I got a new PC running on ubuntu and tried to install the Rsamtools package. got the following error: > source("http://www.bioconductor.org/biocLite.R") > biocLite("Rsamtools") Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???Rsamtools??? is not available does that mean that this package is not available for my linux distribution?? thank you conny -- output of sessionInfo(): > source("http://www.bioconductor.org/biocLite.R") > biocLite("Rsamtools") Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ???Rsamtools??? is not available -- Sent via the guest posting facility at bioconductor.org.

Hi Cornelia, On 12/29/2011 8:16 AM, Cornelia Vesely [guest] wrote: > I got a new PC running on ubuntu and tried to install the Rsamtools package. > got the following error: >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("Rsamtools") > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ??~Rsamtools??T is not available > does that mean that this package is not available for my linux distribution?? > thank you > conny > > > -- output of sessionInfo(): Here you should have the output of running sessionInfo() at an R prompt, which will let us know what versions of things you are running. Please repost with this info. Best, Jim > >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("Rsamtools") > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ??~Rsamtools??T is not available > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

I still have problems installing Rsamtools. The first idea was that my R version was too old - so I updated it to the latest version. still the installation does not work - any ideas? this is just the end of the list after: > biocLite("Rsamtools") Warning: S3 methods ???[<-.CURLOptions???, ???[[<-.CURLOptions??? were declared in NAMESPACE but not found Error in library.dynam(lib, package, package.lib) : shared object ???RCurl.so??? not found ERROR: lazy loading failed for package ???Rsamtools??? * removing ???/home/lab/R/x86_64-pc-linux-gnu- library/2.14/Rsamtools??? * restoring previous ???/home/lab/R/x86_64-pc-linux-gnu- library/2.14/Rsamtools??? The downloaded packages are in ???/tmp/RtmpRyJ4Zm/downloaded_packages??? Warning messages: 1: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ???RCurl??? had non-zero exit status 2: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ???XML??? had non-zero exit status 3: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ???rtracklayer??? had non-zero exit status 4: In install.packages(pkgs = pkgs, repos = repos, ...) : installation of package ???Rsamtools??? had non-zero exit status farther above there was also the error: Error : package ???RCurl??? required by ???rtracklayer??? could not be found ERROR: lazy loading failed for package ???rtracklayer??? -- output of sessionInfo(): R version 2.14.1 (2011-12-22) Platform: x86_64-pc-linux-gnu (64-bit) 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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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] BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tcltk_2.14.1 tools_2.14.1 -- Sent via the guest posting facility at bioconductor.org.