[Bioperl-l] Status 0.7

[Todd Richmond]

On 2/1/01 12:39 AM, "Ewan Birney" <birney@ebi.ac.uk> wrote:

> On Wed, 31 Jan 2001, Todd Richmond wrote:
> 
>> 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.
> 
> Can you run the test scripts from the directory above t/ probably not in
> Macs right? This is the way you are "meant" to run the tests in Unix
> world. 
> 
> We can't change the t/ filenames as this is crucial for making make test
> work in UNIX machines.

You can, of course, manually move all of the .t files up one directory. What
I was getting at was the following statement that appears in 47 of the .t
files:

# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'

The way the files are set up now, this doesn't work. And since some of the
people who are likely to run the tests after install are on Macs, I thought
I'd point out the problem.

>> 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...
>> 
> All due to compiled extensions. No idea what is going on but it looks like
> DynaLoader is foo-barred on Macs.
> 

I'm not sure what you mean by that. Meaning that it should gracefully handle
calls to nonexistent compile extensions? Certainly other compiled extensions
work fine.

> 
>> Chain.t, LiveSeq.t, and Mutator.t all fail because cluck in Carp is not
>> supported.
>> 
> 
> Again, I would claim this is more a Mac Perl problem than bioperl.

It could be. Carp appears to be up to date, and 5.004 should have cluck, but
it doesn't. Maybe the fact that cluck handles stack traces has something to
do with it. I've posted a question to the MacPerl list to see if anyone
knows.
     
>> DB.t    all put one test skipped - can't connect to GenBank?
> 
> No internet connection (see below?)
> 
>> GDB.t    failed 8/11 tests
>>     I'm not sure, but I don't think the LWP stuff is working...

I'll have to investigate this further. LWP works - because I just used CPAN
and that relies on LWP. And the internet connection works - because the bug
reports came through. I'm not behind a firewall, or using proxies, so that
can't be it either.

-- 
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