Re: [Rd] incorrect DLL path for Rbitmap.dll on Windows

2010-11-08 Thread Duncan Murdoch
On 08/11/2010 3:14 PM, Dan Tenenbaum wrote: Hello, I think there is a problem in recent devel builds of R on Windows with various devices from the grDevices package. Thanks, I'll look into this. Duncan Murdoch For example: capabilities() jpeg png tifftcltk

Re: [Rd] incorrect DLL path for Rbitmap.dll on Windows

2010-11-09 Thread Duncan Murdoch
On 08/11/2010 3:14 PM, Dan Tenenbaum wrote: Hello, I think there is a problem in recent devel builds of R on Windows with various devices from the grDevices package. This should be fixed now, as of today's build. Thanks for the report (and thanks to Brian Ripley for fixing it). D

Re: [Rd] Trying to understand the search path and namespaces

2010-11-15 Thread Duncan Murdoch
escription of this a few years ago. It's either on developer.r-project.org, or in an old issue of R News. Duncan Murdoch library(devtools) search() [1] ".GlobalEnv""package:devtools" "package:stats" [4] "package:graphics" &qu

Re: [Rd] Compiling R 2.12.0 from source: error (temp dir)

2010-11-18 Thread Duncan Murdoch
On 18/11/2010 5:40 AM, Janko Thyson wrote: I've created a /tmp directory so I wouldn't have to change TMPDIR. So far, so good. But now I get the error below. Anything I forgot regarding tcltk? Looks as if you forgot to install it. Duncan Murdoch Thx, Janko ERROR: In file inc

Re: [Rd] Compiling R 2.12.0 from source: error (temp dir)

2010-11-18 Thread Duncan Murdoch
ows. Tcl/Tk is included in the Rtools installer, but you have to choose to install it. It looks as though you didn't, or didn't install it in the right place. Duncan Murdoch Append it to 'make all recommended'? I checked 'make --help' which didn't list any su

Re: [Rd] segfault interest?

2010-11-24 Thread Duncan Murdoch
etails on what to include, but don't follow the instructions there for submission, because they're out of date: go to https://bugs.r-project.org instead. Duncan Murdoch regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.com) _

Re: [Rd] R Tools & Vista_x64: Problem compiling RMySQL?

2010-11-26 Thread Duncan Murdoch
by looking at "objdump -x libmySQL.dll". objdump.exe is distributed as part of the MinGW distribution in Rtools.) Duncan Murdoch I upgraded to "Rtools212.exe" yesterday but immediately got errors from "R CMD check RMySQL_0.7-5.tar.gz". After the first e

Re: [Rd] Bug in parseNamespaceFile or switch( , ... ) ?

2010-11-27 Thread Duncan Murdoch
ve been "=" =, "<-" = { Without the extra = sign, the "=" was taken as the default value of the switch, and the stop() was never reached. Conceivably switch() should complain if it is called with more than one default. Duncan Murdoch Details:

Re: [Rd] Bug in parseNamespaceFile or switch( , ... ) ?

2010-11-27 Thread Duncan Murdoch
On 27/11/2010 6:50 PM, Duncan Murdoch wrote: On 27/11/2010 5:58 PM, Charles C. Berry wrote: parseNamespaceFile() doesn't seem to detect misspelled directives. Looking at its code I see switch(as.character(e[[1L]]), , stop(gettextf("unknown namespace dir

[Rd] switch() disallowing multiple default values Re: Bug in parseNamespaceFile or switch( , ... ) ?

2010-11-28 Thread Duncan Murdoch
more typos like this in the base code besides the one in parseNamespaceFile. I expect it will turn up quite a few more in CRAN and Bioconductor packages. Please let me know right away if you've got correct code that generates the warnings or errors. Duncan Murdoch In R-devel they&#

Re: [Rd] Bug in parseNamespaceFile or switch( , ... ) ?

2010-11-28 Thread Duncan Murdoch
On 27/11/2010 7:09 PM, Duncan Murdoch wrote: On 27/11/2010 6:50 PM, Duncan Murdoch wrote: On 27/11/2010 5:58 PM, Charles C. Berry wrote: parseNamespaceFile() doesn't seem to detect misspelled directives. Looking at its code I see switch(as.character(e[[1L]]), ,

Re: [Rd] Sweave choking on \\ in filename

2010-11-29 Thread Duncan Murdoch
n below. This is fixed in R-patched. (It would have been fixed in 2.12.0 if more people tested the betas...). Duncan Murdoch Best regards, Thierry > Sweave("Q:\\BMK\\cursussen\\interne_opleiding\\deelnemerslijst.Rnw", syntax="SweaveSyntaxNoweb") Writing to file deel

Re: [Rd] Windows Rdevel version - no Rgui.exe?

2010-11-30 Thread Duncan Murdoch
: "This is a combined Windows 32/64 bit binary build of the 2010-11-27 r53672 development snapshot of R (which will eventually become R-2.13.0).". Do you think this is an error on my part or do you see the same thing, It may be an error in that build; I'll take a look.

Re: [Rd] Windows Rdevel version - no Rgui.exe?

2010-11-30 Thread Duncan Murdoch
d it looks okay. Might have been a temporary glitch. If you see it again, please let me know. Duncan Murdoch cheers, Keith Keith Satterley Bioinformatics Division The Walter and Eliza Hall Institute of Medical Research Parkville, Melbourne, Victoria,

Re: [Rd] Reordering entries in package manual PDF's

2010-12-01 Thread Duncan Murdoch
page comes first. Duncan Murdoch Is there an easy way to specify the order of the entries in the generated documentation? Browsing through the R manual and mailing list archives did not find anything. Rd is all I need, so I would not like to start using any of the more advanced documentation

Re: [Rd] Reordering entries in package manual PDF's

2010-12-01 Thread Duncan Murdoch
3. Look in src/library/tools/R for the file containing the source to ..Rd2dvi(); you'll find it in Rd2dvi.R. You can also see deparsed versions just by printing the tools:::..Rd2dvi function, but they may not be as useful as the original source. I hope

Re: [Rd] Competing with one's own work

2010-12-03 Thread Duncan Murdoch
't just be published in a contributed package. (That's why bug fixes are easy, and big additions to the base packages are not.) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Competing with one's own work

2010-12-03 Thread Duncan Murdoch
n base R is because someone in the core team is in a better position to maintain the code than an outside package maintainer would be. Duncan Murdoch John, thanks for raising an important issue. Thanks& Best, Ravi. --- Ravi Varadhan

Re: [Rd] Competing with one's own work

2010-12-05 Thread Duncan Murdoch
mmended package.) So just because a package is good quality and contains useful or important code, it shouldn't necessarily become a recommended package. I don't think there are clear rules about when it should, just as there aren't for other R changes. Duncan Murdoch Of the 16 re

Re: [Rd] directory structure of R 2.12.0 distribution

2010-12-08 Thread Duncan Murdoch
there's a description in the R Admin manual as well as the Writing R Extensions manual. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Suggested change to integrate.Rd

2010-12-08 Thread Duncan Murdoch
ove it, or replace it. All the tools for converting the .Rd or .Rnw source into various formats are there. Duncan Murdoch Spencer On 12/8/2010 2:22 PM, John Nolan wrote: Well, you can't idiot-proof things, but you can give clear descriptions and warnings. To take things to the e

Re: [Rd] How to call DBLEPR in Fortran code to be used by R

2010-12-10 Thread Duncan Murdoch
example of dblepr in Writing R Extensions work for you? Duncan Murdoch Thanks, Marian Talbert ASRC Management Servics Contracted To: US Geological Survey Fort Collins Science Center 2150 Centre Ave., Bldg C Fort Collins, CO 80526 Phone: 970-226-9108 [[al

Re: [Rd] errors in getconnection or scan

2010-12-13 Thread Duncan Murdoch
an html page? Testing for valid html is hard. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] errors in getconnection or scan

2010-12-13 Thread Duncan Murdoch
for it. You can catch the error using html <- try(readLines(con), silent=TRUE) if (inherits(html, "try-error")) cat("Error!") Duncan Murdoch 2010/12/13 Duncan Murdoch mailto:murdoch.dun...@gmail.com>> On 13/12/2010 12:36 PM, Arthur Charpentier wrote:

Re: [Rd] embed Sweave driver in .Rnw file

2010-12-14 Thread Duncan Murdoch
ix=somedir/" option to Sweave? That needs to be there before TeX is run. I sometimes put a dir.create("somedir", showWarnings=FALSE) call in an early chunk in the document to create it. Duncan Murdoch Thanks, Dominick On Tue, Dec 14, 2010 at 7:21 AM, Friedrich Leisch&l

