[R-SIG-Mac] Cannot list Bioconductor packages

[peter dalgaard]

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 <federico.calboli at helsinki.fi> 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
> 
> federico.calboli at helsinki.fi
> 
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-mac

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com