[Bioperl-l] Updated Makefile.PL

Sendu Bala bix at sendu.me.uk
Fri Oct 20 10:44:29 EDT 2006


Hi,
I've just committed an updated Makefile.PL to HEAD for bioperl-live. 
Could some people test it on multiple platforms and confirm it is ok 
(try out the different possible options as well)?

(NB. in the below, 'pre-reqs' are things the makefile considers optional 
dependencies)

Note that some pre-reqs have been removed:
# DBD::mysql (nothing in Bioperl-live uses it; Bioperl modules may end 
up requiring it but only after the user makes an explicit choice by 
typing 'DBD::mysql' in their own code to supply as an option to Bioperl 
code)
# File::Temp (standard in 5.6.1)


This pre-req was wrong:
# Data::Stag::Writer
and has been replaced with:
Data::Stag::XMLWriter


Also, I note that very many Bioperl modules need IO::String, including 
Bio::SeqIO, so I'm not sure to what extent we can pretend it is an 
optional module. I didn't make any change though.


I don't know if these changes affect the Windows ppm Nathan, or anything 
else (Bundle?)?

The INSTALL docs need updating with these new and improved pre-reqs 
(note that some pre-reqs had wrong/not enough Bioperl modules listed as 
needing them); does someone want to correct the wiki (based on the new 
Makefile.PL) and then Chris can re-create the text version?


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