Re: [Rd] embed Sweave driver in .Rnw file

2010-12-14 Thread Duncan Murdoch
s. So it's only a problem when you distribute the .tex output of Sweave, not when you distribute the .Rnw input. (I understand there are circumstances where this is unavoidable, but you shouldn't be surprised when object files aren't portable.) Duncan Murdoch Thanks, Dominick

Re: [Rd] Surprising behavior of letters[c(NA, NA)]

2010-12-17 Thread Duncan Murdoch
ector, so it gets recycled to the length of letters, whereas c(NA, 3) and the others are numeric vectors, so they aren't recycled, they're converted to integer indices. So the surprise is due to not recognizing that NA is logical. You wouldn't expec

Re: [Rd] Surprising behavior of letters[c(NA, NA)]

2010-12-17 Thread Duncan Murdoch
On 17/12/2010 10:18 AM, Gabor Grothendieck wrote: On Fri, Dec 17, 2010 at 9:58 AM, Duncan Murdoch wrote: > On 17/12/2010 9:32 AM, Gabor Grothendieck wrote: >> >> Consider this: >> >> >letters[c(2, 3)] >> [1] "b" "c" >>

Re: [Rd] Surprising behavior of letters[c(NA, NA)]

2010-12-17 Thread Duncan Murdoch
d. Values corresponding to TRUE in the index vector are selected and those corresponding to FALSE are omitted." The "must" in that quote is too strong; the Language Definition gets it right. Perhaps the behaviour described in the Intro manual

Re: [Rd] diagnosing a CMD check failure

2010-12-17 Thread Duncan Murdoch
tools::.check_packages directly. The problem is coming in the local function run_tests. Duncan Murdoch > sessionInfo() R version 2.13.0 Under development (unstable) (2010-11-11 r53555) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics g

Re: [Rd] Surprising behavior of letters[c(NA, NA)]

2010-12-18 Thread Duncan Murdoch
On 18/12/2010 9:12 AM, Radford Neal wrote: Duncan Murdoch writes: The relevant quote is in the Language Definition, talking about indices by type of index: "Logical. The indexing i should generally have the same length as x. If it is shorter, then its elements will be recycl

Re: [Rd] Rcmd SHLIB error

2010-12-19 Thread Duncan Murdoch
ime to diagnose or fix this in the next couple of months. If you have spare time, you might want to try older versions of the Rtools (perhaps mixing new compilers with old Rtools/bin and Cygwin DLLs). Duncan Murdoch __ R-devel@r-project.org mailing list

Re: [Rd] Rcmd SHLIB error

2010-12-19 Thread Duncan Murdoch
On 19/12/2010 7:01 AM, Gabor Grothendieck wrote: On Sun, Dec 19, 2010 at 6:39 AM, Duncan Murdoch wrote: On 19/12/2010 6:06 AM, Gabor Grothendieck wrote: On Sat, Dec 18, 2010 at 8:23 PM, Dominick Samperi wrote: On Sat, Dec 18, 2010 at 5:24 PM, Gabor Grothendieck wrote: I am

Re: [Rd] Rcmd SHLIB error

2010-12-19 Thread Duncan Murdoch
On 19/12/2010 10:04 AM, Gabor Grothendieck wrote: On Sun, Dec 19, 2010 at 9:07 AM, Duncan Murdoch wrote: On 19/12/2010 7:01 AM, Gabor Grothendieck wrote: On Sun, Dec 19, 2010 at 6:39 AM, Duncan Murdoch wrote: On 19/12/2010 6:06 AM, Gabor Grothendieck wrote: On Sat, Dec 18, 2010 at 8

Re: [Rd] Rcmd SHLIB error

2010-12-19 Thread Duncan Murdoch
On 19/12/2010 3:09 PM, Gabor Grothendieck wrote: On Sun, Dec 19, 2010 at 10:31 AM, Duncan Murdoch wrote: On 19/12/2010 10:04 AM, Gabor Grothendieck wrote: On Sun, Dec 19, 2010 at 9:07 AM, Duncan Murdoch wrote: On 19/12/2010 7:01 AM, Gabor Grothendieck wrote: On Sun, Dec 19, 2010 at

