[Bioperl-l] Status 0.7

Todd Richmond todd@andrew2.stanford.edu
Thu, 01 Feb 2001 12:22:34 -0800

On 2/1/01 6:30 AM, "Jason Stajich" <jason@chg.mc.duke.edu> wrote:

> On Wed, 31 Jan 2001, Todd Richmond wrote:
>> Chain.t, LiveSeq.t, and Mutator.t all fail because cluck in Carp is not
>> supported.
> And you cannot install Carp from CPAN?

CPAN (on Macs) claims that CPAN is up-to-date. I suppose I could grab Carp
from 5.6 and cross-my fingers...

>> 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.

Actually, the file separator is ':' on the Mac. Most of my scripts start
with a little section that sets filename length, path separators, etc based
on OS. I'm not sure how you could handle this in a global way for the
Bioperl package. Is there module for figuring out all the OS specific items
and setting up variables for them?

>> 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

LWP works just fine - I've discovered that IO::String is what's causing
these modules to fail. It can't create a new Bio::DB::GenBank object, so it
never even gets to try to connect to the external databases. I'm looking
into this, but I'm not sure that there is any way around it.

>> 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.

There are other ways to make/handle tempfiles that work on Macs - we just
need to figure out a way to get BioPerl to check to see if it's running
under MacOS and use an alternative method.

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