Question

How to get rid of "Update all/some/none? [a/s/n]:"

1

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jacorvar ▴ 40

@jacorvar-8972

Last seen 12 months ago

European Union

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

rgl mgcv nlme package installation • 17k views

ADD COMMENT • link updated 8.8 years ago by Gordon Smyth 51k • written 8.8 years ago by jacorvar ▴ 40

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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 REPLY • link 8.8 years ago Martin Morgan 25k

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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 REPLY • link 8.8 years ago Gordon Smyth 51k

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

ADD REPLY • link 8.8 years ago Martin Morgan 25k

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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 REPLY • link 8.8 years ago Martin Morgan 25k

score 5 · Accepted Answer · 2016-01-31

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Dan Tenenbaum ★ 8.2k

@dan-tenenbaum-4256

Last seen 5 months ago

United States

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

biocLite("IRanges", suppressUpdates=TRUE)

More information at ?biocLite .

ADD COMMENT • link 8.8 years ago Dan Tenenbaum ★ 8.2k