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 = crep.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