[Bioperl-l] bioperl on Mac OSX

Jason Stajich jason.stajich at duke.edu
Sun Feb 6 16:24:10 EST 2005

Telling us "tests fail" doesn't give enough information for someone to 
help you.

Note that on OSX you can also install Bioperl via fink and this may be 
easier for you.

Failed tests for Bundle::BioPerl means you probably wouldn't have 
installed all the auxiliary modules, but it depends on which ones you 
forced through that would make a difference.  You need some C libraries 
installed to make use of some of the the XML parser libraries for 
example, but this is not relevant to RemoteBlast.

At least these modules are needed to get Bio::Tools::Run::RemoteBlast 
running - I know this by looking at the use statements in the module 
its self and the test in t/RemoteBlast.t.  You can always test to see 
if a module can be loaded by doing 'perl PATH/To/Module'.   Does this 
succeed for the modules in question?

IO::String, LWP, LWP::UserAgent

Check to see what is actually installed and in your PERL5LIB path.  Are 
you do the install in the system perl directory or your local directory 
by providing the PREFIX option?

$ perldoc LWP
$ perldoc HTTP::Request::Common
$ perldoc HTML::Parser

We can't really diagnose much without specific errors so if you could 
describe exactly what fails wrt RemoteBlast that would make it possible 
for us to help.  If you run the tests in the bioperl core package what 
kind of messages do you get.

$ perl -I. -Ilib t/RemoteBlast


Jason Stajich
jason.stajich at duke.edu

On Feb 6, 2005, at 4:00 PM, Arya Akmal wrote:

> Yes, I did in fact install Bundle::Bioperl ... although not quite 
> completely, it would appear. There were a very large number of failed 
> tests, so I forced the installation. I can, for instance, retrieve 
> genbank sequences, but cannot perform remote BLAST queries at NCBI. So 
> this would seem to indicate that I have installed at least part of the 
> HTTP::Request::Common module, but apparently not 
> Bio::Tools::Run::RemoteBlast.
> thanks again.
> -arya
> On Feb 5, 2005, at 11:31 AM, Jason Stajich wrote:
>> You need to install the dependancies if you want all of the 
>> functionality.
>> When you tried to install from CPAN did you install Bundle::BioPerl?  
>> This is described in the INSTALL document.
>> http://bioperl.org/Core/Latest/INSTALL
>> -jason
>> --
>> Jason Stajich
>> jason.stajich at duke.edu
>> http://www.duke.edu/~jes12/
>> On Feb 4, 2005, at 10:42 AM, Arya Akmal wrote:
>>> Hello-
>>>  I've had some trouble installing the bioperl bundle on Mac OSX 
>>> (specifically 10.3.7). I've tried both though cpan and by 
>>> downloading the  bioperl tarfile and making it. The problem is that 
>>> a large number of the tests fail. I can do a forced install, but 
>>> find that a significant part of the functionality is missing ... as 
>>> an example, the HTML HeadParser.pm module is missing, so I cannot do 
>>> remote NCBI BLAST queries. Is this a common problem on OSX 
>>> platforms, and are there any workarounds?
>>> thanks.
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l

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