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

[Dan Tenenbaum]

On Wed, Mar 27, 2013 at 3:08 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:
> 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)
>
>

Or it could be a problem with Revolution R.
FWIW I installed the windows version of Revolution R and it does not
have this problem, but I don't have access to a Red Hat machine so I
wasn't able to test the Linux version.

Dan



> 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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor