similar to: Problem on running update

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

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

>>>>> Martin Morgan <mtmorgan at fredhutch.org> >>>>> on Mon, 11 May 2015 10:18:07 -0700 writes: > On 05/10/2015 08:19 AM, Martin Morgan wrote: >> Loading an S4 object from a file without first loading the library sometimes (?, >> the example below and actual example involves a virtual base class and the show >> generic)

Hello, I have a problem with read.affy.mixed function. I want to read in together a set of CEL files from chip types Affymettrix HGU133A_2 and HGU133_Plus_2. I have my files to be read in in one directory together with a white space delimited file describing them (covdesc). In this directory I give a command: > merge <- read.affy.mixed() Error in merged[[i]] : subscript out of

Hi Martin, It is really a 'PATH' problem. After adding C:\Program Files\Graphviz2.20\bin to the 'PATH' environment variable, the Rgraphviz package can be loaded without any error messages. Sorry that I ONLY set my 'PATH' environment variable correctly for R but not for Graphviz. Thank you and Duncan so much for your great help. Howard On Tue Mar 30 18:12:54

Hi Martin, Indeed it does (and I should have confirmed myself with R-patched and R-devel before posting...) Thanks, and sorry for the noise. Kevin On Tue, Aug 25, 2015, 13:11 Martin Morgan <mtmorgan at fredhutch.org> wrote: > On 08/25/2015 12:54 PM, Kevin Ushey wrote: > > Hi all, > > > > The following fails for me (on OS X, although I imagine it's the same >

as.factor / as.ordered is not written as a generic. This differs from as.numeric, as.matrix, and other as.*. The following seems to address this and does not break make check-all. FWIW, the patch is against r55563, because with r55564 I see /home/mtmorgan/src/R-devel/src/main/dounzip.c:75:15: error: storage size of ?dt? isn?t known /home/mtmorgan/src/R-devel/src/main/dounzip.c:88:5: warning:

To test two environments for object equality (Lisp EQ), I can use 'identity': > e1 <- environment(local(function()x)) > e2 <- environment(local(function()x)) > identical(e1,e2) # compares object identity [1] FALSE > identical(as.list(e1),as.list(e2)) # compares values as name->value mapping [1] TRUE # (is there a

Dear list I am running some simulations in R involving reading in several hundred datasets, performing some statistics and outputting those statistics to file. I have noticed that it seems that the time it takes to process of a dataset (or, say, a set of 100 datasets) seems to take longer as the simulation progresses. Has anyone else noticed this? I am curious to know if this has to do with how R

Hi, from the man page ?methods, I expected to be able to build pairs (class,package) for a given S3 method, e.g., print, using attr(methods(print), 'info'). However all the methods, except the ones defined in base or S4 methods, get the 'from' value "registered S3method for print", instead of the actual package name (see below for the first rows). Is this normal

invoking parLapply without a cluster fails to find a previously registered cluster > library(parallel) > setDefaultCluster(makePSOCKcluster(2)) > parLapply(X=1:2, fun=function(...) {}) Error in cut.default(i, breaks) : invalid number of intervals This is because in parLapply length(cl) is determined before defaultCluster(cl) is called. By inspection, this appears to be true of

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

With C:\Users\User>R --version R version 2.14.0 RC (2011-10-23 r57410) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-mingw32/x64 (64-bit) running download.file('http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/E-TABM-25.raw.1.zip', tempfile()) sometimes gets 52% (according to the dialog box) of the way through, and then

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" PkgA promotes 'unique' to a generic and exports that DESCRIPTION: Imports: methods R/f.R: setGeneric("unique") NAMESPACE: export(unique) and PkgB creates and exports a method on unique DESCRIPTION Imports: methods, PkgA R/f.R: setClass("B",

Hi, I'm subsetting a named vector using character indices. My vector of indices (or keys) is 10x longer than the vector I'm subsetting. All my keys are distinct and only 10% of them are valid (i.e. match a name of the vector being subsetted). It is surprisingly slow: x1 <- 1:1000 names(x1) <- paste("a", x1, sep="") keys <- sample(c(names(x1),

This bug appears intermittently in R CMD check when reference classes have finalize methods. The problem is that garbage collection can be run after the methods package is no longer available. It affects (periodically) the Bioconductor AnnotationDbi package as well as packages that contain Rcpp classes. To reproduce: library(methods) a = setRefClass("A",

Hi, Today we've seen the following problem with the R-2.12 that we use for our Windows builds: > installed.packages() Error: subscript out of bounds After some investigation we discovered that the cause of this failure was that 1 of the 890 packages currently installed on the machine (Windows Server 2003 R2) had its DESCRIPTION file empty:

Hi everybody! I'm creating an object of a S4 class that has two slots: ListExamples, which is a list, and idx, which is an integer (as the code below). Then, I read a data.frame file with 10000 (ten thousands) of lines and 10 columns, do some pre-processing and, basically, I store each line as an element of a list in the slot ListExamples of the S4 object. However, many operations after this

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

In fact, this does reproduce on R-devel: > options(download.file.method = "libcurl") > options(repos = c(CRAN = "https://cran.rstudio.com/", CRANextra = + "http://www.stats.ox.ac.uk/pub/RWin")) > install.packages("lattice") ## could be any package Installing package into ?/Users/kevinushey/Library/R/3.3/library? (as ?lib? is