[Bioperl-l] how to stop prerequisite modules auto-installing

Chris Fields cjfields at illinois.edu
Sun Jul 26 16:21:23 EDT 2009

On Jul 26, 2009, at 2:33 PM, Sendu Bala wrote:

> Joel Martin wrote:
>> Hello,
>>   I went to test bioperl-live and Build.PL started updating
>> modules in my perl install w/o prompting me, frightening!  I
>> really need to test modules and other groups here need to
>> test them before they're updated so we don't break anything
>> when some module's api changes.
>>   I did svn co of bioperl-live then
>> perl Build.PL PREFIX=/scratch/bioperl-live
>> saw some output including
>> "I think you ran Build.PL directly, so will use CPAN to install  
>> prerequisites on demand"
>> then it went to cpan and tried updating Data::Stag in my perl  
>> install.
>> How can I ask it to prompt me before updating modules ( so
>> I can put the updated versions somewhere for it to find
>> that isn't the live perl install )?
> Unfortunately, for those few (5) modules that are currently  
> "absolutely required", it doesn't ask, it just updates.

This is bad; we should never assume the intent of the user.  I would  
rather prompt for these, then bail if the answer is 'no' for any  
'requires' modules.  Leave it up to the user to make the decision to  
update; if they want they will install the latest required modules,  
otherwise there isn't much we can do.

> Data::Stag actually has a comment next to it suggesting it isn't  
> even "absolutely required". So you could just comment that line out  
> completely in Build.PL as a temporary fix.

If you do any work with UniProt, then Data::Stag *is* required. It is  
used by Bio::Annotation::TagTree, the replacement for  
Bio::Annotation::StructuredValue (this has been the case for a couple  
years now I believe).  The Data::Stag update is small but required as  
well, BTW, unless you want warnings popping up.

> Otherwise, since it will be using CPAN to install modules, you can  
> just arrange beforehand for CPAN to install to your desired location  
> using the CPAN configuration system.


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