Re: [Rd] Bug report 14459 -- procedure for handling follow-up issues

2010-12-21 Thread Duncan Murdoch
when there are simple workarounds. (The workaround in your case is not to use the named chunk.) Duncan Murdoch John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics& Its Applications, Room 1194, John Dedman

Re: [Rd] Bug report 14459 -- procedure for handling follow-up issues

2010-12-21 Thread Duncan Murdoch
ld be more helpful to keep working with 2.12.1-patched, to flush out any more bugs, or to contribute patches. Duncan Murdoch John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics& Its Applications, Room 1

Re: [Rd] Error in generating sweave-tex -> pdf file

2010-12-22 Thread Duncan Murdoch
\usepackage{Sweave} line after the opening \documentclass line. Duncan Murdoch In this example we embed parts of the examples from the help page into a \ LaTeX {} document : <>= y=2 y = y +1 @ which shows that the location parameter of the Ozone distribution varies significantly from month

Re: [Rd] Error in generating sweave-tex -> pdf file

2010-12-22 Thread Duncan Murdoch
On 22/12/2010 1:30 PM, carol white wrote: Should the Sweave package be in /usr/share/texmf/tex/latex/? How about Sweave.sty? I meant Sweave.sty, there's no separate Sweave package. It should be in the R home directory, somewhere within share/texmf. Duncan Murdoch Thanks - Ori

Re: [Rd] License statement

2010-12-22 Thread Duncan Murdoch
nse it in whatever way you and they agree is reasonable. But don't trust what I write as legal advice. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Error in generating sweave-tex -> pdf file

2010-12-23 Thread Duncan Murdoch
ns on where to get it. If that doesn't help, you might get help on this list by stating the versions of everything you're using: R, your OS, and TeX. Duncan Murdoch - Original Message ---- From: Duncan Murdoch To: carol white Cc: r-devel@r-project.org Sent: Wed, December 22, 2

Re: [Rd] Error in generating sweave-tex -> pdf file

2010-12-23 Thread Duncan Murdoch
current release handled things better. But the thing that appears to be missing on your system is texinfo, and that's not part of R. Duncan Murdoch Cheers, - Original Message From: Duncan Murdoch To: carol white Cc: r-devel@r-project.org Sent: Thu, December 23, 2010 1:21:14

Re: [Rd] environment question

2010-12-27 Thread Duncan Murdoch
me. > > > 2 Is a function like EM allowed to alter objects that it finds through > the environment, ones that are not passed as arguments? I understand > that a function cannot alter an object that is passed explicitly, but > what about the ones it grabs from the environment? Y

Re: [Rd] R-forge out?

2010-12-29 Thread Duncan Murdoch
On 29/12/2010 12:44 PM, Paul Gilbert wrote: Is anyone else having trouble connecting to R-forge svn? (Perhaps I missed an outage announcement, or is it bad weather?) I've also had trouble since yesterday. The main web page also appears to be down... Duncan Mu

Re: [Rd] problem building R 2.12.1 64-bit on Windows 7

2010-12-30 Thread Duncan Murdoch
at the end shows it was). That is made using src/extra/zlib/Makefile.win. I don't see any calls to "sed" in there, but there's one in the implicit rule to make the .dll (in src/gnuwin32/MkRules), namely $(SED) -n $(SYMPAT) Do you have a definition for SYMPAT that overrides ours, or SYMPAT64 (which is used in ours)? If that's not it, you could remove the @ sign from the beginning of that line in MkRules, and see what it is trying to do just before it dies. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Indexing request

2011-01-07 Thread Duncan Murdoch
lly an alias, but perhaps there are cases where that would be undesirable. I'll add it as an alias here. I've passed on a message about the problem on that page, and it should eventually be fixed. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Indexing request

2011-01-07 Thread Duncan Murdoch
On 11-01-07 5:52 AM, Prof Brian Ripley wrote: On Fri, 7 Jan 2011, Duncan Murdoch wrote: On 11-01-07 12:08 AM, David Winsemius wrote: I just tried ?Constants at the console and was disappointed that the so-named base help page would not come up. > ?Constants No documentation

Re: [Rd] as.environment.list provides inconsistent results under torture

2011-01-12 Thread Duncan Murdoch
make sure the argumetns are protected.) Do we have an isProtected() function to use in debugging? It should check if something is in the protection stack or is protected for some other reason, so it doesn't look trivial to write. Duncan Murdoch Best, luke On Tue, 11 Jan 2011, Sim

