Re: [Rd] S4 Method Rd Warning

2010-08-30 Thread Duncan Murdoch
eased. Could you try 2.11.1-patched or the devel version of 2.12.0 and see if you still get the warnings? Duncan Murdoch The warning says : * checking Rd \usage sections ... WARNING Bad \usage lines found in documentation object 'enrichmentCalc': S4method{enrichmentCalc}{GenomeDataLis

Re: [Rd] introspective capabilities

2010-08-30 Thread Duncan Murdoch
oking in attr(body(f), "srcref"). See ?srcref for the format; there aren't a lot 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

Re: [Rd] introspective capabilities

2010-09-01 Thread Duncan Murdoch
On 01/09/2010 9:27 AM, Christophe Rhodes wrote: Duncan Murdoch 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 th

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

2010-09-03 Thread Duncan Murdoch
flush out 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-r

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

2010-09-03 Thread Duncan Murdoch
fine. Are you using a NAMESPACE, and declaring your method as a method? If you 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 si

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

2010-09-08 Thread Duncan Murdoch
ms to have made some bad decisions 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
nment 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 wrote: On Wed, Sep 8, 2010 at 12:37 PM, Duncan Murdoch wrote: On 08/09/2010 1:21 PM, Jeffrey Horner wrote: Hi all, I'm setting up a development environment on Windows as the subject implies.

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

2010-09-09 Thread Duncan Murdoch
of silently eating the error: it might have been a typo, that just 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] Non identical numerical results from R code vs C/C++ code?

2010-09-10 Thread Duncan Murdoch
For example, suppose epsilon is the smallest number such that 1 + epsilon is not equal to 1. Then 1 + (epsilon/2) + (epsilon/2) will evaluate to either 1 or 1 + epsilon, depending on the order of computing the additions. Duncan Murdoch Thank you, Ren

Re: [Rd] Non identical numerical results from R code vs C/C++ code?

2010-09-10 Thread Duncan Murdoch
esults. The result will still be 'double' anyway right? Yes, you do need to return type double. Duncan Murdoch On 10/09/2010 13:00, Duncan Murdoch wrote: On 10/09/2010 6:46 AM, Renaud Gaujoux wrote: Hi, suppose you have two versions of the same algorithm: one in pur

Re: [Rd] Windows build

2010-09-10 Thread Duncan Murdoch
7;s where the logs of all the tests of examples are saved. But I can guess at the problem: you don't have 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&#

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

2010-09-11 Thread Duncan Murdoch
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 Murdo

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 ' gets stalled duri

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

2010-09-12 Thread Duncan Murdoch
s where people 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-de

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, >>

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&#x

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

2010-09-14 Thread Duncan Murdoch
oblem with this change 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 ch

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

2010-09-16 Thread Duncan Murdoch
eton is calling to produce the bad man pages. My own feeling is that package.skeleton should produce a package that is installable, but it shouldn't pass "R CMD check" unless there's some manual intervention to fill in the details. I think that is the current state of affairs,

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

2010-09-16 Thread Duncan Murdoch
we should create all the directories: it's mainly aimed at beginners, who might find that intimidating. Advanced users 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 DESCR

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

2010-09-21 Thread Duncan Murdoch
ample 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 Forner wrote: > Hello, > >

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

2010-09-22 Thread Duncan Murdoch
, I can reproduce the problem, 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 l

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

2010-09-27 Thread Duncan Murdoch
. You can put your logo 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

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

2010-09-30 Thread Duncan Murdoch
ier\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

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

2010-10-01 Thread Duncan Murdoch
could. Environments only have one parent. If you read 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_funct

Re: [Rd] Eval and the enclos argument

2010-10-02 Thread Duncan Murdoch
meaningful (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 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) || is.pairlist(envir)) parent.

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Duncan Murdoch
pdating your LaTeX inputenc package. 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 Ito replace it with another command, or

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Duncan Murdoch
rrent R version, delete the old file. Duncan Murdoch Renaud 2010/10/3 Duncan Murdoch : 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=cjW7lImMaNC6

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

2010-10-04 Thread Duncan Murdoch
t a name 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 ___ Aust

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 dow

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

2010-10-05 Thread Duncan Murdoch
beta. 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 lin

Re: [Rd] Recursion error after upgrade to R_2.11.1 [Sec=Unclassified] [Sec=Unclassified]

2010-10-07 Thread Duncan Murdoch
t;> callNextMethod(<...>), on the hopes that the method >> eventually called would take care not to make too many copies >> on slot assignment. >> >> Martin >> TR> Hmmm, not sure what you mean here? My code passes objects

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

2010-10-08 Thread Duncan Murdoch
other situations (e.g. if te was a list to start, 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. Dun

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

2010-10-08 Thread Duncan Murdoch
x27;s a bug, because NULL assignment in data.frames would not convert them to lists, for example. I think you're probably right. Thanks for looking into it. It's quite inconvenient when you have to manipulate named expression. Have to use constructs like et<-et[!names(et)%in%"

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 wrote: On 08/10/2010 12:24 PM, Vitalie Spinu wrote: On Fri, Oct 8, 2010 at 12:14 PM, Duncan Murdoch wrote: Vitalie Spinu wrote: Hello Everyone! NULL replacement will change expression

Re: [Rd] Missing libpthread in RTools

2010-10-15 Thread Duncan Murdoch
ry are standard in Cygwin. 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 ___

Re: [Rd] R 2.12.0 doesn't install properly under Windows Vista

2010-10-16 Thread Duncan Murdoch
). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] R 2.12.0 doesn't install properly under Windows Vista

2010-10-17 Thread Duncan Murdoch
from being included in the installer. So you'll need to debug what's going wrong in your build process that stops Rgui.exe from being built. Duncan Murdoch Sorry to be a pest. Thanks, Erin Erin M. Hodgess, PhD Associate Professor Department of Computer and Mathematical Science

Re: [Rd] R 2.12.0 problems with Windows XP 32-bit binary installer

2010-10-17 Thread Duncan Murdoch
ht place. Generally that's an i386 subdirectory for 32 bit, and an x64 directory for 64 bit. I don't know why a 32 bit DLL wouldn't work with 32 bit R 2.12.0, but if it was installed for 2.11.1, it might not be in the right place. Duncan Murdoch _

Re: [Rd] Sweave and absolute escaped backslashed Windows paths in R 2.12.0

2010-10-25 Thread Duncan Murdoch
Brian Diggs wrote: I've noticed a change in behavior in R 2.12.0 from 2.11.1 regarding the treatment of absolute paths in the file argument of Sweave in a Windows environment. Looks like a bug to me, probably related to the new error reporting. Duncan Murdoch Consider the minimal Rnw

Re: [Rd] Sweave and absolute escaped backslashed Windows paths in R 2.12.0

2010-10-25 Thread Duncan Murdoch
On 25/10/2010 6:24 PM, Duncan Murdoch wrote: Brian Diggs wrote: I've noticed a change in behavior in R 2.12.0 from 2.11.1 regarding the treatment of absolute paths in the file argument of Sweave in a Windows environment. