[Bioperl-l] a thought on Bio::Root::Build

Chris Fields cjfields at illinois.edu
Fri Jan 23 20:02:00 UTC 2009

On Jan 23, 2009, at 11:35 AM, Sendu Bala wrote:

> Mark A. Jensen wrote:
>> Is it a reasonable convenience for the user who has run ./Build.PL
>> with a non-default set of install directories to ask CPAN::Shell
>> to use those directories when installing prerequisites (unless the  
>> user's MyConfig.pm is saying something else)?
> Seems like a good idea to me. If you've thought about it and are  
> confident it should be OK, go ahead and commit.

One small bit to add here, and it may not be related, but I have  
noticed a very interesting error popping up with a majority of the  
CPAN Testers cases using CPANPLUS (example here: http://www.nntp.perl.org/group/perl.cpan.testers/2009/01/msg3113770.html) 

[MSG] [Thu Jan 22 08:14:29 2009] Loading YACSmoke database "/Volumes/ 
[MSG] [Thu Jan 22 08:14:32 2009] Checking whether your kit is  
complete... Looks good Checking prerequisites...

- ERROR: IO::String is not installed

[ERROR] [Thu Jan 22 08:14:32 2009] Could not create Module::Build  
object: mkdir /Users/cpan/.cpan/CPAN: Permission denied at /Volumes/ 
Media/smoke/rel/perl-5.10.0/lib/5.10.0/CPAN/HandleConfig.pm line 539
Note that the CPAN module is being called from within CPANPLUS (likely  
via Bio::Root::Build), I think causing a permissions issue.  Not a  
huge worry (the tests are marked UNKNOWN) but I'm wondering if we  
should bypass automatic installation of required modules if called  
from within the CPAN/CPANPLUS shell for this reason.  Either that or  
try to determine whether CPAN or CPANPLUS is being used and then use  
the correct shell for retrieving and installing modules.


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