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Question: How to get rid of "Update all/some/none? [a/s/n]:"
1
gravatar for jacorvar
22 months ago by
jacorvar30
European Union
jacorvar30 wrote:

Dear BioC community,

Every time I install a bioconductor package as biocLite('oligo'), I'm always asked (after installing it) if I'd like to update the following packages:

Old packages: 'rgl', 'mgcv', 'nlme'
Update all/some/none? [a/s/n]: n

Does anyone know how to solve this? It doesn't cause me a problem, but it's annoying to be prompted every time.

Thanks

ADD COMMENTlink modified 22 months ago by Gordon Smyth32k • written 22 months ago by jacorvar30

Do you mean that you have previously answered 'a', the update fails (or does not?), and you continue to be prompted to update those packages? Or that you don't want to update those packages (in which case the answer is as Dan indicated below).

ADD REPLYlink written 22 months ago by Martin Morgan ♦♦ 20k
1

My guess is that the OP is using R-devel for Windows and is getting a message from biocLite() like this:

Packages which are only available in source form, and may need compilation of
  C/C++/Fortran: ‘mgcv’ ‘nlme’
  These will not be installed

I have been getting this message for a couple of weeks. CRAN is providing Windows binaries for these packages for R-release but not for R-devel. biocLite() keeps prompting to install these packages even though they are not actually available for the operating system being used.

I eliminated the problem for myself by installing each of the packages from source under Windows using Rtools 3.3.

ADD REPLYlink modified 22 months ago • written 22 months ago by Gordon Smyth32k

I think that CRAN would normally provide these; I'll ask what's up and report back.

ADD REPLYlink written 22 months ago by Martin Morgan ♦♦ 20k

These packages are part of the daily R(-devel) snapshot, and CRAN does not build the binaries. So one could (1) install the current snapshot of R-devel, or (2) install Rtools and install the packages from source (e.g., via biocLite(c("nlme", "mgcv"), type="source")). (1) seems preferable, since the packages may use features only available in the most recent R-devel snapshot.

ADD REPLYlink modified 22 months ago • written 22 months ago by Martin Morgan ♦♦ 20k
5
gravatar for Dan Tenenbaum
22 months ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:

Add the argument suppressUpdates=TRUE when you call biocLite(). Example:

biocLite("IRanges", suppressUpdates=TRUE)

More information at ?biocLite .

 

ADD COMMENTlink written 22 months ago by Dan Tenenbaum ♦♦ 8.2k
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