similar to: R 2.13.0 on Windows: R CMD check and '"du"' not found

Hello, I wonder if it is unwise to name a bundle the same as one of its packages. For instance, I now have a huge package called 'aroma' that I basically want to split up in several smaller packages, say 'aroma.core', 'aroma.io', 'aroma.explore', 'aroma.trial', 'aroma.deprecated' etc, which simplifies maintenance but also the overview. For

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"),

Hi, I have found an unwanted feature in the Rd to LaTeX convertion regarding \preformatted inside a \section. I have created an Rd example below, which generates an error in the following 'R CMD check' step * creating aroma.affine-manual.tex ... OK * checking aroma.affine-manual.tex ... ERROR LaTeX errors when creating DVI version. This typically indicates Rd problems. I believe

Hi, I'm trying to write a function in C for implementation with .Call. When compiling using R CMD SHLIB characters seem to be added to the function name. Here's the complete C code from the file summariseMCMC.c: #include<R.h> #include<Rdefines.h> #include<Rinternals.h> void summariseMCMC(SEXP data) { PROTECT(data=AS_NUMERIC(data)); UNPROTECT(1); } Then

Hi. Is it possible to make gpr from raw? library(aroma) #read gpr file gpr <- GenePixData$read("gpr123.gpr", path=aroma$dataPath) # gpr -> raw raw <- as.RawData(gpr) # raw -> ma ma <- getSignal(raw, bgSubtract=FALSE) ma.norm <- clone(ma) #normalization normalizeWithinSlide(ma.norm, "s") #ma -> raw raw2 <- as.RawData(ma) I want to make gpr data from

During installation of a package, Makevars/Makefile in src/ is processed. I've always considered the purpose of this for compiling native code. Is that it's solely purpose, or is it alright to use it also for non-code compilation purposes, e.g. building inst/ subdirectories on the fly? If not, are there other means to create non-static inst/ subdirectories during installation? The

Dear list, in R under wheezy the following error occurs: > library(cairoDevice) > Cairo() Error in Cairo() : Graphics API version mismatch It seems to be Debian-specific, as I tried the same under OpenSUSE 11.3 and it worked. I tried installing cairoDevice via `apt-get install r-cran-cairodevice' and with `install.packages("cairoDevice")' in R (without any

Hi, I got an interesting programming challenge: How do you inspect an object which is assigned via delayedAssign() and that throws an error as soon as it is "touched" (=the value is evaluated)? Is it possible? MINIMAL EXAMPLE: $ R --vanilla > delayedAssign("foo", stop("Hey!")) (If you find this minimal example silly/obvious, please skip down to the real

Hi All, I am trying to compile R 2.13.0 r53834 on 64-bit Windows 7 (home premium) using Rtools212.exe from Duncan Murdoch's site. I (think) I followed the installation guide for Windows. When installing Rtools, made sure I was installing 64-bit tools (including tcltk), etc. I created a copy of MkRules.local where I selected 64 bit instead of 32 architecture. When I run:

Hi All, It seems that the question of how may people use (or download) R, and it's packages is one that comes up on a fairly regular basis in a variety of forums (There was also recent thread on the subject on Stack Overflow). A couple of students at UCLA (including myself), wanted to address the issue, so we set up a system to get and parse the cran.stat.ucla.edu APACHE logs every night, and

Hello, I've been having some trouble working with the aroma package and have realized that it's my ebimage is at the root of the problem. The package builds but during testing it fails because of an undefined symbol as seen below: installing to /usr/local/lib64/R/library/EBImage/libs ** R ** inst ** preparing package for lazy loading ** help *** installing help indices **

waited for the aroma of burnt electronics. There wasn't any so I went to the next room and plugged in a telephone on the wall outlet. I picked up the handset and it rang my asterisk box. I dont have any phone service. The phone is working fine and have used it for hours listening to podcasts. And I can plug it to any phone in the house. Now I am thinking if I can plug another phone

Hi, sessionInfo() has been proven really useful, but you still often have to ask for additional information in order to help troubleshooting. For instance, for troubleshooting the aroma.affymetrix, it is very helpful to know what the current working directory is, for other packages certain system environment variables might be useful and so on. One solution could be to provide support for hook

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hi, Apologies if this is the wrong list to be sending this question to. I am trying to install a copy of the R tools required to create / compile packages on windows. After downloading Rtools from http://www.murdoch-sutherland.com/Rtools/ windows keeps complaining that "The setup files are corrupted". This has happened with both the Rtools213.exe and the Rtools212.exe downloads, and

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@biostatsun1

Hi, I'm trying to remove/delete a directory usingR. I've tried the following with no success: % Rterm --vanilla > getwd() [1] "C:/Documents and Settings/hb/braju.com.R/aroma.affymetrix/test" > dir.create("foo") > file.info("foo") size isdir mode mtime ctime atime foo 0 TRUE 777 2007-02-28 14:52:10

Hello, I've got a DESCRIPTION file with a the first line: Package: Repitools But, when I run R CMD INSTALL Repitools I get: * installing *source* package Repitools ... ** R ** data ** inst ** preparing package for lazy loading Warning in FUN(X[[1L]], ...) : Created a package name, "2011-04-20 09:05:40", when none found ** help *** installing help indices ** building package

Dear developers, I am a maintainer of the CORElearn package which uses OpenMP multithreading to speed up some computations. When producing a new release we tested the package with the latest R 2.12.0. On Linux the package works normally. On Windows we installed a recommended version of Rtools (Rtools212) but the linker fails with the messages below. ... g++

Everyone is back at work and starting to use computers on our smallest network which has Internet access through a rather old Linksys router.? Two systems were left on and screen-locked over the extra long weekend.? There does not appear to have been any Internet access interruption in our absence. A Firefox browser on one system was left pointing to a commonly used web site: