search for: setrepositori

I have some questions and observations about these: Will these replace manually setting options(CRAN), which doesn't work in R-2.1.0? In R-2.1.0, setRepositories() looks to see if options("repos") contains a CRAN entry and will not override that CRAN entry even if the $R_HOME/etc/repositories file (which setRepositories reads from) contains a CRAN entry. Why is this? The user could easily set options("repos") without the help of...

Full_Name: John Gavin Version: 2.1.0 patched 18-04-05 OS: windows XP SP2 Submission from: (NULL) (139.149.1.203) Hi, I suspect that there may be a bug in utils::setRepositories(). Starting with > getOption("repos") CRAN CRANextra "@CRAN@" "http://www.stats.ox.ac.uk/pub/RWin" I set > options(repos = c( + UBS = "http://wfdevapps:8150/qrms/...

Full_Name: Richard Calaway Version: 2.9.2 OS: Windows Vista Submission from: (NULL) (65.47.30.18) If you call setRepositories(graphics=TRUE), or, equivalently, choose "Select repositories..." from RGui's Packages menu, and then click "Cancel", you are dropped to the command line menu. Choosing "Cancel" should drop you back to the top-level prompt. Also, the command-line menu doesn't...

...or the noise, and thanks for keeping R such a great package! --Rich Calaway _____________________________________________ From: Rich Calaway [mailto:richcalaway at revolution-computing.com] Sent: Wednesday, September 23, 2009 12:32 PM To: 'R-bugs at R-project.org' Subject: RE: Bug 13937 (setRepositories() doesn't allow graceful cancellation from GUI menu) Hi, all- This one was moved to features&FAQ, which appears to be the "works as documented" folder, with the following note: intentional: you do need to set repositories or interrupt R. If this is true, there's still a...

Dear all, My gRbase package imports functionality from the bioconductor packages graph, Rgraphviz and RBGL. To make installation of gRbase easy, I would like to have these bioconductor packages installed in connection with installation of gRbase, but to do so the user must use setRepositories() to make sure that R also installs packages from bioconductor. Having to call setRepositories causes what can perhaps be called an (unnecessary?) obstacle. Therefore I have been experimenting with deferring installation of these bioc-packages until gRbase is loaded the first time using .onAttac...

...ever I didn't see anything that might help in diagnosing the problem. While invoking the options under the "package" menu I get the following errors: > chooseCRANmirror() Warning message: In open.connection(con, "r") : cannot open: HTTP status was '0 (nil)' > setRepositories() > update.packages(ask='graphics') Warning: unable to access index for repository http://www.ibiblio.org/pub/languages/R/CRAN/bin/windows/contrib/2.11 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.11 > utils:::menuInstallPkg...

install/update.packages will have a lot of changes in 2.1.0, and I have been adding some widgets to go along with this. - Rather than just CRAN and BIOC, you have a character vector of repositories. There is a function setRepositories() to set the appropriate option(). - There is no default CRAN, but a function chooseCRANmirror() to set a mirror, which is invoked if you try to access CRAN without setting a mirror. - update.packages(ask="graphics") brings up a listbox for you to de-select packages (all a...

...ank you in advance. Maura > utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- Warning: package 'segmented' is in use and will not be installed > utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed > setRepositories() > utils:::menuInstallPkgs() Error in install.packages(NULL, .libPaths()[1], dependencies = NA, type = type) : no packages were specified > chooseCRANmirror() > utils:::menuInstallPkgs() Warning: package 'segmented' is in use and will not be installed > -- Maura E....

...BioCsoft="http://www.bioconductor.org/packages/2.7/bioc", Rforge="http://r-forge.r-project.org")) options(repos=repos) rm(repos) I'd like to avoid editing the version number. One hack to do so is this code that adds all repositories. setRepositories(ind=1:10) r <- getOption("repos") r <- r[!is.na(r)] options(repos=r) Is there a simpler way? I've searched for quite a while without finding an answer. Incidentally, the help page for "options" says: A Bioconductor mirror can be selected by setting options("...

...op and desktop even I uninstall and install it again. I even can not update the R now. I wonder if you have the similar issue. Thakns! Xin > chooseCRANmirror() Warning message: In open.connection(con, "r") : unable to connect to 'cran.r-project.org' on port 80. > setRepositories() > utils:::menuInstallPkgs() Warning: unable to access index for repository http://www.stats.bris.ac.uk/R/bin/windows/contrib/2.12 Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.12 Error in install.packages(NULL, .libPaths()[1L], depend...

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]]

I installed R-2.1.0 from source on a Linux box running Red Hat Enterprise Linux WS release 4 but install.packages() wouldn't work (see below). When I install R-2.0.1 from RPM on the same system, everything is fine. Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 . . . > options(CRAN = "http://cran.fhcrc.org/") > install.packages("rgenoud") --- Please select a CRAN

Hi, I am having troubles trying to install package "sp" in R (2.13.0) on mac OSX. I have tried installing the package using GUi or function install.packages but it didn't work. Here is the error message I get: also installing the dependency ‘rgdal’ trying URL 'http://cran.univ-lyon1.fr/src/contrib/rgdal_0.6-33.tar.gz' Content type 'application/x-gzip' length

I can't seem to find this anywhere. How do I set the default CRAN repository _site wide_ on a linux box? What I want to do is eliminate the pop-up list of repository locations when using 'install.packages()'. I know how to do this for a single account. Modifying files in /etc/R does not seem to work. (cc me please - I think I'm not subscribed). THK -- Timothy H. Keitt,

Can anyone tell me from where to download the package "RHTMLForms" ? CRAN seems not holding this anymore. I am using Windows Vista OS. Thanks -- View this message in context: http://n4.nabble.com/RHTMLForms-Package-tp997672p997672.html Sent from the R help mailing list archive at Nabble.com.

...must be fairly recent. I think this represents about 50% growth in the last year. Not bad! Does anyone have a program that graphs the growth of R packages? I don't know if that historical data is around. Cheers, Bob http://RforSASandSPSSusers.com Henrique's program: > setRepositories() > myPackageNames <- available.packages() --- Please select a CRAN mirror for use in this session --- [I selected them all] > length(unique( rownames(myPackageNames) )) [1] 3175 [[alternative HTML version deleted]]

I'm new to making bubble plots with R, so I was going to try the following: https://stat.ethz.ch/pipermail/r-sig-geo/2009-August/006258.html Unfortunately, it looks like rgdal is not part of 2.14.  I'm not sure if it was the mirror I selected or something else is going on. > install.packages("rgdal") --- Please select a CRAN mirror for use in this session --- Warning

...rators that capture stdout and redirect to the generated report. As it is now, trying to use menu() and select.list() in such frameworks will cause the menu options to appear in the report and not be visible to the user in an interactive run. This behavior affects other querying functions such as setRepositories(graphics=FALSE) and chooseCRANmirror(graphics=FALSE) so those cannot be used in report generators either. Before anyone argues that one shouldn't use reports that prompts the user, there are several flavors of "report generators/vignettes" that are natural to use also interactively...

Dear R-helpers, I would like to export hierarchical clusters e.g. fit <- hclust(d, method="ward") in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package.

Dear R Users, Is there a version of the Windows binary for RBloomberg that works with R 2.11 ? Thanks in advance, Tolga This email is confidential and subject to important disclaimers and conditions including on offers for the purchase or sale of securities, accuracy and completeness of information, viruses, confidentiality, legal privilege, and legal entity disclaimers, available at