[Bioperl-l] make test!!
Brian Osborne
brian_osborne at cognia.com
Fri Oct 22 17:11:59 EDT 2004
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
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
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