[Rd] Fwd: warning or error upon type/storage mode coercion?

2010-09-15 Thread Karl Forner
-- Forwarded message -- From: Karl Forner karl.for...@gmail.com Date: Wed, Sep 15, 2010 at 10:14 AM Subject: Re: [Rd] warning or error upon type/storage mode coercion? To: Stefan Evert stefa...@collocations.de I'm a Perl fan, and I really really miss the use strict feature. IMHO

Re: [Rd] value returned by by()

2010-09-15 Thread Uwe Ligges
On 14.09.2010 20:50, Seb wrote: On Tue, 14 Sep 2010 12:02:04 +0200, Uwe Liggeslig...@statistik.tu-dortmund.de wrote: It returns a list with athe class attribut set to by, just use: x- by(.) unclass(x) Thanks Uwe, however, that still returns an array when using the data.frame method

Re: [Rd] Suggestion: Add DESCRIPTION 'Date' to R CMD check log header

2010-09-15 Thread Kurt Hornik
Martin Maechler writes: Hi Henrik HB == Henrik Bengtsson h...@stat.berkeley.edu on Tue, 14 Sep 2010 18:26:31 -0700 writes: HB Hi, HB in R CMD check, the version of the package being checked is reported, e.g. HB Thu Sep 9 05:02:30 2010: Checking package R.utils (SVN revision 399) ... HB

[Rd] list2env( list() )

2010-09-15 Thread Romain Francois
Hello, list2env generates an error on empty lists. l - list() list2env( l ) Erreur dans list2env(l) : names(x) must be valid character(length(x)). This is consistent with the requirement that the list must be a __named__ list, so this works: names(l) - character(0) list2env( l )

Re: [Rd] value returned by by()

2010-09-15 Thread peter dalgaard
On Sep 15, 2010, at 10:55 , Uwe Ligges wrote: On 14.09.2010 20:50, Seb wrote: On Tue, 14 Sep 2010 12:02:04 +0200, Uwe Liggeslig...@statistik.tu-dortmund.de wrote: It returns a list with athe class attribut set to by, just use: x- by(.) unclass(x) Thanks Uwe, however, that

Re: [Rd] value returned by by()

2010-09-15 Thread Seb
On Wed, 15 Sep 2010 11:29:23 +0200, peter dalgaard pda...@gmail.com wrote: On Sep 15, 2010, at 10:55 , Uwe Ligges wrote: On 14.09.2010 20:50, Seb wrote: On Tue, 14 Sep 2010 12:02:04 +0200, Uwe Liggeslig...@statistik.tu-dortmund.de wrote: It returns a list with athe class

Re: [Rd] S3 method for package listed in suggest/enhance

2010-09-15 Thread Uwe Ligges
On 01.09.2010 17:38, Hadley Wickham wrote: Hi all, The profr package provides a method for displaying its output with ggplot: ggplot.print. You don't need this ggplot2 to use profr, so ggplot2 is listed under enhances in the DESCRIPTION file. If I have just S3method(ggplot, profr) in my

Re: [Rd] value returned by by()

2010-09-15 Thread Uwe Ligges
On 15.09.2010 15:00, Seb wrote: On Wed, 15 Sep 2010 11:29:23 +0200, peter dalgaardpda...@gmail.com wrote: On Sep 15, 2010, at 10:55 , Uwe Ligges wrote: On 14.09.2010 20:50, Seb wrote: On Tue, 14 Sep 2010 12:02:04 +0200, Uwe Liggeslig...@statistik.tu-dortmund.de wrote: It returns a

Re: [Rd] a small suggestion for improving the building of packages

2010-09-15 Thread Uwe Ligges
On 29.08.2010 22:34, Kyle Matoba wrote: All, I just finished the process of build a package for the first time and found it characteristically (for R) very straightforward and well documented. Whenever I deal with open source software I always endeavor to finish the task I have in mind, and

Re: [Rd] value returned by by()

2010-09-15 Thread Seb
On Wed, 15 Sep 2010 15:15:27 +0200, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Why? It is still accessible as a list, even with S4 object, at least for the cases I tried. R wL - with(warpbreaks, by(warpbreaks[, 1:2], tension, summary)) R setClass(Whatever, +

[Rd] Roxygen: question regarding 'use.Rd2' and creation of DESCRIPTION

2010-09-15 Thread Janko Thyson
Dear List, I ran into the following two problems while using the package 'roxygen': QUESTION 1 I split the relevant R-Code for my package into the following scripts: classes.R (S4), functions.R ('standard' functions), generics.R (S4), methods.R (S4). Function package.skeleton() generates

Re: [Rd] a small suggestion for improving the building of packages

2010-09-15 Thread Liaw, Andy
From: Uwe Ligges On 29.08.2010 22:34, Kyle Matoba wrote: All, I just finished the process of build a package for the first time and found it characteristically (for R) very straightforward and well documented. Whenever I deal with open source software I always endeavor to

Re: [Rd] a small suggestion for improving the building of packages

2010-09-15 Thread peter dalgaard
On Sep 15, 2010, at 17:01 , Liaw, Andy wrote: Or else it may be possible to have some malicious person write a script that automagically generate some large number of bogus packages and submit them to CRAN... Andy Douglas Adams - - There is a theory which states that if ever

Re: [Rd] a small suggestion for improving the building of packages

2010-09-15 Thread Kyle Matoba
Uwe, Yes, this makes good sense. All I am saying is that it is somewhat out of the open-source, the user is smart and we should not _artificially force_ him or her to jump through some hoop. I do not contend that packages destined for CRAN should have anything but the fullest documentation

Re: [Rd] a small suggestion for improving the building of packages

2010-09-15 Thread Marc Schwartz
On Sep 15, 2010, at 10:14 AM, peter dalgaard wrote: On Sep 15, 2010, at 17:01 , Liaw, Andy wrote: Or else it may be possible to have some malicious person write a script that automagically generate some large number of bogus packages and submit them to CRAN... Andy Douglas

Re: [Rd] a small suggestion for improving the building of packages

2010-09-15 Thread Kyle Matoba
Yes, well, anyone clever enough to do this will not be stopped by automatically manipulating some text to fill in the minimal documentation necessary to pass checks. On Wed, Sep 15, 2010 at 8:01 AM, Liaw, Andy andy_l...@merck.com wrote: From: Uwe Ligges On 29.08.2010 22:34, Kyle Matoba

Re: [Rd] Suggestion: Add DESCRIPTION 'Date' to R CMD check log header

2010-09-15 Thread Hervé Pagès
On 09/15/2010 01:55 AM, Kurt Hornik wrote: Martin Maechler writes: Hi Henrik HB == Henrik Bengtssonh...@stat.berkeley.edu on Tue, 14 Sep 2010 18:26:31 -0700 writes: HB Hi, HB in R CMD check, the version of the package being checked is reported, e.g. HB Thu Sep 9 05:02:30 2010:

Re: [Rd] Best way to manage configuration for openMP support

2010-09-15 Thread Karl Forner
Thanks a lot, I have implemented the configure stuff and it works perfectly !! Exactly what I was looking for. I just added AC_PREREQ([2.62]) because the AC_OPENMP was only supported from this version, and AC_MSG_WARN([NO OpenMP support detected. You should should use gcc = 4.2 !!!]) when no

Re: [Rd] Problem with WARNING...headers with CRLF line endings

2010-09-15 Thread cstrato
Dear Duncan, dear Herve, Thank you both for your help and suggestions. I think that you are both right: In principle I do not want to put these files in the source tarball (and I did not in the past), however because of the way R CMD check works this seems to be the only possibility to get

Re: [Rd] Problem with WARNING...headers with CRLF line endings

2010-09-15 Thread Dirk Eddelbuettel
On 15 September 2010 at 22:39, cstrato wrote: | Dear Duncan, dear Herve, | | Thank you both for your help and suggestions. I think that you are both | right: | | In principle I do not want to put these files in the source tarball (and | I did not in the past), however because of the way R CMD

Re: [Rd] Problem with WARNING...headers with CRLF line endings

2010-09-15 Thread cstrato
Dear Dirk, Thank you for this suggestion, however since I am not very good in creating Makefiles I would appreciate if you could explain how to filter at the compile stage. These are the lines which I think are essential: xps.dll: $(MYOBJ) $(LINK) /dll /def:xps.def /out:xps.dll fp10.obj

Re: [Rd] Problem with WARNING...headers with CRLF line endings

2010-09-15 Thread Hervé Pagès
On 09/15/2010 01:51 PM, Dirk Eddelbuettel wrote: On 15 September 2010 at 22:39, cstrato wrote: | Dear Duncan, dear Herve, | | Thank you both for your help and suggestions. I think that you are both | right: | | In principle I do not want to put these files in the source tarball (and | I did not

Re: [Rd] R CMD build cannot create vignettes on Windows if Makefile is used

2010-09-15 Thread Hervé Pagès
Oops, sorry for the noise but after looking at today's BioC build/check results, I realize the problem is still here. At least for some of the 8 packages that had an 'R CMD build' timeout because of the Sweave.sty file not being found. I just happened to run 'R CMD build' by hands yesterday on a

[Rd] running 'make' failed during vignette creation ('R CMD build') on Windows

2010-09-15 Thread Hervé Pagès
Hi, This is a follow-up to the problem reported here: https://stat.ethz.ch/pipermail/r-devel/2010-September/058460.html After I updated R-2.12 to 2010-09-13 r52905 on the Bioc build system, some of the packages that have a Makefile in pkg/inst/doc still don't build on Windows. For example,

Re: [Rd] More strange R CMD build/check errors on Windows

2010-09-15 Thread Hervé Pagès
On 09/14/2010 11:23 AM, Hervé Pagès wrote: Hi Uwe, On 09/14/2010 04:49 AM, Uwe Ligges wrote: ... Brian had some ideas that the problems are related to the shell that is used. Is the problem still apparent in a very recent R-devel from few days ago? I am just back from vacations and have not

[Rd] R-forge: Web server down / no space left

2010-09-15 Thread Henrik Bengtsson
FYI and for the R-forge maintainers information: Trying to access http://r-forge.r-project.org/ at this very moment gives: An error occured in the logger. ERROR: could not extend relation 1663/19060/19983: No space left on device HINT: Check free disk space. /Henrik

Re: [Rd] R-forge: Web server down / no space left

2010-09-15 Thread Dario Strbenac
I tried it now and it works. It might have been something momentary. Original message Date: Wed, 15 Sep 2010 19:14:37 -0700 From: r-devel-boun...@r-project.org (on behalf of Henrik Bengtsson h...@stat.berkeley.edu) Subject: [Rd] R-forge: Web server down / no space left To: R-devel

[Rd] Lack of consistent cross-platform behaviour of tools:::buildVignettes()

2010-09-15 Thread Hervé Pagès
Hi, On both Unix and Windows there is a mechanism to add variables to the environment when R is started. I noticed that, on Unix, this mechanism is not used when R is started normally at the command line but only when it's started using the 'R CMD' syntax. One problem with this is some lack of