Re: [Rd] update.packages(1)

2010-03-27 Thread Duncan Murdoch
to put something first. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] update.packages(1)

2010-03-27 Thread Duncan Murdoch
On 27/03/2010 4:48 PM, Seth Falcon wrote: On 3/27/10 1:43 PM, Duncan Murdoch wrote: On 25/03/2010 3:16 PM, Arni Magnusson wrote: I'm relaying a question from my institute's sysadmin: Would it be possible to modify update.packages() and related functions so that 'lib.loc' accepts integer

Re: [Rd] Setting up TortoiseSVN and PuTTY on Windows for r-forge.r-project.org (Was: Re: Using SVN + SSH on windows)

2010-03-28 Thread Duncan Murdoch
. Duncan Murdoch 2. Double click on the Pageant tray icon to open the 'Pageant Key List' window. 3. Click 'Add Key'. Locate the *ppk file saved by PuTTYgen, e.g. 'henrikb,20100328.ppk'. Open it. 4. In the 'Pageant Key List' window, the key should now be listed, e.g. ssh-rsa 1024 ... rsa-key

Re: [Rd] .Call and .C arguments

2010-03-29 Thread Duncan Murdoch
are different? See FAQ 7.31. Duncan Murdoch Is there a way to pass the arguments differently? I'm using Windows and Visual Studio C++ 2005 Express Edition and R-2.10.1. Please see the two simple examples to understand the issue. # C call from R .C(myroundC,as.double(1204.245)) // C Code

[Rd] RSS feeds now link to bug reports

2010-04-01 Thread Duncan Murdoch
in place. For example, see the item under 2.11.0 BUG FIXES in http://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2010/04/01#n2010-04-01 Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Difference Linux / Windows

2010-04-01 Thread Duncan Murdoch
files that only exist on a subset of the platforms. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] inject html code into Rd file

2010-04-02 Thread Duncan Murdoch
On 02/04/2010 7:13 AM, Romain Francois wrote: Le 02/04/10 13:07, Duncan Murdoch a écrit : On 02/04/2010 6:17 AM, Romain Francois wrote: Hello, I'm trying to inject html code into an Rd file. For example : \name{test} \alias{test} \title{test} \description{ \if{html}{ \Sexpr[stage=render

Re: [Rd] inject html code into Rd file

2010-04-02 Thread Duncan Murdoch
On 02/04/2010 8:06 AM, Duncan Murdoch wrote: On 02/04/2010 7:13 AM, Romain Francois wrote: Le 02/04/10 13:07, Duncan Murdoch a écrit : On 02/04/2010 6:17 AM, Romain Francois wrote: Hello, I'm trying to inject html code into an Rd file. For example : \name{test} \alias{test} \title{test

Re: [Rd] full copy on assignment?

2010-04-03 Thread Duncan Murdoch
in multiple places; one is around line 488 of subassign.c another is around line 1336. In each of these places copies are made in some circumstances, but not in general. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Rd] R CMD check tells me 'no visible binding for global variable ', what does it mean?

2010-04-12 Thread Duncan Murdoch
) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] tiny typo in ?prop.test: if for is

2010-04-19 Thread Duncan Murdoch
, respectively, as specified by \code{alternative}. A confidence interval for the underlying proportion with confidence level as specified by Thanks, I've fixed it. Duncan Murdoch [[alternative HTML version deleted]] __ R-devel@r

Re: [Rd] Rtools for building 64 bit windows packages

2010-04-22 Thread Duncan Murdoch
the compilers. You need the MinGW 64 bit versions of the compilers; they are not nicely packaged yet, but the instructions for finding them are in the new version of the R-admin manual, in the section 3.3, Building R for 64 bit Windows. Duncan Murdoch * If not, is there an officially

Re: [Rd] Question of R CMD check

2010-04-23 Thread Duncan Murdoch
()) ###example codes I did not met this problem before. Any ideas on solving this? Thanks a lot. You need to show us the end of the stam-Ex.Rout file. It will contain the error message. Duncan Murdoch __ R-devel@r-project.org mailing list https

Re: [Rd] segfault with format.POSIXct()

2010-04-23 Thread Duncan Murdoch
On 23/04/2010 7:31 AM, Uwe Ligges wrote: Works for me, both under Windows (32 and 64 bit) and Linux, although I have not package slmisc attached. I've just found that the bug 14267 is related to a POSIXlt formatting bug, so this is likely to be the same thing. Duncan Murdoch Uwe Ligges

Re: [Rd] segfault with format.POSIXct()

2010-04-23 Thread Duncan Murdoch
construct of defining a variable sized array within a block, and that was fine, because it was released at the end of the block, not at the end of the function call. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Rd] Question of R CMD check

2010-04-23 Thread Duncan Murdoch
Is it? If not, I'd like to see the package; could you send me a copy? If it is, then something in one of your examples is messing with it. Do you have any calls to rm() or remove() in your examples? Duncan Murdoch 2010/4/23 Duncan Murdoch murdoch.dun...@gmail.com On 21/04/2010 9:48 PM, rusers.sh

Re: [Rd] S4 Inheritance of environments

2010-04-25 Thread Duncan Murdoch
in the way you're using it is to put it in a container. For S4, that could mean using an environment as a slot, or inheriting from an object like list(e), rather than directly from e. Duncan Murdoch Creating S4 classes containing environments exhibits unexpected behavior/features. These have

Re: [Rd] serial connection patch

2010-04-27 Thread Duncan Murdoch
indicated a GPL v3 license on the web page. GPL2 is not compatible with GPL3, so that makes your contribution unusable by us. Duncan Murdoch I updated the patch to open with O_NOCTTY to prevent opening the tty as the controlling terminal. Looks like this is default in BSD and GNU but maybe not in OS

Re: [Rd] Most recent R manuals [Was: Likely disruption to R-devel builds on Windows]

2010-04-30 Thread Duncan Murdoch
On 30/04/2010 10:22 AM, hadley wickham wrote: Maybe Duncan could apply the same script that's being used for RNEWS to the manuals? An RSS feed of changes to the manuals would be really useful. My script is very NEWS specific. The manuals would be harder. You could get the diffs from svn

Re: [Rd] Most recent R manuals [Was: Likely disruption to R-devel builds on Windows]

2010-04-30 Thread Duncan Murdoch
On 30/04/2010 10:48 AM, Gabor Grothendieck wrote: On Fri, Apr 30, 2010 at 10:39 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 30/04/2010 10:22 AM, hadley wickham wrote: Maybe Duncan could apply the same script that's being used for RNEWS to the manuals? An RSS feed of changes

Re: [Rd] Most recent R manuals [Was: Likely disruption to R-devel builds on Windows]

2010-04-30 Thread Duncan Murdoch
On 30/04/2010 2:11 PM, Gabor Grothendieck wrote: On Fri, Apr 30, 2010 at 11:01 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 30/04/2010 10:48 AM, Gabor Grothendieck wrote: On Fri, Apr 30, 2010 at 10:39 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: On 30/04/2010 10:22 AM, hadley

Re: [Rd] as.character() crashes R 2.11 on Win2008 x64 and Win7 64

2010-04-30 Thread Duncan Murdoch
), '1970-01-01') y lt;- as.character(x) At this point, Rgui crashes. I get this using both the 32 and 64 bit 2.11.0 R builds. I'd appreciate any suggestions for how to eliminate these crashes (particularly with the x64 version). Use R-patched. Duncan Murdoch Thanks, Nick The windows

Re: [Rd] Possible bug in POSIX classes for R 2.11.0?

2010-05-01 Thread Duncan Murdoch
R-patched? This looks like a bug that was fixed there recently. See https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14267 for details. Duncan Murdoch Lester Wollman Corporate Statistician Symmetricom, Inc. lwoll...@symmetricom.com -Original Message- From: Achim Zeileis

Re: [Rd] split() bug? Inconsistent Windows/Linux behavior.

2010-05-04 Thread Duncan Murdoch
On 04/05/2010 6:45 PM, Matt Shotwell wrote: This is odd, I think it may have something to do with this Yes, it's definitely a bug in interaction() rather than split() per se. I'll take a look and see if I can fix it. Duncan Murdoch f - interaction(list(iris[,1], iris[,2])) f[16

Re: [Rd] split() bug? Inconsistent Windows/Linux behavior.

2010-05-04 Thread Duncan Murdoch
This is now fixed in R-devel (revision 51908), and R-patched (r51909). Thanks Jay for the nice reproducible example, and thanks Matt for localizing it to the interaction() function. Duncan Murdoch On 04/05/2010 4:37 PM, Jay Emerson wrote: I didn't see anything on this in the bug reports

Re: [Rd] Sweave Feature Requests and Questions

2010-05-08 Thread Duncan Murdoch
space is cheap. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] update.packages fails with directory not found

2010-05-10 Thread Duncan Murdoch
a string, so it looks as though you've somehow got a path containing the control characters \P, \R, and \L. Did you set the lib.loc argument when you called update.packages? Duncan Murdoch Indeed, the path is missing, though it was there when I issued the update.packages command. ??? -- Mike

Re: [Rd] update.packages fails with directory not found

2010-05-10 Thread Duncan Murdoch
On 10/05/2010 8:28 AM, Mike Prager wrote: On Mon, 10 May 2010 06:33:54 -0400, Duncan Murdoch murdoch.dun...@gmail.com wrote: Mike Prager wrote: Windows XP. I have just updated to R 2.11.0 and then run update.packages. In the series of updates, a few will succeed, then I get a failure like

Re: [Rd] update.packages fails with directory not found

2010-05-11 Thread Duncan Murdoch
no idea if they are effective. Duncan Murdoch Georgi Boshnakov Univeristy of Manchester -- Message: 1 Date: Mon, 10 May 2010 00:07:50 -0400 From: Mike Prager mike.pra...@mhprager.com To: r-de...@stat.math.ethz.ch Subject

Re: [Rd] update.packages fails with directory not found

2010-05-11 Thread Duncan Murdoch
in R-devel, revision 51980 or later. (A build of this revision should be on CRAN by tomorrow, at http://cran.r-project.org/bin/windows/base/rdevel.html .) Duncan Murdoch On 11/05/2010 7:47 AM, Duncan Murdoch wrote: On 11/05/2010 6:35 AM, Georgi Boshnakov wrote: I posted a similar problem

Re: [Rd] update.packages fails with directory not found

2010-05-11 Thread Duncan Murdoch
On 11/05/2010 6:21 PM, Mike Prager wrote: On Tue, 11 May 2010 11:05:45 -0400, Duncan Murdoch murdoch.dun...@gmail.com wrote: I'd appreciate it if you could check whether the problems remain in R-devel, revision 51980 or later. (A build of this revision should be on CRAN by tomorrow

Re: [Rd] update.packages fails with directory not found

2010-05-12 Thread Duncan Murdoch
On 12/05/2010 12:42 PM, Mike Prager wrote: Shortened a bit further. Answers to queries are at the end. MHP Duncan Murdoch wrote on 5/11/2010 7:03 PM: On 11/05/2010 6:21 PM, Mike Prager wrote: On Tue, 11 May 2010 11:05:45 -0400, Duncan Murdoch murdoch.dun...@gmail.com wrote: I'd appreciate

Re: [Rd] ranges and contiguity checking

2010-05-12 Thread Duncan Murdoch
remember where they came from, only arguments to functions do, and functions that make use of this fact mainly do it for decorating the output (nice labels in plots) or making error messages more intelligible. Duncan Murdoch __ R-devel@r

[Rd] Using Sweave in hostile environments

2010-05-13 Thread Duncan Murdoch
outside the environment and use SaveVerbatim to save it, then just put \BUseVerbatim or \LUseVerbatim in place where I need it. But because I'm using Sweave, I somehow need to redefine the Sinput, Soutput and maybe the Schunk environments to do that, and I don't see how to do so. Duncan Murdoch

Re: [Rd] Using Sweave in hostile environments

2010-05-14 Thread Duncan Murdoch
, and they each need to be used explicitly: you'll probably want to look at the .tex file to figure out the names. This is pretty rough and I won't commit it to R, but I've attached the patch file (against R trunk rev 51988) in case anyone else wants to use it. Duncan Murdoch On 13/05/2010 10:19 AM

Re: [Rd] Restrict access to variables in parent environment

2010-05-14 Thread Duncan Murdoch
(), but it will not be pretty. Remember that everything in R is an object, so you won't have access to the base level objects like +, or mean, or any other function. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [Rd] where is libRmath.a libRmath.so

2010-05-14 Thread Duncan Murdoch
are grammatically correct. If you want to say the manual *is* too terse, then you need to install R 2.11.0. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R in sandbox/jail (long question)

2010-05-18 Thread Duncan Murdoch
not easy. Duncan Murdoch All comments and suggestions are welcomed, thanks, -gordon __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing

Re: [Rd] Is it possible to generate an error when a function is reassigned?

