[Bioperl-l] bioperl on Mac OSX
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
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.
$ export BIOPERLDEBUG=1
$ perl -I. -Ilib t/RemoteBlast
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
> thanks again.
> On Feb 5, 2005, at 11:31 AM, Jason Stajich wrote:
>> You need to install the dependancies if you want all of the
>> When you tried to install from CPAN did you install Bundle::BioPerl?
>> This is described in the INSTALL document.
>> Jason Stajich
>> jason.stajich at duke.edu
>> On Feb 4, 2005, at 10:42 AM, Arya Akmal wrote:
>>> 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?
>>> Bioperl-l mailing list
>>> Bioperl-l at portal.open-bio.org
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