[Bioperl-l] make test!!
Brian Osborne
brian_osborne at cognia.com
Mon Oct 25 09:41:32 EDT 2004
Nathan,
I just followed up on your observation that _get_ini_files wasn't being
called since $home didn't exist. The script shouldn't have been relying on
$home being defined. You're right about the fallback situation, Web
retrieval, also being doomed to failure on Win, I'll look into that as well
but for the moment we're OK.
Thanks for your help and your observations,
Brian O.
-----Original Message-----
From: Nathan Haigh [mailto:nathanhaigh at ukonline.co.uk]
Sent: Monday, October 25, 2004 3:07 AM
To: 'Brian Osborne'; bioperl-l at bioperl.org
Subject: RE: [Bioperl-l] make test!!
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
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