[Bioc-devel] BiocInstaller::getUpdatablePackages

Martin Morgan mtmorgan at fhcrc.org
Thu Nov 10 22:31:55 CET 2011

On 11/10/2011 11:49 AM, Wolfgang Huber wrote:
> Hi
> it appears that if one has multiple versions of the same package X in
> different libraries, running biocLite("foo") will in the end print the
> message
> Old packages: X
> Update all/some/none? [a/s/n]
> even if the version of X that would be loaded by library(X) is the
> current one; and replying "a" will then needlessly reinstall the package
> over and over again. This can be particularly tedious if X is large or
> numerous.
> (A use case where this came up is a colleague who uses a shared 'server'
> directory in their library path, as well as a small private library in
> their home directory.)
> Would it be possible / desirable for getUpdatablePackages to be smarter,
> and for each package name worry only about that version that 'library'
> would load?

or adding lib.loc as an argument to biocLite(), specifying the library 
locations for update candidates? I don't think ?library documents which 
library is used when a package is found in several of them.

I'm not 100% sure that I follow your description, especially the 'over 
and over again'. If you answer 'a' then each element of X gets updated 
in the the location it occurs; the next time through biocLite should be 
silent. If some of the libraries (e.g., those on the server) are not 
writeable, then biocLite should warn but not prompt for updating. I 
guess the awkward part is when there are many outdated packages on the 
(writable) server, which are not to be updated, and a few in the private 
library, which are to be updated.

> Best wishes
> Wolfgang
> Wolfgang Huber
> http://www.embl.de/research/units/genome_biology/huber
> _______________________________________________
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