On 01/29/2011 01:15 PM, January Weiner wrote: > Dear Martin, > > thank you so much. This seems to have been the problem. I relied on > the fact that many packages report a problem with R version when they > are loaded, and usually I just updated them whenever I saw the > respective message ("this package has been build for a different > version of R") when I loaded them. > > regards, > > j. > > On Sat, Jan 29, 2011 at 8:52 PM, Martin Morgan <mtmorgan at="" fhcrc.org=""> wrote: >> On 01/29/2011 11:01 AM, January Weiner wrote: >>> Hello, >>> >>> I cannot use ReadAffy() in Ubuntu 10.10 (it works in Ubuntu 10.04). >>> >>>> ab <- ReadAffy() >>> Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : >>> unused argument(s) (extended = TRUE) >>> >>> The reason is that the sub() function from R lacks the optional >>> argument "extended": >> >> Hi January -- >> >> This is likely a version mismatch between your R and Bioc packages; >> follow instructions at >> >> http://bioconductor.org/install/index.html#update-bioconductor- packages >> >> and >> >> source("http://bioconductor.org/biocLite.R") >> update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE) >> >> Or update your R and create a fresh bioc install. >> >> Martin >> >>> >>>> a <- rep( "a", 10 ) >>>> sub( "a", "b", a ) >>> [1] "b" "b" "b" "b" "b" "b" "b" "b" "b" "b" >>>> sub( "a", "b", a, extended=TRUE ) >>> Error in sub("a", "b", a, extended = TRUE) : >>> unused argument(s) (extended = TRUE) >>> >>> No such errors occur in Ubuntu 10.04. >>> >>> The R version that comes with Ubuntu 10.10 is 2.11.1: >>> >>>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> i686-pc-linux-gnu >>> >>> locale: >>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] affy_1.22.1 Biobase_2.4.1 >>> >>> loaded via a namespace (and not attached): >>> [1] affyio_1.12.0 preprocessCore_1.6.0 >>> >>> >>> In Ubuntu 10.04, the version of R is 2.10.1 >>> >>> My question: is that a general problem with R 2.11.1, or a problem >>> with Ubuntu? Is anyone aware of that problem? I am trying to figure >>> out what would be the easiest way of getting back the 2.10.1 version >>> (short of deinstalling all R packages and libraries and manually >>> reinstalling them again), I will post a solution if I find an easy >>> one. On windows it is usual to install pre-built packages; on linux packages are usually built by the R that is doing the installation. So if the R is told to build and install the wrong package, there is no warning. Using biocLite avoids this problem. You could put options(repos=c(CRAN="http://cran.fhrcr.org")) utils::setRepositories(ind=1:6) old.packages() in ~/.Rprofile to be alerted of all currently installed packages that are out of date (though this might get irritating with a slow internet connection / large number of packages. Martin >>> >>> best regards, >>> >>> j. >>> >> >> >> -- >> Computational Biology >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 >> >> Location: M1-B861 >> Telephone: 206 667-2793 >> > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793