similar to: Creating packages in 1.8

Hello, After running R CMD check on my package I received the following error on package dependencies: * using log directory 'C:/z-zBackup/Nuvera Bio on Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck' * using R version 2.9.1 (2009-06-26) * using session charset: ISO8859-1 * checking for file 'nvNormalize/DESCRIPTION' ... OK * checking extension type ... Package *

Hi everyone, Two minor points about ?.Renviron. 1) If R_ENVIRON is not set then R defaults to `${R_HOME}/etc/Renviron', not `${R_HOME}/etc/Renviron.site' as stated. 2) In the details, there is a missing "way" in "`value' is processed in a similar to a Unix shell." Cheers, Jonathan. --please do not edit the information below-- Version: platform =

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

Thanks - it is indeed the first '.' that's the problem... Crispin > -----Original Message----- > From: Liaw, Andy [mailto:andy_liaw at merck.com] > Sent: 07 October 2003 15:21 > To: Crispin Miller > Subject: RE: [R] .First.lib doesn't appear to be running after calling > lib rary() > > > I put .First.lib in the file "zzz.R", and it works for

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Colleagues, I am trying to understand how R (2.12.1) obtains the PATH environment variable in Windows (7 or Vista). Startup {base} directs one to: "R_ENVIRON" -- which equals "" in my systems R_HOME/etc/Renviron.site -- which does not exist Next, it directs to: R_HOME/etc/Rprofile.site -- which also does not exist (the expected behavior in a "factory-fresh"

Hi - so I've dusted off the C bits of my brain and gotten a library written for my package... It passes R CMD check ok, and I've put a file called '.First.lib.R' in the pacakge's 'R' subdirectory. Its permissions are 644. It says: .First.lib <- function(lib,pkg) { library.dynam("foo",pkg,lib); require(affy,quietly=TRUE); } I build and INSTALL

I recently took "." off my PATH for security reasons and now find that R does not work in my home directory where the .Renviron file resides. The fix is simple. In the R shell startup section replace ". .Renviron" by ". ./.Renviron". The relevant section is: # Startup if ${USE_R_ENVIRON}; then # use the one in current dir, or default if [ -r .Renviron ] then .

On Debian/Ubuntu, system wide environment variables and options are set in respectively /etc/R/Renviron.site and /etc/R/Rprofile.site. These files are automatically created when r-base is installed, and do not get overwritten during an upgrade. On Fedora, there is no /etc/R directory. What is the recommended place to define system wide environment variables and options on a Fedora system?

I've rolled up R-1.6.1.tgz a short while ago. This is a minor upgrade, fixing an assortment of minor bugs, and one major one: 1.6.0 introduced a memory leak in deparsing, causing much trouble for people running simulations. You can get it from the developer site at http://cvs.r-project.org/pub/CRAN/src/base/R-1.6.1.tgz or wait for it to be mirrored at a CRAN site near you. Binaries for

I've rolled up R-1.6.1.tgz a short while ago. This is a minor upgrade, fixing an assortment of minor bugs, and one major one: 1.6.0 introduced a memory leak in deparsing, causing much trouble for people running simulations. You can get it from the developer site at http://cvs.r-project.org/pub/CRAN/src/base/R-1.6.1.tgz or wait for it to be mirrored at a CRAN site near you. Binaries for

I am having trouble getting an install of RCurl to work properly on a Unix server. The steps I have taken are: 1. installed cUrl from source without difficulty 2. installed RCurl from source using the command ~/R_HOME/R-devel/bin/R CMD INSTALL -l ~/R_HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get >

I am having trouble getting an install of RCurl to work properly on a Unix server. The steps I have taken are: 1. installed cUrl from source without difficulty 2. installed RCurl from source using the command ~/R_HOME/R-devel/bin/R CMD INSTALL -l ~/R_HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get >

When I install a new version of R (Windows XP) I have to: 1. copy my rw....\etc\Rprofile.site file to the new installation 2. copy the rw....\share\texmf files to the tex subfolder of the miktex root directory and then refresh the miktex name database (I have a batch file that does this for me which I run whenever I install a new version of R.) 3. setup the shortcut key using

Dear Madam/ Sir, I am using?R version 3.4.2.?I want to analyse microarray data. when I want to install "simpleaffy" package I get this error "package ?simpleaffy? is not available (for R version 3.4.2)". I have the same problem with?R version 3.3.2. Could you please help me to solve it? I am working with RStudio 0.99.903.exe. I also have problem in getting the new release of

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Hi, I'm using a command in bioconductor that seems to require a package called hu6800cdf. I've installed this properly but I still get the same error: Could not find array definition file ' hu6800cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I've tried specifying

My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error. On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Hello, Could someone please tell me why the following doesn't work: I have a file C:\Program Files\R\rw1051\etc\Renviron.site, which contains the line: R_LIBS= "C:/Jim/LocalR-Libraries/FromCran"; "C:/Jim/LocalR-Libraries/Cantata" >From the documentation, I gather that I have put this file in the default location, but to be safe I also explicitly set the R_ENVIRON