[Bioc-devel] Package download when using functions from affy and oligo

James W. MacDonald jmacdon at uw.edu
Sat May 5 00:16:36 CEST 2018

>> The warning I get when trying oligo::read.celfiles() on a single CEL file
>> right after installing it about the pd.hugene.1.0.st.v1 package. The even
>> more annoying thing is that on my machine it insists on building from
>> source, whereas on another Windows machine without Rtools, it downloads a
>> binary.
> That is an options setting that gets changed when you install Rtools. The
> 'pkgType' option gets set to 'both' because you can now install both kinds.
> And in install.packages it ends up getting switched from 'both' to
> 'source'. I haven't dug any further into that because I am not sure I see
> why it's a problem. In the end there isn't a difference between installing
> a source or a binary pdInfoPackage, and trying to get it to 'do the right
> thing' might have some unforeseen consequences that I would rather not have
> to worry about. This is really an 'if it ain't broke, don't fix it'
> scenario, IMO.

Now that I think about this, most of the annotation packages (including the
pdInfo packages) are no longer generated as windows binary files. So even
if you don't have Rtools installed you shouldn't get the binary, because it
doesn't exist.

> biocLite("pd.hugene.1.0.st.v1", type = "win.binary")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) 'pd.hugene.1.0.st.v1'

   package 'pd.hugene.1.0.st.v1' is available as a source package but not
as a binary

So maybe you are thinking of an older R installation, from back when we
still made binary versions of annotation packages?



James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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