[Bioperl-l] Status 0.7

Jason Stajich jason@chg.mc.duke.edu
Thu, 1 Feb 2001 09:30:47 -0500 (EST)

On Wed, 31 Jan 2001, Todd Richmond wrote:

> On 1/30/01 10:28 AM, "Hilmar Lapp" <hlapp@gmx.net> wrote:
> > In parallel to fixing known bugs (known from the bug-tracker) the package
> > shall be tested on various systems and against the projects we want to be
> > compatible with (Mac, Win32, Perl 5.004, Ensembl, bioperl-gui, bioperl-corba,
> > which will certainly reveal additional bugs/problems.
> I had a few hours to spare today, so I ran the tests for the bioperl-live
> branch on MacOS 9.1, Perl 5.004.  Besides the difficulty of getting all the
> external dependencies working (which I'll write up for the documentation),
> there's a few problems that will need to be fixed.
> General issues: There's no "make test" on Macs (at least that I've found).
> When running *.t manually, every test script that hard-coded 't/filename' as
> a input file failed. When the 't/' was removed, scripts ran normally.

Todd - are you running them from the bioperl-live dir as in
perl t/SeqIO.t ??
You need to do it this way since we are looking for a relative directory.
Of course, you aren't running this cmdline probably so you can't choose
the relative directory, hmm.  The filenames have to be 't/filename' for
unix so that when we run make test it can find them.  I guess we can try
and be very clever here and contruct the names but the code gets ugly real
quick since we cannot rely on File::Spec to give us nice fileseparators.

Cross platform is going to be interesting... 

> Index.t, SearchDist.t, Variation_IO.t all cause MacPerl to crash - both
> running the script and checking for syntax errors! The latter makes it hard
> for me to diagnose the problem...
> Chain.t, LiveSeq.t, and Mutator.t all fail because cluck in Carp is not
> supported.

And you cannot install Carp from CPAN?

> OddCodes.t, SeqAnal.t, SeqStats.t, and Tools.t all seem to pass the tests
> but give an error message: Bio:Root:RootI.pm Line 118:  Odd number of
> elements in hash list.
will have to look at that.
> SeqFeatureProducer.t    fails - problem with // instead of :: ?
yep, not sure how we're going to deal with this.
> Sim4.t    passes 9/10
>     not ok 5
> # Test 5 got: '/nfs/disk21/birney/prog/wise2/example/human'
> (Cellwall:Documents:Downloads:bioperl-live:t:Sim4.t at line 31)
> #   Expected: 'human'

This has to do with the fact that you are running on the mac and so the
fileseparator is '/' on unix, yet it is '::' on the Mac, so when we go to
split up the filename we are dependant on the system we are running on.  I
guess the logic will have to be a little bit smarter about this or we make
the test less restrictive.

> Blast.t Passes 1..24, can't find gzip to finish tests
This is part of steve's model to support gzip, we should probably make
sure and skip these tests on non unixes.

> BPpsilite.t    fails - doesnąt even get started. Spews error messages and
> ends with:
> # Cellwall:Documents:Downloads:bioperl-live:t:BPpsilite.t has too many
> errors.
> DB.t    all put one test skipped - can't connect to GenBank?
no LWP probably
> GDB.t    failed 8/11 tests
>     I'm not sure, but I don't think the LWP stuff is working...
no LWP
> largefasta.t    fails
> # Can't call method "seek" on unblessed reference, <GEN0> chunk 2.
> File 'MacPerl ź:site_perl:Bio:Seq:LargePrimarySeq.pm'; Line 195
largeprimaryseq is probably not going to work on a mac.
> largepseq.t    failed immediately - couldn't open tempfile
tempfile creation is not going to work in the way we need it to on macs... 

I'm not sure there is going to be a way to make it work on the mac unless
a machead has time to try and find fixes.

> I'll try to get these entered via the web page so that we can track them.
> Todd
> -- 
> Dr Todd Richmond                 http://cellwall.stanford.edu/todd
> Carnegie Institution             email: todd@andrew2.stanford.edu
> Department of Plant Biology      fax: 1-650-325-6857
> 260 Panama Street                phone: 1-650-325-1521 x431
> Stanford, CA 94305
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Jason Stajich
Center for Human Genetics
Duke University Medical Center