similar to: objects masked from packages

Hello everybody, I'm trying to install a package I have built. This package contains three scripts with various functions (S3 as well as S4 classes) I run at first the package.skeleton command with: > package.skeleton("affyAnalysis", namespace=TRUE, code_files =c("defS3.R", "defS4.R", "qc.R")) affyAnalysis is the name of the supposed package and

hi all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o

Dear developers, nearly not worth mentioning, but anyway: there is a tiny typo in a german translation file (in src/library/tools/po/R-de.po: 'erzuege' instead off 'erzeuge'). The attached (if it passes the filters...) patch (for revision 51109) should correct this. Thanks, Martin -- Dr. Martin Becker Statistics and Econometrics Saarland University Campus C3 1, Room 206

Wenn man ihn mal braucht ist er tot. folgende Fehlermeldung ereilt mich seit heute beim starten des R Commander auf dem Mac: > library(Rcmdr) Lade n?tiges Paket: car Lade n?tiges Paket: MASS Lade n?tiges Paket: nnet Error : .onAttach in attachNamespace() f?r 'Rcmdr' fehlgeschlagen, Details: ? Aufruf: structure(.External(.C_dotTclObjv, objv), class = "tclObj") ? Fehler: [tcl]

Hi I'm running the latest R on a presumably up to date Linux server. 'Doing something silly I'm sure, but can't see why my saved PLMset objects come out all wrong. To use an example: Setting up an example PLMset (I have the same problem no matter what example I use) > library(affyPLM) > data(Dilution) # affybatch object > Dilution = updateObject(Dilution)

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 =

Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb

Hi, I am using R and tried to normalize the data within each sample group using RMA. When I tried to import the all the normalized expression data as a single text file and make a boxplot, it showed discrepancy among the sample groups. I tried to scale them or re-normalize them again, so that it can be used for further analysis. Unfortunately, I did not manage it on using AffyPLM package. Would

Dear Sirs, I am using both the Bioconductor adds on (Affy, AffyPLM,...) and the 'standard' R-package. I am trying to select a list of genes which all have expression values below a certain threshold. I have done this by creating a vector which has 0s where the expression is greater than the threshold and 1s where it is less than or equal to it. Multiplying this vector by the expression

Hi, I am trying to install Bioconductor onto R version 2.7.0 for Windows. I installed R, then followed the instructions on http://www.bioconductor.org/download, which state that you should type the following: source("http://bioconductor.org/biocLite.R") biocLite() When I do that, I get the following error: Running biocinstall version 2.2.9 with R version 2.7.0 Your version of R

When I try to load the DCluster package I get the following error message (R 2.5.1; PowerBook G4; Mac OS X 10.4.10) (Load needed package) Lade nötiges Paket: spdep (error: package spdep could not been loaded) Fehler: Paket 'spdep' konnte nicht geladen werden (additional warning message) Zusätzlich: Warning message: (There is no package spdep in:.....) es gibt kein Paket 'spdep'

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 all. I'm having a little trouble with the  function "texteval" (session package). I have used "texteval" in the construction of the function "ExpandData1". "ExpandData1" does not work as expected. However, when I run only the inside code of "ExpandData1" I get the right result. Apparently "texteval" is not working when used

Hi, I know this question has been asked before but I have not seen an answer pertaining to repeated measures anovas. I got a simple data set with two factors: block (3 levels) and prime (2 levels). The dataset (expData) are stuctured so one column (block) states which block a trial is in and one column (prime) states which prime was used in the trial, another column (RT) states reation time for

Hi everyone, I am having installation problems, but this is how it all started: I had some errors running the bioconductor package affyPLM that uses LAPACK/Blas > Pset <- fitPLM(Data) Background correcting PM Normalizing PM Fitting models /usr/local/lib/R/bin/exec/R: relocation error: /usr/local/lib/R/lib/libRlapack.so: undefined symbol: s_copy # thrown out of R .... I was using R

Dear R-list, I have a partly comma separated partly underscore separated string that I am trying to parse into R. Furthermore I have a bunch of them, and they are quite long. I have now spent most of my Sunday trying to figure this out and thought I would try the list to see if someone here would be able to get me started. My data structure looks like this, (in a example.txt file) Subject

Hi all, I downloaded and installed JGR. Then when I tried to load the package in R console, it generated the following error message: > local({pkg <- select.list(sort(.packages(all.available = TRUE))) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) Loading required package: rJava using Java Runtime version 1.5.0 using JAVA_HOME = C:\Program Files\Java\jre1.5.0_01 Loading required

I calculate an anova test in the following way: expdata<-read.table("/home/dorien/UA/meta-music/optimuse/optimuse1-build-desktop/results/results_processedCP", header=TRUE)

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

Hello there, I’m computing the total value of an order from the price of the order items using a “for” loop and the “ifelse” function. I do this on a large dataframe (close to 1m lines). The computation of this function is painfully slow: in 1min only about 90 rows are calculated. The computation time taken for a given number of rows increases with the size of the dataset, see the example with