similar to: Problem installing aroma.affymetrix on Solaris 9 with R-2.6.2

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message

Hello everybody, I am trying to install Rmpi on 64-bit HP-Proliant server. I am facing the following error: * Installing *source* package 'Rmpi' ... Try to find mpi.h ... Found in /usr/local/mpich-1.2.7p1/include Try to find libmpi or libmpich ... Found libmpich in /usr/local/mpich-1.2.7p1/lib Try to find liblam ... checking for main in -llam... no liblam not found. Probably not LAM-MPI

I don't know if this is the correct forum to ask the following question; however, when I search the aroma.affymetrix discussion group, it suggested that I should posted the question to r-help. Here it goes. I followed the instructions on aroma.affymetrix trying to install the packages; following are the steps: > install.packages(c("R.oo", "R.utils"),

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 *

I am developing a package that imports some functions from another package. The imported package (qcc) does not have a namespace and this is causing problems with loading of my package, which has a namespace. Is there a workaround to allow loading the namespace-less package? I searched the archives and found a suggestion that the package should be included in the Depends list, but this has not

Dear Help, After loading the pd.Citrus library and checking the DataFrame, I ran > the R code for: > > 1) 'oligo' > > > > {> library(pd.citrus) > Loading required package: RSQLite > Loading required package: DBI > > data(pmSequence) > > > show(pmSequence) > DataFrame with 341730 rows and 2 columns > fid sequence > <integer>

I have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been

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 >

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of

I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo. R version 2.4.0 Under development (unstable) (2006-08-29 r39012) i386-pc-mingw32 locale: LC_COLLATE=English_United

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 have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

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

Hi there, I got a problem when trying to read in a .cel file using ReadAffy(). R codes: require(affy) ReadAffy(filenames="CH1.CEL") It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried

An embedded and charset-unspecified text was scrubbed... Name: ?????? ?? ????????. URL: <https://stat.ethz.ch/pipermail/r-help/attachments/20080818/dcaa0623/attachment.pl>

Dear RUsers, I am new to R. I am learning how to use R. I am a PC user and run R on windows. I would appreciate if some one could guide me on a few questions I have: 1) I have 4 cel files (2 replicates for NORM and Disease resp). I have been able to run siggenes on this dataset where I have 4 labels in the class file groupsnhi.cl op-> (0,0,1,1) and my data has been read into datrmanhi after

Dear list, I?m using R embedded in another program (coded in tcl/tk) under Windows Vista. In this context I don?t launch Rgui.exe but rather Rtem.exe. Now I have a problem finding libraries not specifically installed as administrator (and which are not in the path ?program files? but in Contacts\Documents of the current user). To be precise, the user launching my tcl/tk program can?t find