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[Bioc-devel] BiocInstaller::getUpdatablePackages

2 messages · Wolfgang Huber, Martin Morgan

Original
Wolfgang Huber
# 
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?


Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
Martin Morgan
#
On 11/10/2011 11:49 AM, Wolfgang Huber wrote:
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guess the awkward part is when there are many outdated packages on the 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.