Re: [Rd] R vs. C

2011-01-17 Thread Duncan Murdoch
). So if you have something that's really slow, think about the fundamental operations, and write those in C, then use R code to glue them together. But if it is fast enough without doing that, then leave it all in R. Duncan Murdoch On 17/01/2011 17:13, Patrick Leyshock wrote: > A

Re: [Rd] format scientific + plotmath potential bug

2011-01-18 Thread Duncan Murdoch
yourself to the CC list there. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] "+" operator on characters revisited

2011-01-23 Thread Duncan Murdoch
chine$integer.max) + 1L and -1L + (.Machine$integer.max + 1L) give different results. When I try it now without parentheses, I get the same answer as the first one, but I don't believe we guarantee that that will always be so. Duncan Murdoch _

Re: [Rd] use of depends, suggests, etc

2011-01-29 Thread Duncan Murdoch
that generates a link if the target is installed, and plain text if not. Seems like it would be overkill, but you must have good reasons to want to link to packages that don't exist on the test machines, so maybe it's worth doing. Duncan Murdoch Kevin On 1/27/2011 4:3

Re: [Rd] Strange behaviour of read and writeBin

2011-02-04 Thread Duncan Murdoch
On 04/02/2011 5:35 AM, Christian Ruckert wrote: To me it seems like writeBin() writes one char/byte more than expected. You want writeChar rather than writeBin to avoid the null termination of strings. Duncan Murdoch > con<- file("testbin", "wb") &

Re: [Rd] keep.source when semicolons separate statements on the one line

2011-02-04 Thread Duncan Murdoch
Thanks for the report. I'll take a look. I'm now past one major time sink, and will have some time to catch up on old problems; I'll add this to that list. Duncan Murdoch On 03/02/2011 7:09 PM, John Maindonald wrote: The following is 'semicolon.Rnw' > \Swea

Re: [Rd] keep.source when semicolons separate statements on the one line

2011-02-05 Thread Duncan Murdoch
On 04/02/2011 3:34 PM, Kevin R. Coombes wrote: This is probably the same underlying bug, but it is not caused by semicolons. Yes, it was the same bug. I think I have it fixed now, and will commit after some more testing. Duncan Murdoch If you use keep,soure=TRUE with expand=FALSE and

Re: [Rd] keep.source when semicolons separate statements on the one line

2011-02-05 Thread Duncan Murdoch
On 05/02/2011 1:18 PM, Duncan Murdoch wrote: On 04/02/2011 3:34 PM, Kevin R. Coombes wrote: This is probably the same underlying bug, but it is not caused by semicolons. Yes, it was the same bug. I think I have it fixed now, and will commit after some more testing. Now committed as r54232

Re: [Rd] Error with named chunks in Sweave with the development version of R

2011-02-07 Thread Duncan Murdoch
Thanks, I'll take a look. The "internal error" message was intended to catch this kind of problem. Duncan Murdoch On 07/02/2011 7:36 AM, Clément Calenge wrote: Dear all, There seems to be a problem with named chunks in Sweave with the version of R under development (downl

Re: [Rd] Error with named chunks in Sweave with the development version of R

2011-02-07 Thread Duncan Murdoch
This should be fixed as of r54259. Duncan Murdoch On 07/02/2011 7:36 AM, Clément Calenge wrote: Dear all, There seems to be a problem with named chunks in Sweave with the version of R under development (downloaded yesterday). When I sweave the file toto.Rnw described at the end of this mail

Re: [Rd] R 2.12.1 Windows 32bit and 64bit - are numerical differences expected?

2011-02-10 Thread Duncan Murdoch
that there are precision differences coming from there. I think we'd be interested in knowing what they are even if they are beyond our control, so I would appreciate it if you could track down where the difference arises. Duncan Murdoch BACKGROUND A colleague was trying to repl

Re: [Rd] R 2.13.0 on Windows: R CMD check and '"du"' not found

2011-02-13 Thread Duncan Murdoch
rceforge.net/projects/unxutils/) in the bin/ directory of Rtools (e.g. C:/Rtools/bin/) provides a workaround. I'll see about adding it with the next update. Duncan Murdoch sessionInfo() R version 2.13.0 Under development (unstable) (2011-02-11 r54330) Platform: x86_64-pc-mingw32/x64 (64-b

