[Bioperl-l] make test!!
Nathan Haigh
nathanhaigh at ukonline.co.uk
Sat Oct 23 16:28:22 EDT 2004
Sorry but I don't have time to expand on this at the moment, I will tomorrow morning!
Having said that, if I make the change I suggested to Bio::DB::registry.pm and run the test file you e-mailed me I get the
following:
perl -w -I. t\Registry.t
1..12
ok 1
ok 2
ok 3
ok 4
ok 5
ok 6
ok 7
ok 8
ok 9
ok 10
ok 11
ok 12
So, this seems to work for me! I have Activestate komodo that allows debugging step by step, and this Is how I found the error. I
will e-mail you details about this bug in the morning.
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,
>
> Registry.t shouldn't fail if there's no $HOME set since it uses
> $OBDA_SEARCH_PATH, it sets OBDA_SEARCH_PATH for its own use, and it also
> supplies its own *ini file. To prove this to myself I just unset HOME on my
> machine and Registry.t still works (and $OBDA_SEARCH_PATH was unset as well,
> I never use it).
>
> So, I understand your point but the absence of $HOME shouldn't be the
> problem. Registry.pm is part of the OBDA system so the user is responsible
> for either seeing that $HOME is set or setting $OBDA_SEARCH_PATH, either
> will work (and in UNIX you could put the *ini file in /etc/bioinformatics).
> Questions: did this change you made in your local Registry.pm fix
> Registry.t? What are the errors using the Registry.t I sent you last night?
>
> So you have both modules and the Berkeley DB library? There's goes my latest
> hypothesis!
>
> The problem here is that I'm just guessing when it comes to ActiveState, and
> you can see that my guesses aren't always on target. What would be great is
> if someone using ActiveState would sit down with the Perl debugger and step
> through the code line by line so we'd know _exactly_ where the failures are.
> Can someone help us here? If you're not familiar with the debugger this
> would be a good opportunity to learn about it, it's a fantastic tool (and
> absolutely required if you want to improve your coding skills). I'm not just
> talking about Registry but about the other errors that Nathan is showing us.
>
> Brian O.
>
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Nathan Haigh
> Sent: Friday, October 22, 2004 3:30 AM
> To: 'Brian Osborne'; 'Bioperl'
> Subject: RE: [Bioperl-l] make test!!
>
> I have the following versions installed:
> DB_File 1.810
> BerkeleyDB 0.25
> And I'm pretty sure I have the library (I remember using a BTree quite a
> while back).
>
> Having just had a look at Bio::DB::Registry, _load_registry refers to the
> ENV variable HOME. Windows doesn't have such a variable by
> default, so the user must either set it themselves, and failing this,
> Bio::DB::Registry should assume a default e.g. C:/
>
> Therefore I've changed this sub to read:
> sub _load_registry {
> my ($self) = @_;
> my $home;
>
> if (defined $ENV{"HOME"}) { $home = $ENV{"HOME"} } # use this if it's
> set
> elsif ($^O eq 'MSWin32') { $home = 'C:/' } # def windows home
> if $ENV{HOME} isn't set
> else { $home = (getpwuid($>))[7] }
>
> my @ini_files = _get_ini_files($home);
>
> unless (@ini_files) {
>
> etc etc
>
>
> I don't know if you still need to test for failure of getpwuid, since you
> should never get to this stage on windows - I can't think
> of a reason why the c: drive is inaccessible!
>
> Nathan
>
> > -----Original Message-----
> > From: Brian Osborne [mailto:brian_osborne at cognia.com]
> > Sent: 22 October 2004 01:22
> > To: nathanhaigh at ukonline.co.uk; 'Bioperl'
> > Subject: RE: [Bioperl-l] make test!!
> >
> > Nathan,
> >
> > OK, thank you. Some of the messages you're seeing from Registry.t are
> > warnings, not errors, but at any rate there are still errors. So am I
> > correct in assuming that you have the modules DB_File and BerkeleyDB
> > installed, as well as the Berkeley DB library?
> >
> > I can't do more with Index.t, as I said I was just guessing there. My
> first
> > instinct is still to suspect something is wrong with Fcntl, Storable, or
> > DB_File, these are used by DB/FileCache and the problem with Index.t lies
> > with DB/InMemoryCache or DB/FileCache, most likely the latter. Someone
> using
> > ActiveState Perl is going to have to address this one.
> >
> > 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
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