[BioC] automatic package installs

[James W. MacDonald]

Hi Patrick,

Votruba, Patrick G. wrote:
> Hello,
> 
> My colleague recently received the following error message and it has
> caused some concern among our system administrators.  The
> getProbePackage function tries to download and install a package that's
> not locally available and fails because the user doesn't have write
> permission to the library directory.  There are, however, a core group
> of R users who do have write permission and we'd like to prevent
> unintentional package installations.  Is there an easy way to disable
> this function?

Not really, but if one is trying to run a function that requires a 
particular package to work, is it really an unintentional package 
installation?

Anyway, the canonical method to handle such situations is to create a 
local library in one's home directory (or somewhere that the particular 
user has write access), and then set .libPaths() to include that 
directory. Then the package will be installed there, the user can do the 
intended analysis, and the 'usual' R library directory is unaffected.


> 
> Also, this has sparked some debate as to whether bioconductor software
> also automatically updates existing packages.  If so, can this also be
> disabled?

I don't know of any BioC software that automatically updates existing 
packages. If there are some, you would need to disable them 
individually, as AFAIK, this isn't a common practice.

> 
> Do automatic package installs/updates occur for all packages or just a
> subset (e.g. annotation packages)?

I only know of two packages that do automatic installs of packages; affy 
and gcrma. These packages will install cdf packages (affy) or probe 
packages (gcrma), both of which are necessary for the respective 
packages to function. The only way to disable the automatic installs for 
these packages is to not have write access to the library, which as you 
found causes them to error out.

Best,

Jim




-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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