On Tue, 22 Jan 2008, James W. MacDonald wrote: > This is questionable advice for many CRAN packages, and horrible advice > for a Bioconductor package. If there are any dependencies (and BioC > packages often have many, and their dependencies may have > dependencies...) you can end up in download hell, all because you have > ignored the functionality that exists in R to handle such things.
But unfortunately the advice below is equally 'questionable'. > As other posters have noted, you can use setRepositories(). You can also > set this in your .Rprofile file with something like > > options(repos=(CRAN="http://ACloseRepository")) > > so you don't have to do anything interactively. That is not what setRepositories() does: it is what chooseCRANmirror() does and does not help here. > Then use install.packages(), with dependencies=TRUE if you think there > may be dependencies (although I don't think it hurts if there are none). The default (dependencies=NA) was chosen for good reasons ... it selects the dependencies you need to run the package, and not others needed to e.g. check it. > For Bioconductor packages, use biocLite() > > source("http://www.bioconductor.org/biocLite.R") > biocLite("GEOquery") which advice should be clarified by noting that is just a wrapper to the R facilities to handle multiple repositories, and if you are going to learn to use those anyway for other repositories it is not necessary to do it via the wrapper. setRepositories(ind=c(1,3:6)) # Windows ind = c(1,2, 4:7) ... use install.packages for any CRAN or BioC package *BUT* beware that some packages have incompatible versions on the two repositories and that this will pick the largest version number for such. > Best, > > Jim > > > Gabor Csardi wrote: >> Eleni, download the package (I assume you know where it is), >> on Linux you will need the source package. Then from R type >> >> install.packages("<the file you downloaded>", repos=NULL) >> >> Gabor >> >> On Tue, Jan 22, 2008 at 11:26:12AM +0200, Eleni Christodoulou wrote: >>> Hi all, >>> >>> I am trying to install the package "GEOquery" in unix. I have downloaded the >>> standard version of R and this package is not contained in the default. I >>> know that I can select repositories under windows but I don't know how to do >>> it in unix. Does anyone have any idea on this? >>> >>> Thank you in advance, >>> Eleni >>> >>> [[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. >> > > -- > James W. MacDonald, M.S. > Biostatistician > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > ______________________________________________ > 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. > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ 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.