similar to: Buglet in install.packages warning message

In the context of installing a Bioconductor package using our biocLite() function, install.packages() warns > install.packages("RUVSeq", repos="http://bioconductor.org/packages/2.14/bioc") Installing package into '/home/mtmorgan/R/x86_64-unknown-linux-gnu-library/3.1-2.14' (as 'lib' is unspecified) Warning message: package 'RUVSeq' is not available

Hello all, I've had the following apropos alternative in my ~/.Rprofile for some time, and have found it more useful than the current version. Basically, my version ignores case when searching. If others find this useful, perhaps apropos could be suitably patched (and I'd be willing to create such a patch). + seth Here is my version of apropos: APROPOS <- function (what, where =

Dear all, Is there a reason, why there is no +-operator for aes (i.e. uneval) objects (as there is for themes and gg objects)? I had a couple of cases where such an operator would be useful, for instance to combine the result of aes and aes_string in functions. Any flaws with the following proposition: `+.uneval` <- function(e1, e2) { dup <- names(e1) %in% names(e2) if (any(dup)) {

Dear all, Sometimes I have the situation where a function takes a data.frame and an additional argument describing come columns. For greater flexibility I want to allow for either column names or column indices. What I usually do then is something like the following: -------------8<------------- f <- function(datf, cols) { nc <- seq_along(datf) cn <- colnames(datf) colOK <-

Dear all, Maybe, I am doing something wrong, but using R-2.5.0 on my Intel-Mac, I have problems using function callNextMethod() in method initialize. I am loading the following code as file "testS4.R": setClass("baseClass", representation(myname = "character", mydir = "character", "VIRTUAL"),

Hi, install.packages() seems to be broken in latest R-devel snapshot (2010-07-19 r52561) if you are using an R/R.version$platform-library/x.y directory. > .libPaths() [1] "/home/hpages/R/x86_64-unknown-linux-gnu-library/2.12" [2] "/home/hpages/R-2.12/library" > install.packages("car") Error in sprintf(gettext(fmt, domain = domain), ...) : too

I've noticed that install.packages() [https://svn.r-project.org/R/trunk/src/library/utils/R/packages.R] and update.packages() [https://svn.r-project.org/R/trunk/src/library/utils/R/packages2.R] sometimes output to stdout and sometimes to stderr. It looks like stderr is used (e.g. via cat()) when the message is part of querying the user, e.g. update.packages <- function(lib.loc = NULL,

I'm writing SQL queries, and it's very handy to be able to use sQuote for string parameter values. It makes me wish that I could use an sQuote-like function for enclosing column names and other identifiers in backticks, i.e., select `foo` from `table`. Obviously I can do this with paste(), I'm just asking for syntactic sugar. Oh, a buglet: the sQuote help page, See Also section, the

Norm, thanks for the help. Applying the fix solves the issue I mentioned but now I have more issues. I can install clang, but when running I cannot compile and link files. If I compile with -c flag it works but compiling the following x.c file gives an error: x.c: int main(void) { return 0; } > ./clang x.c /project/helder/scratch/packages2/bin/ld: unrecognized option '-C'

I'm looking for ideas for creating high-quality plots for use in projected presentations (powerpoint, etc) --- ideally high-quality png, jpg, bmp. The graphics produced using the postscript device look very good. Those generated with win.graph(), png are plagued by the jaggy lines. So far, the only way I can use the postscript plots in my presentations is using separate screen capture

Hi, namespaceImportFrom in base/R/namespace.R has the following: fdef <- methods:::getGeneric(genName, impenv) The definition of getGeneric is in methods/R/RMethodUtils.R starts with: getGeneric <- ## return the definition of the function named f as a generic. ## ## If there is no definition, throws an error or returns ## NULL according to the value of

Hi, in R-3.0 I get the following error when calling lsfit with more observations than variables, which seems to come from an error in the formatting of the error message (note that this was not happening in 2.15.3): > nobs <- 5; nvar <- 6; lsfit(matrix(runif(nobs*nvar), ncol=nvar), runif(nobs), intercept=FALSE) Error in sprintf(ngettext(nry, "%d response", "%d

Git is a source code management system like CVS, svn, arch, and others. It would be nice to add exclude support to R CMD build and INSTALL so that the .git subdir of an R package is handled appropriately. Here is a possible patch: diff --git a/src/scripts/INSTALL.in b/src/scripts/INSTALL.in index 75da9db..09e5ab5 100644 --- a/src/scripts/INSTALL.in +++ b/src/scripts/INSTALL.in @@ -863,7

Hi all, One of the things I find most problematic in R is the partial matching of names in lists. Robert and I have discussed this and we believe that having a mechanism that does not do partial matching would be of significant benefit to R programmers. To that end, I have written a patch that modifies the behavior of "[[" as follows: 1. [[ gains an 'exact' argument with

Hi there, I am a bioinformatician working in DFCI. I am new to R. Yesterday I installed the R-1.7.1 to my Linux (since I am not able to find R-1.8 on the webpage). But I have some package installation problems ... 1. install.packages2() function isn't available. If I type at R prompt: >install.packages2("Biobase") Error: couldn't find function

I think there are some missing words in "R Internals"'s description of the P_ macro. It currently has "A macro as a wrapper for ngettext", which I think ought to be something like "The macro P_ may be used as a wrapper for ngettext". The following patch also makes the 2 alternate definitions of P_ have the same argument names, StringS and StringP. Expanding the

Hi, Is there an alternative to type2char that is available for use in package code? It would be useful for producing more informative error messages. + seth

A short overview of the problem: Automatic domain in ngettext() does not work when used inside a package. How to test: 1. Download the small test package "minimal_1.0-0.tar.gz" attached to the bug report. 2. As the package contains Finnish translations, start R with Finnish language settings. Prepending "LANGUAGE=fi " to the command line that starts R works for me on Linux, if

Regarding the following code, warning(sprintf(ngettext(has.errors, "scheduled core %s encountered error in user code, all values of the job will be affected", "scheduled cores %s encountered errors in user code, all values of the jobs will be affected"), paste(has.errors, collapse = ", ")), domain = NA) has.errors is a vector whose elements are the

Hi, I have a S3 package with namespace called "myS3Pkg". Inside my package I would like to create a S4 class which extends (adds 2 slots) another S4 class from some other package. The class should be created in "myPkg" environment (and not global environment). Using: setClass("myS4class", representation("otherS4class", mydata = "numeric"),