similar to: R CMD check: unknown option ?--outdir==RCHECK?

For 'R CMD check', it appears that option '--outdir' is not recognized and generates warning "unknown option '--outdir'". R CMD check --help says: Usage: R CMD check [options] pkgs [...] Options: [...] -o, --outdir=DIR directory used for logfiles, R output, etc. (default is 'pkg.Rcheck' in current directory,

Dear R devel I am experiencing a problem using R CMD check. I tried to specify the argument outdir, but get every time the error message: Warning: unknown option ‘--outdir==RCHECK’ This happens both on R 2.15.2 Linux, as well as R 3.0.1 Windows, with latest Rtools. Is it just that I am not passing the argument the right way, or is there an issue with R CMD check? I tried to write the argument

I installed R on my Windows laptop in C:\Program Files\R\R-2.15.2 and am able to open RGUI (640bit), see packages and run commands. However, when I test the installation and run the basic tests and all the tests on the standard and recommended packages i.e.: library("tools") testInstalledBasic("both") testInstalledPackages("base", errorsAreFatal

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Hi, another Rd related issue I encountered is that if an error occurs in an \Sexpr in an Rd file, then on get the following error: * checking for portable compilation flags in Makevars ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted

Hi again, following my previous post on RCurl, I cannot install Rcpp either: g++ -m32 -I/home/renaud/bin/R/2.15/lib64/R/include -I/home/renaud/bin/R/2.15/lib64/R/include/i386 -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c r_cast.cpp -o r_cast.o g++ -m32 -shared -L/usr/local/lib64 -o Rcpp.so Date.o DateVector.o Datetime.o DatetimeVector.o Dimension.o DottedPair.o

Hi again, following my previous post on RCurl, I cannot install Rcpp either: g++ -m32 -I/home/renaud/bin/R/2.15/lib64/R/include -I/home/renaud/bin/R/2.15/lib64/R/include/i386 -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c r_cast.cpp -o r_cast.o g++ -m32 -shared -L/usr/local/lib64 -o Rcpp.so Date.o DateVector.o Datetime.o DatetimeVector.o Dimension.o DottedPair.o

Hi, when I run R CMD check with flag --as-cran, the process hangs at stage: * checking CRAN incoming feasibility ... I am pretty sure it is a proxy issue. I looked at the check code in the tools package and it seems that the issue is in the local function `.repository_db()` (defined in `tools:::.check_package_CRAN_incoming()`), which eventually calls `url()` with argument

Hi, running install.packages() to install a package from a local repository (i.e., starts with file:///) appears to delete the PACKAGES file that is in the src/contrib/ directory. This happens on a cluster running Scientific Linux release 6.4 (Carbon), but not on my Ubuntu local machine. Subsequent calls to install.packages() complain about src/contrib/PACKAGES not existing, although there still

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, I have a set of user defined package which I have installed in 2.8.1 for quite some time. I installed 2.11.0 and 2.11.1 a couple of days ago while still having 2.8.1 version in my system. For the package, package.skeleton works fine in R 2.11. However, it comes problem when I run Rcmd check/intall. The intall.out shows below. I further tested that I reran R-2.8.1/bin/R CMD check in

Full_Name: Enrico Pegoraro Version: 2.7.2 OS: Windows (Vista or Xp PRO) Italian Submission from: (NULL) (87.4.189.202) If you send these lines of code: outdir="c:/pippo" file.path(outdir,"pluto.html") R replies correctly: [1] "c:/pippo/pluto.html" But if you change the first steps to: outdir="" file.path(outdir,"pluto.html") R replies

Hi, in R 2.12.1, R CMD check hangs when building a vignette that uses a foreach loop with the doMC parallel backend. This does not happen in R 2.13.1, nor if I use doSEQ instead of doMC. All versions of multicore, doMC and foreach are the same on both my R installations. Has anybody encountered a similar issue? Thank you. Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the

Hello! I want to detect some environment on a remote host (in C program, getenv()), but it is failed. Here is a little program which I try to run on a remote host with command: "#ssh myhost myecho" /* myecho */ #include <stdio.h> main (){ char *dir; if ((dir = getenv("MYDIR")) != NULL) printf ("environment is %s\n",dir);

Hi, all, I'm looking a utility for removing a directory from within R. Currently, I'm using: foo <- function(...) { mydir <- tempdir() dir.create(mydir, showWarnings = FALSE, recursive = TRUE) on.exit(system(sprintf("rm -rf %s", mydir))) ## do some stuff in "mydir" invisible() } However, this is assumes "rm" is available. I know of

Hi, I am trying to use "read.pnm" from the package "pixmap" to read more than 10 thousand image files in "mydir". > file.list <- dir( "mydir", full=T) > for( i in 1:length(file.list) ) { print(i) x <- read.pnm(file.list[i]) } In the beginning it was fine. But after reading 1020 images or so, the read.pnm function seems to crash on

Hi, suppose you have two versions of the same algorithm: one in pure R, the other one in C/C++ called via .Call(). Assuming there is no bug in the implementations (i.e. they both do the same thing), is there any well known reason why the C/C++ implementation could return numerical results non identical to the one obtained from the pure R code? (e.g. could it be rounding errors? please

Hi, Basically, I want to preserve some of directories on destination side conditionally and hence, I choose to use --filter option mentioned in rsync man pages. I noticed that --filter option works as expected when I don't have --relative option used but in below case it doesn't work. rsync -avz --relative --delete --filter='H /mydir2' --exclude='- /preserve' mydir1/.

Hello I am using Sweave to generate some pdf reports using R on a Windows platform and would like to control the output directory that the generated .tex file goes to. Basically I use the following commands in a batch file: set outdir=c:/output/1234 Rscript -e Sweave('C:/pathpathpath/script.Rnw') Which produces script.tex Sweave has the option of specifying an output directory for

Hi All, This might be simple question, I need to retrive data for modelling from the databases. Eveytime date values changes so I countnot fix date value in the code, it is required to pass as parameter. When I pass the date as parameter, it throws error. (ERROR: column "start_dt" does not exist Position: 285) My script is as below, please guide me where am I going wrong? All parameters