2010-05-23 Thread Duncan Murdoch
an important function you'll still cause local problems, but you may find it easier to fix them. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Indexing bug?

2010-05-26 Thread Duncan Murdoch
)] as.character(x) [1] c b a c results[as.character(x)] cb NAc 45 NA4 Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Indexing bug?

2010-05-26 Thread Duncan Murdoch
Duncan Murdoch wrote: Is this expected behaviour? x - factor(c(c, b, a,c)) results - c(c=4, b=5) results[x] giving results[x] NAbc NA NA54 NA (i.e. it appears to give results[levels(x)] Thanks to all for pointing out my misinterpretation.It's clearly not a bug

Re: [Rd] segfault on 2.11.0 with large POSIXct vector using as.character

2010-05-26 Thread Duncan Murdoch
looking for bugs. But if those eyes are closed, the model doesn't work. Duncan Murdoch invisible(as.character(Sys.time()+1:7e4)) invisible(as.character(Sys.time()+1:8e4)) invisible(as.character(Sys.time()+1:9e4)) Error: segfault from C stack overflow invisible(as.character(Sys.time()+1

Re: [Rd] Bug with ..0

2010-05-30 Thread Duncan Murdoch
a case of you doing something you shouldn't, and the error handling not slapping you on the wrist. Duncan Murdoch ff - function(..0, ...) ..0 ff(32, 3) [1] 3 R.version.string [1] R version 2.11.0 Patched (2010-04-26 r51822) win.version() [1] Windows Vista (build 6002

Re: [Rd] Bug with ..0

2010-05-30 Thread Duncan Murdoch
; see isDDName in src/main/dstruct.c. Also, why is it reserved? What is the future intended use? As far as I know, there is none. It is reserved simply because it follows the pattern of ..n. It would not be hard to make ..0 specially unreserved, but what would be the point? Duncan Murdoch

Re: [Rd] GUI's and R background processes

2010-06-15 Thread Duncan Murdoch
the calculation. You probably only want one processor to do this, and let it check on the other cores to see if there are any results ready. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] with(x, Recall()) Crash

2010-07-06 Thread Duncan Murdoch
thought I'd pass along the offending code. I've tested the crash on R 2.11.1 (on Linux and Mac), but not in devel versions of R. Thanks for posting that. It does still exist on R-devel, and as you say, it shouldn't. I'll fix it. Duncan Murdoch HTH, Robert x - 1 with(x, Recall

Re: [Rd] Large discrepancies in the same object being saved to .RData

2010-07-07 Thread Duncan Murdoch
, this doesn't take up much space in memory, but when you save the object to disk, a copy of the whole environment will be made, and that can end up wasting up a lot of space if the environment contains a lot of things that aren't needed by the formula. Duncan Murdoch Cheers, Julian

Re: [Rd] Telling Windows how to find DLL's from R?

2010-07-09 Thread Duncan Murdoch
Windows can find it (there are other tricks, but they apply at the Windows level, not at the R level). I haven't tried this, but can't you use Sys.setenv() to change the PATH to what you want? Presumably you'll want to change it back afterwards. Duncan Murdoch

Re: [Rd] Large discrepancies in the same object being saved to .RData

2010-07-10 Thread Duncan Murdoch
On 10/07/2010 2:33 PM, Paul Johnson wrote: On Wed, Jul 7, 2010 at 7:12 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 06/07/2010 9:04 PM, julian.tay...@csiro.au wrote: Hi developers, After some investigation I have found there can be large discrepancies in the same object

Re: [Rd] Large discrepancies in the same object being saved to .RData

2010-07-10 Thread Duncan Murdoch
of a function and what the pointer in a ‘EXTPTRSXP’ points to) is not included in the calculation. If you really want to know how much space an object will take when saved, probably the only reliable way is to save the object and look at how much space the file takes. Duncan Murdoch Bill

Re: [Rd] Large discrepancies in the same object being saved to .RData

2010-07-11 Thread Duncan Murdoch
does. I've just changed the default print method for formulas to display the environment if it is not globalenv(), which is the rule used for closures as well. So now in R-devel: as.formula(y ~ x) y ~ x as before, but as.formula(y ~ x, env=new.env()) y ~ x environment: 01f83400 Duncan

