Re: [Rd] scan() doesn't like '1.#IND'

2012-02-08 Thread Dan Tenenbaum
2012/2/8 Duncan Murdoch : > On 12-02-08 8:59 PM, Hervé Pagès wrote: >> >> Hi, >> >> Since C++ code compiled with g++ 4.6.3 on Windows (the version included >> in latest Rtools) now can produce things like '1.#IND' when writing >> doubles to a file (using the<<  operator), I wonder whether scan() >>

Re: [Rd] scan() doesn't like '1.#IND'

2012-02-08 Thread Duncan Murdoch
On 12-02-08 8:59 PM, Hervé Pagès wrote: Hi, Since C++ code compiled with g++ 4.6.3 on Windows (the version included in latest Rtools) now can produce things like '1.#IND' when writing doubles to a file (using the<< operator), I wonder whether scan() shouldn't support those things. Right now (wi

[Rd] scan() doesn't like '1.#IND'

2012-02-08 Thread Hervé Pagès
Hi, Since C++ code compiled with g++ 4.6.3 on Windows (the version included in latest Rtools) now can produce things like '1.#IND' when writing doubles to a file (using the << operator), I wonder whether scan() shouldn't support those things. Right now (with recent R devel and latest Rtools) we g

Re: [Rd] capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame

2012-02-08 Thread Hervé Pagès
Thanks Martin. H. On 02/08/2012 12:55 AM, Martin Maechler wrote: Martin Morgan on Tue, 7 Feb 2012 19:31:41 -0800 writes: > On 02/07/2012 04:08 PM, Hervé Pagès wrote: >> Hi, >> >> This is what I get with recent R devel on a 64-bit Ubuntu laptop: >> >> >

[Rd] R devel: R CMD build now sources ~/.Rprofile

2012-02-08 Thread Henrik Bengtsson
I've just noticed that with a recent R devel on Windows, R CMD build sources ~/.Rprofile, e.g. > RCMD build Running ~/.Rprofile > R CMD build Running ~/.Rprofile FYI R --no-init-file & R --vanilla still avoid this. > sessionInfo() R Under development (unstable) (2012-02-08 r58297) Platform: x86

Re: [Rd] FORTRAN compilation error

2012-02-08 Thread Simon Urbanek
On Feb 8, 2012, at 3:16 PM, David L Lorenz wrote: > I get an error when trying to compile a FORTRAN source file for use in a > package that I am developing. The error, reported in 00install.out is > below. > > * installing *source* package 'USGSstats' ... > ** libs > > *** arch - i386 > C:/PR

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread Simon Urbanek
On Feb 8, 2012, at 5:31 PM, Roebuck,Paul L wrote: > What would be involved in modifying rJava's .jpackage() method > to search in both locations ('java' and/or 'jars') for JAR files > to be added to the CLASSPATH on JVM initialization? > Well, it wouldn't take much but I don't like that idea. Th

Re: [Rd] RFC: Proposal to make NROW() and NCOL() slightly more general

2012-02-08 Thread Hervé Pagès
Hi Martin, On 02/07/2012 08:32 AM, Martin Maechler wrote: Martin Maechler on Mon, 6 Feb 2012 15:35:36 +0100 writes: >> On Sat, Feb 4, 2012 at 10:38 AM, Martin Maechler >>wrote: >> > The help has >> > >> >> Description: >> > >> >> 'nrow' a

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread Roebuck,Paul L
What would be involved in modifying rJava's .jpackage() method to search in both locations ('java' and/or 'jars') for JAR files to be added to the CLASSPATH on JVM initialization? On 2/8/12 4:12 PM, "William Dunlap" wrote: > We don't "mandate" a given JDK (including the compiler, > javac), but

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread William Dunlap
We don't "mandate" a given JDK (including the compiler, javac), but we do supply the JRE. We do require that the java compiler be able to produce code that the JRE accepts (we test-run javac with a variety of common version-type flags to try to find one that works with our JRE). It is source:pkg/

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread Simon Urbanek
Unfortunately we cannot mandate JDK so packages have to use the build stage for compilation so the S+ model doesn't work. I think java is more consistent than src/java -> jars Sent from my iPhone On Feb 8, 2012, at 3:27 PM, William Dunlap wrote: > For what it is worth, the S+ package system u

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Hadley Wickham
> It's hard to provide a reproducible example because it depends on > exactly what package you have installed where, but I had hoped that > this would at least illustrate my problem - R CMD install doesn't seem > to be respecting R_LIBS.  I'm trying to understand whether this is a > bug, or somethi

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread William Dunlap
For what it is worth, the S+ package system uses the java directory in source packages to store java source code (under pkg/java/src/, using the usual directory structure that follows the class structure under there), prebuilt jar files (in pkg/java/prebuiltjars, no subdirectories), and a Makevars

[Rd] FORTRAN compilation error

2012-02-08 Thread David L Lorenz
I get an error when trying to compile a FORTRAN source file for use in a package that I am developing. The error, reported in 00install.out is below. * installing *source* package 'USGSstats' ... ** libs *** arch - i386 C:/PROGRA~1/R/R-214~1.1/etc/i386/Makeconf:194: warning: overriding recipe

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Hadley Wickham
2012/2/8 Uwe Ligges : > > > On 08.02.2012 19:36, Hadley Wickham wrote: >>> >>> I wonder it works that far. It won't for me on Windows nor Linux, because >>> system2 passes the whole thing shQuoted to the shell. Hence it is highly >>> shell dependent what happens with the ill formed command. >> >> >

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Dirk Eddelbuettel
On 8 February 2012 at 20:05, Uwe Ligges wrote: | Anyway, this won't work under a Windows shell, I believe. At least, I do | not know how to set an env variable and run RCMD INSTALL in a Windows | shell as a one liner - independent of R. FWIW this issue was addressed by Oleg years ago in cfuncti

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Uwe Ligges
On 08.02.2012 19:36, Hadley Wickham wrote: I wonder it works that far. It won't for me on Windows nor Linux, because system2 passes the whole thing shQuoted to the shell. Hence it is highly shell dependent what happens with the ill formed command. Well I was using the env argument to system2,

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Dirk Eddelbuettel
On 8 February 2012 at 19:26, Uwe Ligges wrote: | | | On 07.02.2012 19:13, Hadley Wickham wrote: | > Hi all, | > | > Am I using the correct syntax to set a custom R_LIBS when running R | > CMD INSTALL from the command line? | > | > I get: | > | > R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rap

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Hadley Wickham
> I wonder it works that far. It won't for me on Windows nor Linux, because > system2 passes the whole thing shQuoted to the shell. Hence it is highly > shell dependent what happens with the ill formed command. Well I was using the env argument to system2, which claims to be cross-platform (at lea

Re: [Rd] Using custom R_LIBS with R CMD install

2012-02-08 Thread Uwe Ligges
On 07.02.2012 19:13, Hadley Wickham wrote: Hi all, Am I using the correct syntax to set a custom R_LIBS when running R CMD INSTALL from the command line? I get: R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-08e68ca/ # Desktop : R_LIBS=/Users/hadley/R-dev R CMD INSTALL aL3xa-rapport-

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread Roebuck,Paul L
On 2/7/12 5:37 PM, "Simon Urbanek" wrote: > On Feb 7, 2012, at 4:34 PM, Roebuck,Paul L wrote: > >> We have an R package which needs to include a JAR file. >> Is there a canonical directory for it? > > rJava defines "java" for that purpose (see ?.jpackage). > How canonical that is may be open fo

Re: [Rd] Canonical package directory name for JAR files?

2012-02-08 Thread Kevin R. Coombes
It may not (yet) be canonical, but it is (a) easy to remember and (b) likely to be recognized easily by someone looking at the structure. On 2/7/2012 5:37 PM, Simon Urbanek wrote: On Feb 7, 2012, at 4:34 PM, Roebuck,Paul L wrote: We have an R package which needs to include a JAR file. Is ther

Re: [Rd] Options for keeping files when package re-install or update.

2012-02-08 Thread Uwe Ligges
User defined files are not touched if you update a package *unless* you put it into the directory structure of the package, where a user defined file is not intended to be ... Uwe On 08.02.2012 01:02, 전희원 wrote: Hi! All I want to keep some file which user defined when re-installing or updat

[Rd] Options for keeping files when package re-install or update.

2012-02-08 Thread 전희원
Hi! All I want to keep some file which user defined when re-installing or updating package. Is there any way to do? Thanks. --Heewon-- [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/list

[Rd] Error in data.frame(srcfile = NA_character_ ...) using R CMD check

2012-02-08 Thread Joris Meys
Hi all, I'm running into an error when using R CMD check on a package I inherited and I'm now trying to clean up. There are known issues with the Rd files (they definitely need to get updated) resulting in a couple of warnings, but the error occurs before check reaches the Rd files. Below is a sni

Re: [Rd] capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame

2012-02-08 Thread Martin Maechler
> Martin Morgan > on Tue, 7 Feb 2012 19:31:41 -0800 writes: > On 02/07/2012 04:08 PM, Hervé Pagès wrote: >> Hi, >> >> This is what I get with recent R devel on a 64-bit Ubuntu laptop: >> >> > mydf <- data.frame(a=1:2080, b=1001:2040, c=letters, d=LETTERS,