[BioC] duplicate 'row.names' are not allowed from biocLite.R

[Valerie Obenchain]

Hi Pawel,

After looking at the biocLite.R file:

     readLines("http://bioconductor.org/biocLite.R", 100)

the problem appears to be here:

p <- file.path(R.home(\"etc\"), \"repositories\")
a <- tools:::.read_repositories(p)

If you run these lines from an R session does it reproduce the error?

     p <- file.path(R.home("etc"), "repositories")
     a <- tools:::.read_repositories(p)

If yes, 'repositories' may have been corrupted with a dupliacted row or 
improper line ending etc. If that is the case you will need to reinstall 
R. You can look at 'repositories' by typing,

     readLines(file.path(R.home("etc"), "repositories"), 100)


Valerie

On 03/26/2013 07:11 AM, Pawel Eljasz wrote:
> here is abit of the traceback:
>
> 13: stop("duplicate 'row.names' are not allowed") at
> biocLite.R#32
> 12: read.table(file = file, header = header, sep = sep,
> quote = quote,
>           dec = dec, fill = fill, comment.char =
> comment.char, ...) at biocLite.R#32
> 11: utils::read.delim(file, header = TRUE, comment.char =
> "#", colClasses = c(rep.int("character",
>           3L), rep.int("logical", 4L))) at biocLite.R#32
> 10: tools:::.read_repositories(p) at biocLite.R#3
>
>
>
> On 03/26/13 11:37, Pawel Eljasz wrote:
>> dear all
>>
>> possibly novice kind of question,
>> I get this:
>>
>> Error in read.table(file = file, header = header, sep =
>> sep, quote = quote,  :
>>    duplicate 'row.names' are not allowed
>>
>> when run:
>> source("http://bioconductor.org/biocLite.R")
>>
>> on one RHEL 6.3 two other R version, plain-distro 2.15.2
>> and 2.13.2 are ok, no complaining there
>> yet 2.14.2, which in fact is Revo_Core-6.1.0-1 fails in
>> fashion described above
>>
>> can you suggest any fix or what might be wrong?
>> many thanks
>>
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>
>
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