Sent: Wednesday, October 20, 2004 10:20 AM
> > > To: 'Bioperl'
> > > Subject: RE: [Bioperl-l] make test!!
> > >
> > > Apologise for all the pervious messages! I just wanted to get this onto
> > the
> > > mailing list:
> > >
> > > I have managed to do a "nmake test" (WinXP) on bioperl-live.
> > >
> > > System: WinXP Pro
> > > ActiveState Perl 5.8.0 build 804
> > > Nmake v6.00.8168.0
> > >
> > > A note beforehand:
> > > The error message I had previously got, and heard others have also
> > received
> > > on other OS's. That contain a "line too long" error when
> > > trying "make test", is due to the limitations of the particular OS.
> > Versions
> > > of ExtUtils::MakeMaker >= 6.06 (current version: 6.21)
> > > have got round this problem by splitting long command lines from
> Makefiles
> > > into a series of smaller commands.
> > >
> > > Test Summary:
> > > Failed Test Stat Wstat Total Fail Failed List of Failed
> >
> > --------------------------------------------------------------------------
> > --
> > > ---
> > > t\Index.t 22 5632 41 21 51.22% 21-41
> > > t\Registry.t 22 5632 11 9 81.82% 3-11
> > > t\seqread_fail.t 255 65280 13 0 0.00% ??
> > > 115 subtests skipped.
> > > Failed 3/192 test scripts, 98.44% okay. 30/8816 subtests failed, 99.66%
> > > okay.
> > > NMAKE : fatal error U1077: 'I:\Programming\Perl\Perl5.8.0\bin\perl.exe'
> :
> > > return code '0xff'
> > > Stop.
> > >
> > > Particulars:
> > > t\Index......................NOK 21Can't call method "length" on an
> > > undefined value at t\Index.t line 124, <GEN6> line
> > > 54.
> > > t\Index......................dubious
> > > Test returned status 22 (wstat 5632, 0x1600)
> > > DIED. FAILED tests 21-41
> > > Failed 21/41 tests, 48.78% okay
> > > t\Registry...................ok 2/11The getpwuid function is
> unimplemented
> > > at K:\Downloads\FlashGet\Software\Bioinform
> > > atics\BioPerl\1\bioperl-live\blib\lib/Bio/DB/Registry.pm line 116.
> > > t\Registry...................dubious
> > > Test returned status 22 (wstat 5632, 0x1600)
> > > t\seqread_fail...............ok 1/13
> > > ------------- EXCEPTION: Bio::Root::Exception -------------
> > > MSG: BioFetch Error 4: ID [XXX111] not found in database
> > > [embl][http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[embl-id:
> > > XXX111]|[embl-acc:XXX111]+-ascii+-vn+2+-noSession].
> > > STACK: Error::throw
> > > STACK: Bio::Root::Root::throw
> > >
> >
> K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li
> > > b/Bio/Root/R
> > > oot.pm:328
> > > STACK: Bio::DB::BioFetch::postprocess_data
> > >
> >
> K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\l
> > > ib/Bio/DB/BioFetch.pm:406
> > > STACK: Bio::DB::WebDBSeqI::get_seq_stream
> > >
> >
> K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li
> > > b/Bio/DB/WebDBSeqI.pm:525
> > > STACK: Bio::DB::WebDBSeqI::get_Stream_by_id
> > >
> K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\
> > > lib/Bio/DB/WebDBSeqI.pm:287
> > > STACK: Bio::DB::WebDBSeqI::get_Seq_by_id
> > >
> >
> K:\Downloads\FlashGet\Software\Bioinformatics\BioPerl\1\bioperl-live\blib\li
> > > b
> > > /Bio/DB/WebDBSeqI.pm:153
> > > STACK: main::fetch t\seqread_fail.t:69
> > > STACK: t\seqread_fail.t:81
> > > -----------------------------------------------------------
> > > t\seqread_fail...............dubious
> > > Test returned status 255 (wstat 65280, 0xff00)
> > > after all the subtests completed successfully
> > >
> > >
> > > Nathan
> > >
> > > > -----Original Message-----
> > > > From: bioperl-l-bounces at portal.open-bio.org
> > > [mailto:bioperl-l-bounces at portal.open-bio.org] On Behalf Of Aaron J.
> > Mackey
> > > > Sent: 14 October 2004 21:27
> > > > To: Bioperl
> > > > Subject: [Bioperl-l] make test!!
> > > > Importance: High
> > > >
> > > >
> > > > I've had only a very few people send me feedback about the current
> > > > state of bioperl-live "make test" on your favorite
> > > > old/crotchety/obscure platforms. I'm writing the Change log and
> > > > thinking about branching, but I'm an experimentalist, I need data!
> > > >
> > > > Get a bioperl-live HEAD checkout, do a "cvs update -PAd" to make sure
> > > > you have everything, "make distclean" if you've built from the cvs
> > > > checkout before, and start from scratch with the usual litany: perl
> > > > Makefile.PL; make; [setenv BIOPERLDEBUG 1;] make test; email Aaron.
> > > >
> > > > Setting BIOPERLDEBUG is very noisy, but it's the end result I care
> > > > about, not so much all the verbiage (unless there's specific verbiage
> > > > related to the end result ...)
> > > >
> > > > Thanks,
> > > >
> > > > -Aaron
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l at portal.open-bio.org
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