similar to: How to make an <pkg>/configure file executable on Windows/NTFS?

Hello, I believe I have found a bug in the R INSTALL script (src/scripts/INSTALL.in). The problem comes up when a user tries to specify more than one "--config-args" (or, I imagine, "--config-vars") on the R CMD INSTALL line. In such a case, no error message is generated, but the first specification is silently overwritten by the second specification. The process therefore

I don't know if this is the correct forum to ask the following question; however, when I search the aroma.affymetrix discussion group, it suggested that I should posted the question to r-help. Here it goes. I followed the instructions on aroma.affymetrix trying to install the packages; following are the steps: > install.packages(c("R.oo", "R.utils"),

During installation of a package, Makevars/Makefile in src/ is processed. I've always considered the purpose of this for compiling native code. Is that it's solely purpose, or is it alright to use it also for non-code compilation purposes, e.g. building inst/ subdirectories on the fly? If not, are there other means to create non-static inst/ subdirectories during installation? The

If it was any other environment than the global, you could use substitute: e <- new.env() delayedAssign("foo", stop("Hey!"), assign.env = e) substitute(foo, e) delayedAssign("foo", stop("Hey!")) substitute(foo) Hadley On Mon, Jan 26, 2015 at 12:53 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote: > Hi, I got an interesting programming

Hi, I got an interesting programming challenge: How do you inspect an object which is assigned via delayedAssign() and that throws an error as soon as it is "touched" (=the value is evaluated)? Is it possible? MINIMAL EXAMPLE: $ R --vanilla > delayedAssign("foo", stop("Hey!")) (If you find this minimal example silly/obvious, please skip down to the real

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@biostatsun1

Hi, sessionInfo() has been proven really useful, but you still often have to ask for additional information in order to help troubleshooting. For instance, for troubleshooting the aroma.affymetrix, it is very helpful to know what the current working directory is, for other packages certain system environment variables might be useful and so on. One solution could be to provide support for hook

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hi, I'm trying to remove/delete a directory usingR. I've tried the following with no success: % Rterm --vanilla > getwd() [1] "C:/Documents and Settings/hb/braju.com.R/aroma.affymetrix/test" > dir.create("foo") > file.info("foo") size isdir mode mtime ctime atime foo 0 TRUE 777 2007-02-28 14:52:10

So apparently (being a linux novice) I didn't realize it was insufficient to simply have the file marked as executable. It turns out the default TMP directory on my machine is mounted with a noexec flag so no files in that directory are allowed to be executed. The solution is to set an environment variable TMPDIR=some new directory I created (eg. /home/myusername/tmp) Then R uses that

I had the same thought in the shower this morning but I was disappointed to find that SElinux was disabled on the system. My next step will be to install a previous version of R on the system. My problem is that I am planning a shiny server installation and at least half of the apps on the current system depend on these libraries that will not install. -- W. Michael Conklin EVP Marketing &

Duncan Murdoch writes: > On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. > > I don't know what is causing this bug. Perhaps a Linux user can

Hi All, It seems that the question of how may people use (or download) R, and it's packages is one that comes up on a fairly regular basis in a variety of forums (There was also recent thread on the subject on Stack Overflow). A couple of students at UCLA (including myself), wanted to address the issue, so we set up a system to get and parse the cran.stat.ucla.edu APACHE logs every night, and

On Mon, Jan 26, 2015 at 12:24 PM, Hadley Wickham <h.wickham at gmail.com> wrote: > If it was any other environment than the global, you could use substitute: > > e <- new.env() > delayedAssign("foo", stop("Hey!"), assign.env = e) > substitute(foo, e) > > delayedAssign("foo", stop("Hey!")) > substitute(foo) Hmm... interesting

On 22/06/2017 5:02 PM, Conklin, Mike (GfK) wrote: > I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. I don't know what is causing this bug. Perhaps a Linux user can reproduce it and fix it. Here's what I see:

I am using debug on the .install_packages function...stepping through. Once the temporary folder is created and the tar file expanded I run file_test and get a FALSE back indicating that the configure file is not executable. [1] "/tmp/RtmpMM6iC1/R.INSTALLc5ca415e4310/stringi" Browse[2]> dir(new) [1] "DESCRIPTION" "INSTALL" "LICENSE"

Hello, I wonder if it is unwise to name a bundle the same as one of its packages. For instance, I now have a huge package called 'aroma' that I basically want to split up in several smaller packages, say 'aroma.core', 'aroma.io', 'aroma.explore', 'aroma.trial', 'aroma.deprecated' etc, which simplifies maintenance but also the overview. For

This patch makes it possible do module installs in this way: $ R INSTALL --with-hdf5=/packages . Is there a better/conventional way to do this kind of thing that I'm not seeing? diff -c -r1.29 INSTALL.in *** src/scripts/INSTALL.in 2000/01/24 19:48:48 1.29 --- src/scripts/INSTALL.in 2000/01/26 01:26:11 *************** *** 107,112 **** --- 107,116 ---- lib=${2}; shift ;;

On 22/06/2017 3:42 PM, Conklin, Mike (GfK) wrote: > Not much progress..... I step through debug and it gets to the do.install() function which immediately errors with the same "configuration not executable" error. I believe that is a locally defined function, which means you can set a breakpoint within it but only if R is compiled with source info, or you can manually call

Hi, I'm trying to write a function in C for implementation with .Call. When compiling using R CMD SHLIB characters seem to be added to the function name. Here's the complete C code from the file summariseMCMC.c: #include<R.h> #include<Rdefines.h> #include<Rinternals.h> void summariseMCMC(SEXP data) { PROTECT(data=AS_NUMERIC(data)); UNPROTECT(1); } Then