[Bioperl-l] make test!!
Nathan Haigh
nathanhaigh at ukonline.co.uk
Fri Oct 22 03:30:08 EDT 2004
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
> > > Bioperl-l at portal.open-bio.org
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