Looks like R.app forgot to adapt to
> tools:::.BioC_version_associated_with_R_version
function ()
numeric_version(Sys.getenv("R_BIOC_VERSION", "3.1"))
<bytecode: 0x7fd10ac08d50>
<environment: namespace:tools>
I.e. in newer R, you need to use
tools:::.BioC_version_associated_with_R_version() to get the version.
You might want to check newer R.app builds off of http://r.research.att.com or
wait for Simon to chime in with harder info than what I have.
Or,... You could just edit the offending R file by hand. If neither of us have
done anything out of the ordinary, I think you'll find it in
/Applications/R.app/Contents/Resources/GUI-tools.R
Or,... Upon actually reading the above code section, I think that a noninvasive
procedure is preemptively to use
options("BioC.repos"= z) where z is obtained from, um,
mirror <- getOption("BioC_mirror", "http://www.bioconductor.org";)
# ver <- "3.1"
ver <- as.character(tools:::.BioC_version_associated_with_R_version())
z <- paste(mirror, "packages",
ver, c("bioc", "data/annotation", "data/experiment", "extra"),
sep = "/"))
-Peter D.
On 23 Apr 2015, at 09:58 , Federico Calboli <[email protected]>
wrote:
> Hi All,
>
> I am using R version 3.2.0 (2015-04-16) and R.app GUI 1.65 (6931)
> x86_64-apple-darwin13.4.0. I am using the package installer to install and
> update packages. I have the following problem: when I try and list
> Bioconductor packages (binaries or source) I get the following message:
>
> Error in as.character(tools:::.BioC_version_associated_with_R_version) :
> cannot coerce type 'closure' to vector of type 'character'
>
> No idea what is going on or how to fix it, and in fact I have no idea whetehr
> this is a OS X specific issue or not (but I cannot test on a different OS).
> If this *is* a OS X issue I would be grateful if someone can figure out
> what’s missing.
>
> Best
>
> F
>
>
> --
> Federico Calboli
> Ecological Genetics Research Unit
> Department of Biosciences
> PO Box 65 (Biocenter 3, Viikinkaari 1)
> FIN-00014 University of Helsinki
> Finland
>
> [email protected]
>
> _______________________________________________
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [email protected] Priv: [email protected]
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