similar to: Add .git to SCM excludes for build and INSTALL scripts

Hi all, I'm trying to build from source on Linux and getting the following error when it tries to build the help for 'nlme': <snip> ranef.lme text html latex example reStruct text html latex example /home/sfalcon/sw/R-related/R-1.8.1/bin/INSTALL: line 1: 8133 Segmentation fault ${R_CMD} perl

Hi, I use rsync 3.0.2 for daily incremental backups: rsync -aAzHRxby -f '. -' --numeric-ids --delete-during --delete-excluded \ --suffix='' --backup-dir=$BACKUP_ROOT/$BACKUP_HOST/${TODAY} \ ${DESTINATION}$BACKUP_ROOT/$BACKUP_HOST/current <<< $EXCLUDE_PATTERNS Sometimes I add a new item to $EXCLUDE_PATTERNS but then the excluded files are backed up in

I'm in the process of packaging R (and R modules) for future inclusion in Fedora Extras, and I've managed to get several hundred modules installed without issue, however, the GO metadata package is refusing to comply. Since I'm packaging this in rpm format, I can't use any of the automated functions for build, I've got to do it locally through R. The following steps work for

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

I've been experimenting with install.packages and it's new ability to track down dependencies from a list of repositories and encountered this: install.packages(c("foo", "bar"), repos="http://cran.r-project.org", dependencies=c("Depends", "Suggests")) dependencies 'foo' are not availabledependencies 'bar'

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

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 =

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, 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

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"),

Hi, On Windows, package files in the inst/ subdir are installed after the lazyload creation. This differs from Linux where inst/ is installed _before_ lazyload creation. Since packages may need data in inst, I think the order on Windows should be changed. Perhaps like this: diff --git a/src/gnuwin32/MakePkg b/src/gnuwin32/MakePkg index 57af321..868e8f1 100644 --- a/src/gnuwin32/MakePkg +++

Hi, Using latest R 2.5.0 Patched, I'm unable to install the Matrix package from cran.fhcrc.org. I get: Creating a new generic function for "isSymmetric" in "Matrix" Creating a new generic function for "unname" in "Matrix" Error in conformMethod(signature, mnames, fnames, f) : In method for function "!": formal arguments omitted in

Hi all, The write_PACKAGES function has a 'fields' argument that allows a user generating a PACKAGES file to specify additional fields to include. For symmetry, it would be nice for the available.packages function to be able to read those extra fields when specified. Similarly, it would be useful for installed.packages to have a 'fields' argument. This would allow a user to

Hi all, The dict package provides a dictionary (hashtable) data structure much like R's built-in environment objects, but with the following differences: - The Dict class can be subclassed. - Four different hashing functions are implemented and the user can specify which to use when creating an instance. I'm sending this here as opposed to R-packages because this package will

Full_Name: Ben Goodrich Version: 2.6.1 OS: Debian Submission from: (NULL) (128.103.222.166) bzr is another version control system and adds a .bzr folder to the top-level directory of a package, similar to .svn and .git for subversion and git respectively. However, while R CMD build removes directories called .svn, .git, and some others, it does not remove .bzr . As a result, the .bzr folder is

Hi, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")

Having used JUnit and PyUnit, I was pleased to see the release of the RUnit package on CRAN. I'm wondering if there are any RUnit users out there that would be willing to share some tips on how they organize their code to work with RUnit. Specifically, I'm wondering about the best way to load/import/source the functions to be tested. I would like to end up with a script, testall or some

promptClass fails to identify methods associated with the class. Here is a fix: Index: promptClass.R =================================================================== --- promptClass.R (revision 41719) +++ promptClass.R (working copy) @@ -165,7 +165,7 @@ if (nmeths > 0) { .meths.body <- " \\describe{" for (i in 1:nmeths) { - .sigmat

I'm having problems getting R CMD check to work correctly on Windows 7 (64 bit) in a package that uses C code. What I want to do is to be able to pass the equivalent of the "--force-biarch" option to check, but this is only supported for INSTALL. Background: I'm writing a package (RNetica) which forms a link between R and a third-party library (Netica.dll). The vendor supplies

I'm having problems getting R CMD check to work correctly on Windows 7 (64 bit) in a package that uses C code. What I want to do is to be able to pass the equivalent of the "--force-biarch" option to check, but this is only supported for INSTALL. Background: I'm writing a package (RNetica) which forms a link between R and a third-party library (Netica.dll). The vendor supplies