[R] select repositories under linux
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.
Re: [R] select repositories under linux
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. -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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.
Re: [R] select repositories under linux
hits=-2.6 tests=BAYES_00 X-USF-Spam-Flag: NO On Tue, 2008-01-22 at 11:26 +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 GEOquery is part of the Bioconductor project. See the web site for this project for instructions on how to install bioconductor and associated packages: http://www.bioconductor.org/ Installation instructions for GEOquery appear to be here: http://bioconductor.org/packages/2.1/bioc/html/GEOquery.html HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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.
Re: [R] select repositories under linux
See setRepositories() On 22/01/2008, Eleni Christodoulou [EMAIL PROTECTED] 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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.
Re: [R] select repositories under linux
Agreed, i had no idea that this is a Bioconductor package. G. On Tue, Jan 22, 2008 at 09:49:50AM -0500, 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. 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. 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). For Bioconductor packages, use biocLite() source(http://www.bioconductor.org/biocLite.R;) biocLite(GEOquery) 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 -- Csardi Gabor [EMAIL PROTECTED]UNIL DGM __ 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.
Re: [R] select repositories under linux
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. 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. 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). For Bioconductor packages, use biocLite() source(http://www.bioconductor.org/biocLite.R;) biocLite(GEOquery) 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.
Re: [R] select repositories under linux
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, UKFax: +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.
