[R-SIG-Mac] Cannot list Bioconductor packages

[Federico Calboli]

> On 23 Apr 2015, at 12:53, peter dalgaard <pdalgd at gmail.com> wrote:
> 
> 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.

Just tried R.app GUI 1.66 (6935) x86_64-apple-darwin13.4.0 and I have the same message:

Error in as.character(tools:::.BioC_version_associated_with_R_version) : 
  cannot coerce type 'closure' to vector of type 'character'

> 
> 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

Hence I edited GUI-tool.R by hand — which works.

BW

F




> 
> 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
> 
> 
> 
> 
> 
> 
> 
> 
> 


--
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