similar to: Could not install aroma.affymetrix

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

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 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

Hi, Gordon Smyth brought the following problem to my attention. PROBLEM/"BUG": Using R v1.9.0 alpha for Windows and the latest Rtools from Brian Ripley you get the following problem trying to R CMD build a package (or a bundle); >R CMD build R.basic * checking for file 'R.basic/DESCRIPTION' ... OK * preparing 'R.basic': * checking whether 'INDEX' is

Full_Name: Henrik Bengtsson Version: rw1022 OS: Windows Me Submission from: (NULL) (216.175.126.55) When ${R_HOME}/share/perl/maketitle.pl tries to generate a TITLE that is longer than $lc-3 (=13) characters long, it repeats the package name on line two. Example: Now it generates an output like: com.braju.graphics com.braju.graphics Bla bla bla... But, I believe it should

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

I tried different versions of sma**.tar.gz file either with "R CMD INSTALL -l packagepath sma**.tar.gz", "R INSTALL -l path sma**.tar.gz" and under R windows by "install.packages("sma_0.5.15.tar.gz",repos=NULL)" . I got same error ====== * installing *source* package 'sma' ... ** Creating default NAMESPACE file Warning in .write_description(db,

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

FYI, I'm sure the following is a temporary issue, but in case it slips through, I want to raise it here. On Windows 7 64-bit, running Rcmd check on R devel gives: * using R version 2.13.0 Under development (unstable) (2011-02-11 r54330) * using platform: x86_64-pc-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'aroma.core/DESCRIPTION' ... OK * this is

Hi, I've got a version of rowMedians(x, na.rm=FALSE) for matrices that handles missing values implemented in C. It has been optimized for memory and speed. To avoid coercing integers to doubles, and hence allocate an additional 200% memory, there is one C function for integers and one for doubles. The rowMedians() implementation is currently sitting in my non-CRAN package R.native

Full_Name: Henrik Bengtsson Version: 1.3.0 OS: Windows Me Submission from: (NULL) (216.175.122.171) I realized that the title of packages in the library index when they are in a bundle is the title of the bundle and not the package. It looks like the TITLE file, which apparently is used for generating the library index, takes the value of the bundle's title and not the package's title.

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

I am looking for an online (easily accessible) form of the samples of genetic data for those with cancer and those without cancer. Can anyone direct me in the right place? Thanks, Jim [[alternative HTML version deleted]]

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

Full_Name: Henrik Bengtsson Version: 1.5.1 OS: WinMe Submission from: (NULL) (217.210.0.243) In the Perl script $R_HOME/bin/check there is a bug under the section "Check R code for syntax errors" where the 'Rfiles <- c(...)' is build up. If there are too many files in @Rfiles the source code line generated will be too long and weird things will happen, e.g. strange

Does anyone know if it is possible to add a dictionary file of known words that becomes part of the *built* package to tell 'R CMD check --as-cran' not to report these words as misspelled. I want this dictionary to come with the *.tar.gz such that it will be available regardless where the package is checked. For instance, currently I get: * using log directory

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

To reply to Yves Gauvreau question (Jan 24, 2001) about how to set values within function, it is possible to do without without using the "<<-" assignment operator or other nasty tricks. I had the same problem and I did a nasty workaround two weeks ago implementing the functionality of reference variables, but today I "ran into" the [R] help page for ".Alias".

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 **