similar to: Problem installing Biobase on Solaris

Hi Everybody, I am having a problem with loading Biobase package. I typed 2 lines below at R prompt > source ("http://boconductor.org/biocLite.R") > biocLite (lib="/usr/local/lib/R/library") which attempted to install a bunch of packages with varying degree of success. Out of 29, 13 failed. Biobase is one of them. As a matter of fact, when I looked at logs, most

Hi I am using Rserve for R2.3.1. every time after I load Biobase library, a new Graphics window frame pops up. Could any onw know how can avoid it. Best Saeede class testReserve { public static void main(String[] args) { RServeConnection rsCon = null; Rconnection c = null; Process proc = null; try { Runtime rt = Runtime.getRuntime(); proc

Hi, Recently I try to install Biobase component using the tutorials from cran.r-project.org/doc/Rnews/Rnews_2006-5.pdf I tried u <- "http://bioconductor.org/biocLite.R" > source(u) > biocLite("pkgDepTools", dependencies=TRUE) Running biocinstall version 2.0.8 with R version 2.5.1 Your version of R requires version 2.0 of Bioconductor. Warning in

Hello, I wanted to install MergeMaid package in v 2.2.1. I could install it but couldn't use without its dependant, Biobase. at biobase installation, I got the following error message In method for function "split": expanding the signature to include omitted arguments in definition: drop = "missing" Error in .MakeSignature(new("signature"), def, signature) :

Hello experts, I would like consult you some questions regarding RFE 6334757 and CR 6322205 (disk write cache). ========================================== RFE 6334757 disk write cache should be enabled and should have a tool to switch it on and off CR 6322205 Enable disk write cache if ZFS owns the disk ========================================== The cu found on SPARC Enterprise T5140,

Does anyone know about this device? SESX3Y11Z 32 GB 2.5-Inch SATA Solid State Drive with Marlin Bracket for Sun SPARC Enterprise T5120, T5220, T5140 and T5240 Servers, RoHS-6 Compliant This is from Sun''s catalog for the T5120 server. Would this work well as a separate ZIL device for ZFS? Is there any way I could use this in a T2000 server? The brackets appear to be

We are trying to setup a Windows server that will allow any of our users to build a binary R package given a source package. The idea is to have a central R installation and allow users to install packages to their own package library for the purposes of binary package building. It seems, however, that write access to $R_HOME is required as part of the install step even when -l is used to

Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns:

Neither biocLite nor the GUI menus can install packages on my system. Here is relevant output: > version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 11.1 year 2010 month 05 day 31 svn rev 52157 language R version.string R version 2.11.1 (2010-05-31) > source("http://bioconductor.org/biocLite.R") BioC_mirror =

I''m moving some data off an old machine to something reasonably new. Normally, the new machine performs better, but I have one case just now where the new system is terribly slow. Old machine - V880 (Solaris 8) with SVM raid-5: # ptime du -kds foo 15043722 foo real 6.955 user 0.964 sys 5.492 And now the new machine - T5140 (latest Solaris 10) with ZFS

I've been having problems building vignettes in bioconductor packages with R-devel. Turns out that Rdevel/share/texmf/hyperref.cfg wants Blue and Red predefined, when only blue and red are defined (as of rsync Rdevel, Sept 10th). This is on a Debian unstable system (Sept 9th version). Might not apply to all other tetex systems. Seems to have bitten the bioconductor build system, though.

Full_Name: Colin A. Smith Version: 1.8.0 OS: Mac OS X 10.2.6 Submission from: (NULL) (216.102.90.18) Both Biobase and my package annaffy use S4 classes to define methods for "[". Both packages use the save image method of installation. (See annaffy 1.0.3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: >

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

Hi, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")

On 10/11/2006 2:48 PM, Seth Falcon wrote: > Hi, > > Reading help("Documentation"), I'm led to believe that a help call > like: > > ?myFun(x, sqrt(wt)) > > Will search for help on the appropriate method in the case that myFun > is generic. This isn't working for me. Here is an example using the > Biobase package: > > ## If Biobase is

I'm seeing weird issues in methods initialization, i.e. loading marrayClasses loads Biobase, and when explicitly done, as in library(Biobase) library(marrayClasses) is fine, but when Biobase is loaded via a require statement in marrayClasses' .First.Lib, I end up with: Warning message: In the method signature for function "coerce", class "exprSet" has no

Hi there, I am a bioinformatician working in DFCI. I am new to R. Yesterday I installed the R-1.7.1 to my Linux (since I am not able to find R-1.8 on the webpage). But I have some package installation problems ... 1. install.packages2() function isn't available. If I type at R prompt: >install.packages2("Biobase") Error: couldn't find function

If I try to build a package with a vignette R CMD build Biobase I see * checking for file 'Biobase/DESCRIPTION' ... OK * preparing 'Biobase': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to re-build vignettes * creating vignettes ... OK * cleaning src Error in setwd(pkgname) : cannot change working directory Execution halted This is

I am having trouble with the library function of R Version 1.5.0 for Mac OS X Carbon when I try to load libraries that did not come with the R installation. For example, I put the Biobase library from bioconductor.org in the 'library' folder. R cannot find it, even though it can find the pre-installed libraries: > library() # this lists standard libraries such as 'boot',

Dear ALL I want to load "HTSanalyzeR", It 's necessary to load "igraph" package. This time I see this error: library(igraph) library(HTSanalyzeR) Loading required package: GSEABase Loading required package: Biobase Error: package 'Biobase' is not installed for 'arch=i386' > I 'll be glade if you help me [[alternative HTML version deleted]]