Re: [Rd] R.exe crashes on R v2.12.0dev (Windows Vista)

2010-07-26 Thread Duncan Murdoch
... Duncan Murdoch Locale ID:1033 Additional Information 1: 8772 Additional Information 2: 9431192a7274b0ee769861df31ecee58 Additional Information 3: f768 Additional Information 4: 930d06d3f6aed4162dca7601993082f5 Anyone knows if there anything else I can do to provide

Re: [Rd] R.exe crashes on R v2.12.0dev (Windows Vista)

2010-07-26 Thread Duncan Murdoch
tried it.) Duncan Murdoch /Henrik On Mon, Jul 26, 2010 at 1:30 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 26/07/2010 5:15 AM, Henrik Bengtsson wrote: Just FYI: Problem remains (on same system) with R version 2.12.0 Under development (unstable) (2010-07-21 r52590): Problem

Re: [Rd] R CMD build wiped my computer (from R-help)

2010-07-29 Thread Duncan Murdoch
that filename. So I'll have to leave this for a Unix-alike user. Duncan Murdoch unlink RColorBrewer/R/residuals.MCMCglmm.R unlink RColorBrewer/R/ColorBrewer.R~ rmdir RColorBrewer/R * checking for LF line-endings in source and make files * checking for empty or unneeded directories * building

Re: [Rd] transpose of complex matrices in R

2010-07-30 Thread Duncan Murdoch
don't quite understand why). You should call base::t.default, not base::t. Then this will work. The same solution fixes the one below, though you won't even need the base:: prefix on t.default. Duncan Murdoch 3. Try to define a t.complex() function: t.complex - function(x){t(Conj(x

Re: [Rd] Disappearance of the file quot;NEWSquot;

2010-08-03 Thread Duncan Murdoch
or not. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] problem with dl tag in tools::Rd2HTML

2010-08-05 Thread Duncan Murdoch
On 05/08/2010 5:18 PM, Michael Lachmann wrote: Duncan Murdoch-2 wrote: What version are you using? I don't see that in current R patched. I see this in version 2.11.1. This is the code I ran to generate it: page - utils:::.getHelpFile(?options) tools::Rd2HTML(page,out=t.html

Re: [Rd] [R-SIG-Mac] Question about line type in contour() function (R 2.11.1)

2010-08-06 Thread Duncan Murdoch
On 05/08/2010 8:46 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote: On Aug 5, 2010, at 5:20 PM, Duncan Murdoch wrote: On 05/08/2010 7:18 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote: I'm running R 2.11.1 (MacBook Pro and OS X 10.6.4) and am trying to set a line type

Re: [Rd] [R-SIG-Mac] Question about line type in contour() function (R 2.11.1)

2010-08-06 Thread Duncan Murdoch
On 06/08/2010 7:52 AM, Duncan Murdoch wrote: On 05/08/2010 8:46 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote: On Aug 5, 2010, at 5:20 PM, Duncan Murdoch wrote: On 05/08/2010 7:18 PM, David B. Thompson, Ph.D., P.E., D.WRE, CFM wrote: I'm running R 2.11.1 (MacBook Pro and OS X 10.6.4

Re: [Rd] parent.frame(1) of a S4 method is not a calling environment.

2010-08-17 Thread Duncan Murdoch
in the signature. Slightly unpleasant, though. You could use formulas for that. If you pass in formula = ~ x + y*z then environment(formula) will be the right evaluation environment, and formula[[2]] will be the unevaluated x + y*z. Duncan Murdoch Standardised, simpler syntax like

[Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?

2010-08-19 Thread Duncan Murdoch
, so that the default behaviour (which has always been equivalent to expand = TRUE) would be the only behaviour. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?

2010-08-19 Thread Duncan Murdoch
On 19/08/2010 3:17 PM, Marc Schwartz wrote: On Aug 19, 2010, at 2:07 PM, Duncan Murdoch wrote: I am trying to improve the error reporting in Sweave documents, so that if you have a syntax error in a code chunk, it will tell you which line of your input file contained the error

Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?

2010-08-19 Thread Duncan Murdoch
On 19/08/2010 4:29 PM, Claudia Beleites wrote: I never used it. I got curious, though. What would be a situation that benefits of this option? When I put it in, I thought it would be for people who were writing about Sweave. Duncan Murdoch Maybe a use case could be found by brute force

Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?

