[Bioc-devel] biocLite should warn when called from a non-current R version

Simon Anders anders at embl.de
Thu Jun 20 09:03:12 CEST 2013

Hi Martin

good to see that Herve agrees with me, and I reiterate my point, because 
I consider this issue very important.

The average user does _not_ expect that a function like 'biocLite', 
which has the express purpose of downloading and installing packages, 
does not pull the newest package. I know that to you, as an an 
experienced Bioc person, this has become second nature, but believe me: 
It is unusual and very surprising for anybody used to other systems.

The message hence has to very clearly and unambiguously state the 
following fact: "The biocLite function will NOT install the most recent 
released versions of Bioconductor packages."

I insist that this should be mentioned in this direct manner. Your 
formulation may imply it to the careful reader but not to a user in a 
hurry. Merely mentioning that there are newer versions will _not_ bring 
across the point that calling the biocLite installation script will not 
install these!

I really do not see the problem with saying clearly that biocLite will 
not pull the newest version. Is this something we are ashamed of and 
don't want to admit straight out?

And I frankly see no need to warn users already in this message that 
updates can break existing workflows. Everybody who has ever used any 
software knows this.


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