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