Re: [Rd] Request: Suggestions for "good teaching" packages, esp. with C code

2011-02-15 Thread Duncan Murdoch
or assignment. f2<- function(){ return(a=5) } This is a mistake: return() doesn't take named arguments. It is lenient and lets you get away with this error (treating it the same as return(5)), and returns the 5, visibly. Duncan Murdoch f2() Kevin Wright On Tue, Feb 15, 2

Re: [Rd] Avoiding name clashes: opinion on best practice naming conventions

2011-02-16 Thread Duncan Murdoch
will not be visible to other packages without a prefix, so they won't clash. Your package will be guaranteed to see its own functions first. A user can still have a clash between your exported functions and some other package's exports, but with fewer functions exported, that wil

Re: [Rd] Request: Suggestions for "good teaching" packages, esp. with C code

2011-02-16 Thread Duncan Murdoch
de may be quite disadvantageous in certain situations. As far as I know there is no such effect. I suspect what you saw just triggered a bug in the C code that had stayed hidden before. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.

Re: [Rd] How to make a package with help pages in multiple languages?

2011-02-22 Thread Duncan Murdoch
omatically attached when the original is attached, if the locale says to use that language? Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Sexpr problem

2011-02-25 Thread Duncan Murdoch
es of the note are generated using \Sexpr). If you put together a simple .Rd file that shows the difference you're seeing, I'll take a look. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] hook for when R quits

2011-03-11 Thread Duncan Murdoch
On 11/03/2011 1:37 PM, Michael Lawrence wrote: Thanks for the suggestion, but I don't think that R finalizes all of its objects when it quits. At least a simple test suggests that on Linux. Did you use onexit=TRUE? On Windows that appears to work... Duncan Murdoch Michael On Fri, M

Re: [Rd] hook for when R quits

2011-03-11 Thread Duncan Murdoch
On 11/03/2011 3:11 PM, Henrik Bengtsson wrote: On Fri, Mar 11, 2011 at 11:07 AM, Prof Brian Ripley wrote: > On Fri, 11 Mar 2011, Duncan Murdoch wrote: > >> On 11/03/2011 1:37 PM, Michael Lawrence wrote: >>> >>> Thanks for the suggestion, but I don'

Re: [Rd] Feature request: txtProgressBar with ability to write to arbitrary stream

2011-03-15 Thread Duncan Murdoch
Bar) <- tpbEnv you'll get clear messages if it is out of scope when you try to use it. Duncan Murdoch Best, Matt On 03/15/2011 05:37 AM, Andreas Borg wrote: > Hi all, > > I use txtProgressBar to monitor progress of large computations. What I > miss is the ability to r

Re: [Rd] object not found whilst loading namespace

2011-03-15 Thread Duncan Murdoch
f input The files are concatenated into one big file which is sourced. You've got an unclosed parenthesis/brace/bracket in this file, but some later file closed it -- so that file probably has an extra closing one. Duncan Murdoch Thanks anyway, Max On Tue, Mar 15, 2011 at 9:48 P

Re: [Rd] Detecting bad lexical scoping

2011-03-17 Thread Duncan Murdoch
rules. The language def section on environments made me hurt. Quoting Uwe Ligges, "No". Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Duncan Murdoch
find the source of warnings if it proves too difficult. Thanks for considering this idea... That sounds like a good idea. It would be easier to experiment with if you provided the offending file. (Yes, the lack of a name makes it hard to find that file, but it's easier for you than for al

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Duncan Murdoch
Writing R documentation files' in manual 'Writing R Extensions'. "Documentation object 'ellipse.glm'" tells me the \name{} inside the .Rd file, which is enough to uniquely identify the file. Are you not seeing this part of the message? Duncan Murdoch __

Re: [Rd] Feature request: display file name in R CMD check warning

2011-03-17 Thread Duncan Murdoch
On 11-03-17 12:33 PM, Dan Tenenbaum wrote: On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch wrote: On 16/03/2011 7:55 PM, Dan Tenenbaum wrote: Hi, I came across the following warning in R CMD check (it only occurred on Windows): The \usage entries for S3 methods should use the \method

Re: [Rd] [Patch suggestion] Adding 3rd arg to tempfile() to set extension

2011-03-18 Thread Duncan Murdoch
I think this is a good idea; I'll put it into r-devel and possibly r-alpha. Duncan Murdoch On 18/03/2011 1:54 PM, Dirk Eddelbuettel wrote: The other day I was working on an example which used tempfile() to create file for use by the graphics device. And while I love tempfile()---as