2010-08-19 Thread Duncan Murdoch
? Duncan Murdoch mainloop,keep.source=TRUE,expand=FALSE= for (i in 1:nSamples) { getInfoAboutThisSample for (j in 1:nChromosomes) { getChromosomeDataForCurrentSample normalizeChromosomeData findSegments computeSignificance writeResults } } @ Each of the chunks is itself a fairly long piece

Re: [Rd] Sweave *, showWarnings=TRUE ?

2010-08-20 Thread Duncan Murdoch
advantage of in many places. If that is expanded, my Sweave changes should take advantage of it automatically. Duncan Murdoch In a course on using R (for beginners), I would really like to show warnings that code chunks produce. Currently, the warnings are printed to the console when I run 'R CMD

Re: [Rd] Does anyone use Sweave (RweaveLatex) option expand=FALSE?

2010-08-30 Thread Duncan Murdoch
On 19/08/2010 5:25 PM, Duncan Murdoch wrote: On 19/08/2010 5:07 PM, Kevin Coombes wrote: I use it, frequently. The idea for it goes back to some of Knuth's original literate programming ideas for developing weave and tangle when he was writing TeX (the program). I want to be able

Re: [Rd] introspective capabilities

2010-08-30 Thread Duncan Murdoch
of user-level utility functions for working with this. For packages, the relevant option is keep.source.pkgs at the time the package is installed. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] introspective capabilities

2010-09-01 Thread Duncan Murdoch
On 01/09/2010 9:27 AM, Christophe Rhodes wrote: Duncan Murdoch murdoch.dun...@gmail.com writes: On 27/08/2010 7:52 AM, Christophe Rhodes wrote: Hi, Is there any way, from R code, to perform introspection as to where certain names acquired their values? There's the keep.source option

Re: [Rd] Weird erratic error and illogical error message, could someone explain this?

2010-09-03 Thread Duncan Murdoch
the bug more quickly if the latter is the problem.) If you're only running R code, then this looks like a bug in R, but it might still be worth trying gctorture to make it reproducible. We won't be able to fix it if we can't reproduce it. Duncan Murdoch ... my long-running code [as I said, cannot

Re: [Rd] Stats not loaded? Method for as.ts() results in error

2010-09-03 Thread Duncan Murdoch
don't, R will have to guess what the methods are, and it might be getting mixed up because of the unusual name of the generic. Duncan Murdoch Did anyone of encounter a similar problem or could help me out with a hint? Thank you very much, Janko

Re: [Rd] Development environment for R extentions on Windows

2010-09-08 Thread Duncan Murdoch
lately that make it harder and harder to work with. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] CMD check: checking data for non-ASCII characters is very time consuming

2010-09-08 Thread Duncan Murdoch
variable to skip this check. For the full list of check configuration variables, see the Tools section of the R Internals manual. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Development environment for R extentions on Windows

2010-09-08 Thread Duncan Murdoch
On 08/09/2010 5:37 PM, Jeffrey Horner wrote: On Wed, Sep 8, 2010 at 1:01 PM, Jeffrey Horner jeffrey.hor...@gmail.com wrote: On Wed, Sep 8, 2010 at 12:37 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 08/09/2010 1:21 PM, Jeffrey Horner wrote: Hi all, I'm setting up a development

Re: [Rd] An ls error which is not an error...

2010-09-09 Thread Duncan Murdoch
coincidentally looks like the name of something on the search list. So I will try to change the error to an informative warning. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Windows build

2010-09-10 Thread Duncan Murdoch
the recommended packages installed. They're needed to run the tests. In Windows you get them by make rsync-recommended make recommended Getting them in other OS's is slightly different, but I forget the details. See the R Installation and Administration manual. Duncan Murdoch

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

2010-09-11 Thread Duncan Murdoch
they adjust to the new organization of the share/texmf directory, things will be fine again. The reorg is described in this NEWS item: * Directory R_HOME/share/texmf now follows the TDS conventions, so can be set as a texmf tree ('root directory' in MiKTeX parlance). Duncan Murdoch I

