similar to: getOption("repositories")

I currently set the Bioconductor repository in my .Rprofile using this code (which needs editing for every version number change of Bioconductor): # Choose repositories repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", CRANextra="http://www.stats.ox.ac.uk/pub/RWin",

On 25/08/2017 1:19 PM, Sam Albers wrote: > Hi there, > > I am trying to distinguish between getOption() and Sys.getenv(). My > understanding is that these are both used to set values for variables. > getOption is set something like this: option("var" = "A"). This can be > placed in an .Rprofile or at the top of script. They are called like this >

Hi there, I am trying to distinguish between getOption() and Sys.getenv(). My understanding is that these are both used to set values for variables. getOption is set something like this: option("var" = "A"). This can be placed in an .Rprofile or at the top of script. They are called like this getOption("var"). Environmental variables are set in the .Renviron file

Hello, Is it possible to change the default repositories? I've already changed the list in the repositories file under etc/ this is how my repositories file under R/etc looks like: row name menu_name URL default source win.binary mac.binary CRAN CRAN @CRAN@ TRUE TRUE TRUE TRUE BioC Bioconductor http://www.bioconductor.org TRUE TRUE TRUE FALSE

A post on the Bioconductor mailing list https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html suggests that install.packages now references .Rprofile (?), whereas in R-2-8 it did not. Is this intentional? The example is, in .Rprofile library(utils) install.packages("Biobase", repos="http://bioconductor.org/packages/2.4/bioc") then

Dear all, i was working under R 1.6.2 but i wanted to install bioconductor under WinXP, and because R 1.7.1 contains the TclTk package and automatic installation of bioconductor packages, so i install it. Everything is fine except this message which appear after the installation of packages. "> local({a<- CRAN.packages(CRAN=getOption("BIOC")) +

Hi R users: I got the following message when I use the pixmap library on R 1.7.0 over w2K platform (on R 1.6.2 it runs right). pixmapGrey(matrix(c(0,1),128,128)) Error in .class1(object) : Object "from" not found I download the library .zip file from: http://cran.r-project.org/bin/windows/contrib/1.7/pixmap_0.3-2.zip Other question: When I try to "Install package(s) from

Dear R-Helpers, I'm fiddling with my .Rprofile in Windows XP & R 2.7.0 Beta. I prefer to manually save my workspace but automatically save my command history via the .Rprofile. That is working fine once I found that "utils::" was required before the loadhistory & savehistory functions. What I would like to do is add a separator line with a date between the histories of each

Hi, After some reading and experimentation I found that I cannot solve this problem: 1. I am starting R and check: > system("pwd") /home/woodstock/hoffmacw/R/test > system("echo $HOME") /home/woodstock/hoffmacw > system("echo $R_PROFILE") /home/woodstock/hoffmacw/R > system("ls $R_PROFILE/.Rprofile") /home/woodstock/hoffmacw/R/.Rprofile

Hi all, several packages print messages during loading. How do I avoid to see them when the packages are in the defaultPackages? Here is an example. With this in ~/.Rprofile ,----[ ~/.Rprofile ] | old <- getOption("defaultPackages") | options(defaultPackages = c(old, "filehash")) | rm(old) `---- I get as last line when starting R: ,---- | filehash: Simple key-value

Hi, I am a student studying Biostatistics at University. We have been advised to install R and R commander. I managed to do this successfully, except I wasn't able to complete the final step - which would enable both R and R commander to launch when I open the R icon on my desktop. However, I haven't been able to save it and for this to work. The last instructions we were given are:

i am able to install zip files of packages from local zip files using the file.choose() for the package argument in install.packages() function in R console and also from the Packages menu>install from local zip files. But if there are many packages to install (say >15 or 20), then i have to factor in dependencies of 15-20 packages which may be more than 100 or 200 packages in all to be

Dear R-Help group: I have been tinkering with how I want my personal standard library functions to look like. They are not designed to be professional and heavyweight, but lightweight. There are probably dozens of little bugs, because I don't know or have not properly taken care of a variety of internal R code issues. still, I like how this ended up, and there is no learning curve, so I

I noticed about a couple weeks ago that my R start up script starting showing the below errors, following the line "Type 'q()' to quit R" Not sure what I did different and so far it hasn't caused major problems but kind of fear that it will. Can you please help? I also posted my Rprofile below. Attempting to load the environment 'package:R.utils' R.methodsS3 v1.2.2

I am running R version 2.8.1 on Windows XP OS. When I launch R, I would like to automatically read a file containing my database connections, user ids, and passwords into my workspace. I tried including this in my Rprofile.site file: ... local({ old <- getOption("defaultPackages") options(defaultPackages = c(old, "Rcmdr","RODBC", "utils")) }) .First

Hi everyone, I've followed the instructions from R-Admin Section 6.6 for creating a local repository. I've modified my Rprofile.site file to add the local repository to my repos, but I haven't been able to successfully install my package from the repo. Here's the code that I've run. ################################## sessionInfo() getOption("repos")

Hi, Since the installation of R-2.3.0 I have the following problems: 1. Startup .First() produces ------------------ Started in /home/woodstock/hoffmann/Projects/RtoZ/Windwurf/R with '~/R/.Rprofile' edited on 2006-04-28, 11:08 During startup - Warning messages: 1: use of NULL environment is deprecated 2: use of NULL environment is deprecated 3: use of NULL environment is

I think Rprofile.site as installed with R-2.6.2 contains some misleading information. It contains the following lines # set a CRAN mirror # local({r <- getOption("repos") # r["CRAN"] <- "http://my.local.cran" # options(repos=r)})'. Uncommenting these lines and changing the URL will not work. '. at the end of the last line will break the

In my .Rprofile I have the following functions which display the current directory in the main R window title bar, and modify base::setwd() to keep this up to date. I like this because I can always tell where I am in the file system. cd <- function(dir) { base::setwd(dir) utils::setWindowTitle( short.path(base::getwd()) ) } short.path <- function(dir, len=2) { np

Folks: A minor (R 2.2.0) Windows package install annoyance, but I can't figure out how to fix it. If someone could tell me how or point me to the appropriate docs, I would appreciate it. I set my CRAN mirror in my Rprofile.site file. After startup, I get: > getOption('repos') CRAN "http:/cran.cnr.berkeley.edu/" > However, when I then go