similar to: Adding .R to source file keeps R from reading it?

I am updating the Bioconductor package, LMGene. Thus I am modifying someone else's package, editing or writing new documentation, etc. When I modify the man files in LMGene and install the library, it doesn't change the 'help' that R gives you. The 'help' you actually get in R is the same as before. I haven't been able to find an explanation in "Writing R

Full_Name: Guy W. Tillinghast Version: 2.8.0 OS: Windows XP professional Submission from: (NULL) (24.248.24.3) I am encountering difficulty asking R to manipulate the correct columns in Expression Set class (object 4). I download the ALL data with: library(golubEsets) data(Golub_Merge) Note, the data has the samples not in order. This is not R's fault (at least not that I can tell): >

Hi list, Here is an example: ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library? ??? * installing *source* package ?CoreGx? ... ??? ** using staged installation ??? ** R ??? ** data ??? *** moving datasets to lazyload DB ??? ** inst ??? ** byte-compile and prepare package for lazy loading ??? Error : in method for

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

>>>>> Herv? Pag?s >>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes: > Hi list, > Here is an example: > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing > ??? hpages at XPS15:~$ R CMD INSTALL CoreGx > ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?

Hi, After updating R-2.12 on the Bioconductor build system about 1 week ago (we update R every 4-6 weeks for our devel builds), we've started to see something never seen before on Windows: for some BioC packages, 'R CMD build' would produce no output at all (0 byte) and, of course, no source tarball. Even though, the code returned by the command is 0! See an example of this is here:

Dear all, My gRbase package imports functionality from the bioconductor packages graph, Rgraphviz and RBGL. To make installation of gRbase easy, I would like to have these bioconductor packages installed in connection with installation of gRbase, but to do so the user must use setRepositories() to make sure that R also installs packages from bioconductor. Having to call setRepositories causes

Hello, This question popped up on the bioc-devel list, I'm forwarding it here. I know that sources for R-2.14 alpha can be found here: http://cran.r-project.org/src/base-prerelease/ But the OP (below) is asking about Windows binaries. Dan ---------- Forwarded message ---------- From: Stefan McKinnon H?j-Edwards <Stefan.Hoj-Edwards at agrsci.dk> Date: 2011/10/4 Subject: Re:

Dear folks, Please welcome a newbie both to R and the mailing list :). I am currently working on a sequencing project, and heard about R as well as some of its packages for next gen sequencing, and decided to give it a try. Starting with ShortRead, I found a document (http://www.bioconductor.org/packages/2.5/bioc/vignettes/ShortRead/inst/doc/ShortRead_and_HilbertVis.pdf) which does mention

Dear all, When running R CMD check on Windows XP to test my package I get the following warning message: "* checking line endings in C/C++/Fortran sources/headers ... WARNING Found the following sources/headers with CR or CRLF line endings: src/xpsDict.h" The problem is that this file is created by the compiler AUTOMATICALLY during the compilation process, and since the file is

Dear all, i was working under R 1.6.2 but i wanted to install bioconductor under WinXP, and because R 1.7.1 contains the TclTk package and automatic installation of bioconductor packages, so i install it. Everything is fine except this message which appear after the installation of packages. "> local({a<- CRAN.packages(CRAN=getOption("BIOC")) +

Hola, buenas tardes, Hace unos dias que intento cargar unos datos de microarrays del ncbi con versión de R 2.15.2 de 32 bits en windows xp. he utilizado el siguiente codigo: library(Biobase) library(GEOquery) library(limma) gset <- getGEO("GSE6536", GSEMatrix =TRUE) Al hacerlo me da este error: "Error in function (type, msg, asError = TRUE) : couldn't connect to

Hi, I get an error indicating a missing library from the package 'Ruuid'. I suppose this means I should install RGtk. I just thought I'd document the error. Maybe a dependency entry is missing? R 2.9.0 OS X 10.5.8 Thanks, - chris > biocLite('Ruuid') Using R version 2.9.0, biocinstall version 2.4.12. Installing Bioconductor version 2.4 packages: [1] "Ruuid"

Hi all, I am using the package ChIPpeakAnno, and I have a problem with the function getAllPeakSequence. This is related to object oriented programming I think, I have the following message: > peaksWithSequences <- getAllPeakSequence(peakList, upstream = 100, > downstream = 100, genome = Hsapiens) Error in validObject(.Object) : invalid class "GRanges" object: superclass

Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name ("FileName" instead of "Filename") which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers

Hi R users: I got the following message when I use the pixmap library on R 1.7.0 over w2K platform (on R 1.6.2 it runs right). pixmapGrey(matrix(c(0,1),128,128)) Error in .class1(object) : Object "from" not found I download the library .zip file from: http://cran.r-project.org/bin/windows/contrib/1.7/pixmap_0.3-2.zip Other question: When I try to "Install package(s) from

A post on the Bioconductor mailing list https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html suggests that install.packages now references .Rprofile (?), whereas in R-2-8 it did not. Is this intentional? The example is, in .Rprofile library(utils) install.packages("Biobase", repos="http://bioconductor.org/packages/2.4/bioc") then

I currently set the Bioconductor repository in my .Rprofile using this code (which needs editing for every version number change of Bioconductor): # Choose repositories repos <- structure(c(CRAN="http://streaming.stat.iastate.edu/CRAN", CRANextra="http://www.stats.ox.ac.uk/pub/RWin",

The warnings from make.packages.html() on the Apple Mac OS X platform can be dealt with as follows: ------------------------------------------------ (1) make.packages.html() uses the function tempdir() and attempts to create a temporary directory in the default location /tmp/ which fails due to the /tmp directory architecture on the Mac. I set up a .Renviron file in my user account

That might be worth thinking about generally, but it would still be nice to have the base generics pre-defined, so that people are not copy and pasting the definitions everywhere, hoping that they stay consistent. On Wed, Mar 26, 2014 at 6:13 AM, Gabriel Becker <gmbecker@ucdavis.edu>wrote: > Perhaps a patch to R such that generics don't clobber each-other's method > tables