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

2010-09-12 Thread Duncan Murdoch
On 12/09/2010 12:49 AM, Hervé Pagès wrote: Hi Duncan, On 09/11/2010 03:56 AM, Duncan Murdoch wrote: On 11/09/2010 12:52 AM, Hervé Pagès wrote: Hi, I found the following problem with recent R-devel (2010-08-26 r52817) on Windows (32-bit and 64-bit): 'R CMD build pkg' gets stalled during

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

2010-09-12 Thread Duncan Murdoch
use Makefiles to bypass the normal process. Duncan Murdoch AfaIcs this is also how it worked in the past. Best wishes Wolfgang On Sep/11/10 12:56 PM, Duncan Murdoch wrote: On 11/09/2010 12:52 AM, Hervé Pagès wrote: Hi, I found the following problem with recent R-devel (2010-08-26

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

2010-09-13 Thread Duncan Murdoch
Hervé Pagès wrote: Hi Duncan, On 09/12/2010 05:07 AM, Duncan Murdoch wrote: On 12/09/2010 12:49 AM, Hervé Pagès wrote: Hi Duncan, On 09/11/2010 03:56 AM, Duncan Murdoch wrote: On 11/09/2010 12:52 AM, Hervé Pagès wrote: Hi, I found the following problem with recent

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

2010-09-13 Thread Duncan Murdoch
On 13/09/2010 2:38 PM, Hervé Pagès wrote: On 09/13/2010 03:34 AM, Duncan Murdoch wrote: Hervé Pagès wrote: Hi Duncan, On 09/12/2010 05:07 AM, Duncan Murdoch wrote: On 12/09/2010 12:49 AM, Hervé Pagès wrote: Hi Duncan, On 09/11/2010 03:56 AM, Duncan Murdoch wrote: On 11/09/2010

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

2010-09-14 Thread Duncan Murdoch
On 14/09/2010 2:46 PM, Hervé Pagès wrote: Duncan, On 09/13/2010 11:47 AM, Duncan Murdoch wrote: On 13/09/2010 2:38 PM, Hervé Pagès wrote: [...] Thanks for suggesting workarounds but don't you think there is a real problem? As I said, we don't use TEXINPUTS on Windows, we use

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

2010-09-14 Thread Duncan Murdoch
is that some packages might create files with CRLF endings on all platforms, and then check *should* complain about them. My advice would be not to put them in the tarball, and ignore the warning. Or write a Makevars.win that fixes the line endings so that check is happy. Duncan Murdoch

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

2010-09-16 Thread Duncan Murdoch
that causes R CMD build or R CMD INSTALL to fail, please let us know. By the way, I don't think the title can be filled in automatically unless a user has roxygen style documentation, so we don't. But doesn't the roxygen package do that? Duncan Murdoch - Last time I used package.skeleton

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

2010-09-16 Thread Duncan Murdoch
can do what you do. Perhaps an option (default off) to create everything would be a good compromise. Duncan Murdoch I copy a template package directory, edit the template DESCRIPTION file, copy my code into the appropriate subdirectories, and run prompt(func, filename=pkg/man/func.Rd) on each

Re: [Rd] Possible bug or annoyance with library.dynam.unload()

2010-09-21 Thread Duncan Murdoch
first. Pick some CRAN package, tell us what to do with it to trigger the error, and then we can see if it's something special about your package or Roxygen or a general problem. Duncan Murdoch Thanks, Karl On Thu, Sep 16, 2010 at 6:11 PM, Karl Fornerkarl.for...@gmail.com wrote: Hello

Re: [Rd] Possible bug or annoyance with library.dynam.unload()

2010-09-22 Thread Duncan Murdoch
, and it looks like a bug to me. Thanks for the report, I'll put it on the bugs page, and hopefully it will be fixed before the 2.12.0 release. Duncan Murdoch Steps to reproduce the problem: * unarchive it ( tar zxvf foo_0.1.tar.gz ) * cd foo * install it locally ( mkdir local; R CMD INSTALL -l

Re: [Rd] Incorporate graphic files into R-package

2010-09-27 Thread Duncan Murdoch
there, it will be installed when your package is installed, and your Sweave document can find it using system.file(path within package, package=yourpackage) to copy to the output directory. Duncan Murdoch __ R-devel@r-project.org mailing list https

Re: [Rd] bulding a package for Windows (path problem?)