Re: [Rd] system.file() to read a text file from a vignette

2011-03-23 Thread Duncan Murdoch
rror in read.table(system.file("inst", "doc", "extdata", "tv.dat", package = "vcdExtra")) : no lines available in input How can I fix this? Everything in the "inst" directory is moved up a level when it is installed. So you shouldn't mention "inst" in its path. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] argument handling in boot.ci

2011-03-23 Thread Duncan Murdoch
uot;, which means that a copy is distributed with R, but it is not part of R), so suggestions should go to the maintainer. But you need to put together a simple example to illustrate the problem. When I modify the first example in example(boot.ci) to specify type=&

Re: [Rd] Standalone C++ application for processing R parser output(SEXP)

2011-03-24 Thread Duncan Murdoch
as on what is wrong, or how I can go about it? I think you need to think of your program as a new front end for R, even if you're only using a few R functions. See Chapter 8 in the Writing R Extensions manual. Duncan Murdoch __ R-devel@r-proj

Re: [Rd] .Fortran successful, R locks up.

2011-03-25 Thread Duncan Murdoch
library with the environment variable DEBUG set to T to get the debugging information compiled into it. Not sure if you need to do anything on the other systems. Duncan Murdoch Thanks for your time on my behalf! dan Ouput from R session with library "swat" and subroutine "j

Re: [Rd] Rd2pdf and Rd2dvi don't find texi2dvi

2011-03-25 Thread Duncan Murdoch
your shell. I'd try system("texi2dvi --version") in R and compare the result to what you get outside, examine the environment variables PATH and TEX in both places (with Sys.getenv(c("PATH", "TEX")) in R) to look for differences, etc. Duncan Murdoch __

Re: [Rd] bug (or feature) in alpha 2.13?

2011-03-27 Thread Duncan Murdoch
1]> where In the output from "where," there should be information on the line number at which the user code blew up. It's there in 2.12, but not in 2.13, from what I can see. That's not intentional. I'll see what went wrong... Duncan Murdoch ___

Re: [Rd] bug (or feature) in alpha 2.13?

2011-03-27 Thread Duncan Murdoch
On 11-03-27 7:42 AM, Duncan Murdoch wrote: On 11-03-26 7:41 PM, Norm Matloff wrote: The pattern (I can make a simple example if needed): > source("x.R") > options(error=recover) > x<- ... > f(x) # f() from x.R (subscript bou

Re: [Rd] Bug in tools::compactPDF() in 2.13-0-alpha

2011-03-27 Thread Duncan Murdoch
quot;) That won't work: you need the full path to the gs_cmd, not just its home directory. Duncan Murdoch NULL no matter what I do. This is with: sessionInfo() R version 2.13.0 alpha (2011-03-27 r55077) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_G

Re: [Rd] Typo in tools:::format.check_Rd_metadata()

2011-03-29 Thread Duncan Murdoch
.pretty_format(bad[[nm]])) })) Cheers, H. Thanks, will fix. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Reading 64-bit integers

2011-03-29 Thread Duncan Murdoch
ave to read it as two 4-byte numbers and check that the high-order one (which is endianness dependent, of course) is zero. A C-level sanity check seems more efficient and more helpful to me. Seems to me that the S-PLUS solution (output="double") would be a lot more useful. I'd com

Re: [Rd] Rtools and MinGW

2011-04-04 Thread Duncan Murdoch
ver be the same as the regular MinGW version (even if just by update cycle delays). Is there any other way to tell Rtools where to search for MinGW-bin except of setting the globally applicable PATH variable ? Some configuration file or so ? Why not just keep two PATH variables, and put one in pla

Re: [Rd] question about assignment warnings for replacement methods

2011-04-05 Thread Duncan Murdoch
sure how literally to take it). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rtools questions

2011-04-05 Thread Duncan Murdoch
64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Do you h

Re: [Rd] Rtools questions

2011-04-06 Thread Duncan Murdoch
On 11-04-05 7:51 PM, Henrik Bengtsson wrote: > On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote: >> On 11-04-05 6:22 PM, Spencer Graves wrote: >>> >>> Hello: >>> >>> >>> 1. How can I tell when the development version of Rtool

Re: [Rd] Rtools questions

2011-04-06 Thread Duncan Murdoch
On 06/04/2011 8:16 AM, Gabor Grothendieck wrote: On Wed, Apr 6, 2011 at 7:54 AM, Duncan Murdoch wrote: > On 11-04-05 7:51 PM, Henrik Bengtsson wrote: >> On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch >>wrote: >>> On 11-04-05 6:22 PM, Spencer Graves

[Rd] duplicates() function

2011-04-08 Thread Duncan Murdoch
it in C, if there isn't a simple implementation I missed. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Invalid connection after closing?

