[Bioperl-l] Status 0.7

Todd Richmond todd@andrew2.stanford.edu
Wed, 31 Jan 2001 18:03:05 -0800

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.

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

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.

SeqFeatureProducer.t    fails - problem with // instead of :: ?

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'

Blast.t Passes 1..24, can't find gzip to finish tests

BPpsilite.t    fails - doesnąt even get started. Spews error messages and
ends with:
# Cellwall:Documents:Downloads:bioperl-live:t:BPpsilite.t has too many

DB.t    all put one test skipped - can't connect to GenBank?
GDB.t    failed 8/11 tests
    I'm not sure, but I don't think the LWP stuff is working...

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

largepseq.t    failed immediately - couldn't open tempfile

I'll try to get these entered via the web page so that we can track them.


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