2010-09-30 Thread Duncan Murdoch
\Documents\hydrology\development\hydrosim Are you really using version 2.9.2? If so, I think you're on your own. The current release is 2.11.1, and our efforts are concentrated on testing the alpha/beta of 2.12.0 now. Duncan Murdoch Can't locate R/Dcf.pm in @INC (@INC contains: C /ARCHIV~1/R/R

Re: [Rd] scoping goes wrong when some functions are used within others.

2010-10-01 Thread Duncan Murdoch
carefully you'll see that this is documented correctly in (Note: if ‘data’ is already an environment then this is used with its existing parent.) Duncan Murdoch ff- function(x){ y- some_value some_function(y) } ff(x) Error in eval(expr, envir, enclos) : object 'y' not found I tried

Re: [Rd] Eval and the enclos argument

2010-10-02 Thread Duncan Murdoch
(given my reading of the documentation) when envir is not an environment already. Hadley I think that handles the case of envir=NULL. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Eval and the enclos argument

2010-10-02 Thread Duncan Murdoch
On 02/10/2010 10:40 AM, Hadley Wickham wrote: On Sat, Oct 2, 2010 at 8:18 AM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 02/10/2010 7:57 AM, Hadley Wickham wrote: Hi all, I'm trying to understand the default value of the enclos argument of eval: enclos = if(is.list(envir

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Duncan Murdoch
. If that doesn't work, you can see if the problem is in the conversion, by running R CMD Rd2dvi --no-clean dja.Rd and look in the Rd2.tex file that was produced. Duncan Murdoch Your command was ignored. Type I command return to replace it with another command, or return to continue without

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Duncan Murdoch
, delete the old file. Duncan Murdoch Renaud 2010/10/3 Duncan Murdoch murdoch.dun...@gmail.com: On 03/10/2010 12:23 PM, Renaud Lancelot wrote: Dear all, I have a problem with an Rd file containing French accentuated characters. I have uploaded the file at http://filex.cirad.fr/get?k

Re: [Rd] S4 class help pages [Sec=Unclassified]

2010-10-04 Thread Duncan Murdoch
with a hyphen in it. So you're seeing help on subtraction. You can get what you want with class?stats4::mle. I'll see if I can fix the advice from ??. Duncan Murdoch Thanks Troy ___ Australian Antarctic Division

Re: [Rd] SweaveInput + keep.source = TRUE trouble

2010-10-05 Thread Duncan Murdoch
On 05/10/2010 5:38 AM, Claudia Beleites wrote: Dear all, I have trouble with R-beta sweaving files that include definitions with \SweaveInput in combination with keep.source = TRUE Thanks for the report. I'll take a look. Duncan Murdoch Symptom: SInput is taken from too far down

Re: [Rd] SweaveInput + keep.source = TRUE trouble

2010-10-05 Thread Duncan Murdoch
. Duncan Murdoch On 05/10/2010 5:38 AM, Claudia Beleites wrote: Dear all, I have trouble with R-beta sweaving files that include definitions with \SweaveInput in combination with keep.source = TRUE Symptom: SInput is taken from too far down the input file (the shift is the number of lines

Re: [Rd] NULL assignment will change the expression's class into list

2010-10-08 Thread Duncan Murdoch
, the NULL assignment would remove the a entry). A simple workaround is to use te[a] - expression(NULL) or te - te[-1] instead, depending on what you expected to happen. Duncan Murdoch Regards, Vitally. [[alternative HTML version deleted]] __ R

Re: [Rd] NULL assignment will change the expression's class into list

2010-10-08 Thread Duncan Murdoch
conversion from one. Duncan Murdoch Vitally. Duncan Murdoch Regards, Vitally. [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] NULL assignment will change the expression's class into list

2010-10-08 Thread Duncan Murdoch
Vitalie Spinu wrote: On Fri, Oct 8, 2010 at 7:49 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 08/10/2010 12:24 PM, Vitalie Spinu wrote: On Fri, Oct 8, 2010 at 12:14 PM, Duncan Murdochmurdoch.dun...@gmail.com wrote: Vitalie Spinu wrote: Hello

Re: [Rd] Missing libpthread in RTools

2010-10-15 Thread Duncan Murdoch
. Is there any chance to include them in RTools, too? Rtools is for building R, and that library isn't needed in R. If you want it for some particular purpose, can't you just install a copy on your machine? Duncan Murdoch Davor __ R-devel@r-project.org

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