Yes it is. I copied and pasted all the attempted installation messages. The installed Bioconductor environment is the latest released. Just installed yesterday. The dependencies ... well, should be automatically resolved.-
Thank you, Maura -----Messaggio originale----- Da: Martin Morgan [mailto:mtmor...@fhcrc.org] Inviato: mar 23/06/2009 18.55 A: mau...@alice.it Cc: bioconductor-boun...@stat.math.ethz.ch; r-h...@stat.math.ethz.ch; Stefano Rovetta; Francesco Masulli; Chenna Reddy Oggetto: Re: [R] Cannot install pakages from Bioconductor besides the default installation Please ask Bioconductor questions on the Bioconductor mailing list https://stat.ethz.ch/mailman/listinfo/bioconductor Is the below a complete transcript of the outcome of biocLite('biomaRt')? I would have expected to see R attempt to install each package, and then perhaps XML failing to compile. This would mean that first RCurl and then biomaRt would fail to install. Likely XML would fail to install because of outdated system dependencies, but this is just speculation; is this really the complete output of the biocLite('biomaRt') command? Martin <mau...@alice.it> writes: > I am running the last R version on SuSE 11.1. > I installed the Bioconductor environment following the instructions on the > web. As a consequence some > core packages from Bioconductors were installed. > I need to add some more packages. So I tried biomaRt as follows. > It does not get installed correctly. > Please see the following sequence. > Thank you in advance. > Maura > >> source("http://bioconductor.org/biocLite.R";) > Warning messages: > 1: In safeSource() : Redefining 'biocinstall' > 2: In safeSource() : Redefining 'biocinstallPkgGroups' > 3: In safeSource() : Redefining 'biocinstallRepos' >> > biocLite("biomaRt") > Running biocinstall version 2.4.11 with R version 2.9.0 > Your version of R requires version 2.4 of Bioconductor. > Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > argument 'lib' is missing: using > '/home/mauede/R/x86_64-unknown-linux-gnu-library/2.9' > also installing the dependencies 'XML', 'RCurl' > > trying URL > 'http://bioconductor.org/packages/2.4/extra/src/contrib/XML_2.5-1.tar.gz' > Content type 'application/x-gzip' length 676201 bytes (660 Kb) > opened URL > ================================================== > downloaded 660 Kb > > trying URL > 'http://bioconductor.org/packages/2.4/extra/src/contrib/RCurl_0.98-1.tar.gz' > Content type 'application/x-gzip' length 470071 bytes (459 Kb) > opened URL > ================================================== > downloaded 459 Kb > > trying URL > 'http://bioconductor.org/packages/2.4/bioc/src/contrib/biomaRt_2.0.0.tar.gz' > Content type 'application/x-gzip' length 200617 bytes (195 Kb) > opened URL > ================================================== > downloaded 195 Kb > > > The downloaded packages are in > '/tmp/RtmpAtNws1/downloaded_packages' > Warning messages: > 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'XML' had non-zero exit status > 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'RCurl' had non-zero exit status > 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = > dependencies, : > installation of package 'biomaRt' had non-zero exit status >> > library(biomaRt) > Error in library(biomaRt) : there is no package called 'biomaRt' >> ?getBM > No matches for "getBM" have been found >> ?getSequence > No matches for "getSequence" have been found > > > > > > tutti i telefonini TIM! > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 tutti i telefonini TIM! [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
