[Bioperl-l] Extreme newbie question.

Adlai Burman adlai at refenestration.com
Thu Jun 25 14:59:10 EDT 2009

Hey again, I'm right into trying to install again and I now get a new  

Client not fully configured, please proceed with configuring.
  o conf init urllist

any ideas?


On Jun 25, 2009, at 5:21 PM, Kevin Brown wrote:

> http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
> Or http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink
> That error suggests that the install fails and you need to figure out
> why from the install error messages. I suspect you aren't doing the
> install as root, but as a normal user who lacks the needed permissions
> to change files in certain directories.
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Adlai Burman
>> Sent: Wednesday, June 24, 2009 7:09 PM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Extreme newbie question.
>> I have been trying to install BioPerl for a while now and after
>> pummeling my hard drive (Mac OS 10.5 intel) with several attempts at
>> Fink installation, a >cpan installation and removing my .cpan
>> folder I
>> am still at square 0. I do not want to do anymore damage to my
>> computer, yet I really need a working install (especially to
>> interface
>> with remote DBs like GenBank. Can anyone give me some advice here?
>> After each attempt, I have tried to run perldoc bptutorial.pl and
>> tried test scripts with "use Bio::Perl" in the headers and I just
>> receive  error mesages like the following:
>> Can't locate Bio/Perl.pm in @INC (@INC contains: /home/users/dag/lib/
>> perl5/ /Library/Perl/Updates/5.8.8/darwin-thread-multi-2level
>> /Library/
>> Perl/Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-
>> multi-2level /System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-
>> thread-multi-2level /Library/Perl/5.8.8 /Library/Perl
>> /Network/Library/
>> Perl/5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /
>> Network/Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread-
>> multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /
>> Library/Perl/5.8.1 .) at trsh.pl line 1.
>> I have been working from the OReilly book astering Perl for
>> Bioinformatics and the INSTALL file and have scoured around the
>> BioPerl website and am still stuck.
>> Thanks in advance,
>> Adlai
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>> Bioperl-l at lists.open-bio.org
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