2011-04-08 Thread Duncan Murdoch
ot; In the current implementation, connections are a finite resource, and you need to be able to get rid of them when you are done. close(con) is the way to do that. If you want to re-open it, you need to remember the filename (or extract it before calling close()), and issue another call to

Re: [Rd] duplicates() function

2011-04-08 Thread Duncan Murdoch
should have posted would be x <- cbind(1, c(9,7,9,3,7) ) and I'd still like the same output duplicated(x) [1] FALSE FALSE TRUE FALSE TRUE duplicates(x) [1] NA NA 1 NA 2 Duncan Murdoch -- Joshua Ulrich | FOSS Trading: www.fosstrading.com On Fri, Apr 8, 2011 at 9:59

Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?

2011-04-09 Thread Duncan Murdoch
, all variables must be found in declared dependencies, the search could stop before it got to globalenv(). But it seems unlikely that your students are writing packages with namespaces.) Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Rtools questions

2011-04-09 Thread Duncan Murdoch
On 11-04-06 2:45 PM, Henrik Bengtsson wrote: On Wed, Apr 6, 2011 at 4:54 AM, Duncan Murdoch wrote: On 11-04-05 7:51 PM, Henrik Bengtsson wrote: On Tue, Apr 5, 2011 at 3:44 PM, Duncan Murdoch wrote: On 11-04-05 6:22 PM, Spencer Graves wrote: Hello: 1. How can I tell when the

Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?

2011-04-09 Thread Duncan Murdoch
in a function call like f(data.=ETB){if(missing(data.))data(ETB); data.}. When I run "R CMD check", I get "no visible binding for global variable 'ETB'", even though the function is tested and works during R CMD check. What is ETB? Your code is lo

Re: [Rd] Wish there were a "strict mode" for R interpreter. What about You?

2011-04-10 Thread Duncan Murdoch
On 11-04-09 9:22 PM, Spencer Graves wrote: On 4/9/2011 6:12 PM, Duncan Murdoch wrote: On 11-04-09 7:02 PM, Spencer Graves wrote: On 4/9/2011 2:31 PM, Hadley Wickham wrote: On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnson wrote: Years ago, I did lots of Perl programming. Perl will let you be lazy

Re: [Rd] deparse operators in expressions

2011-04-10 Thread Duncan Murdoch
take a look at src/main/deparse.c. The operators that are labelled as PP_BINARY2 get no spaces. Looking in src/main/names.c, we see those are /, ^, %%, %/% and :. But clearly this is by design, and I think it's unlikely to change. Duncan Murdoch deparse(expression(1/1)) [1] "

Re: [Rd] deparse operators in expressions

2011-04-10 Thread Duncan Murdoch
like +, - and *. I looked it up, and it has been like that since revision 2 when this code was first committed to our repository in 1997. I imagine whoever wrote it was following the pattern of some other language (maybe S), or maybe just their own personal taste. Duncan Murdoch Regards,

Re: [Rd] sort.int(S3object) strips class but not the is.object flag

2011-04-11 Thread Duncan Murdoch
I'll fix this in R-devel, and backport it to 2.13.0-patched. Duncan Murdoch > x<- structure(1:3, class="unrecognizedClass") > y<- sort.int(x) > t<- 1:3 > identical(y, t) # expect TRUE [1] FALSE > identical(as.vector(y), as.vector

Re: [Rd] duplicates() function

2011-04-11 Thread Duncan Murdoch
On 08/04/2011 11:39 AM, Joshua Ulrich wrote: On Fri, Apr 8, 2011 at 10:15 AM, Duncan Murdoch wrote: > On 08/04/2011 11:08 AM, Joshua Ulrich wrote: >> >> How about: >> >> y<- rep(NA,length(x)) >> y[duplicated(x)]<- match(x[duplicated(x)] ,x)

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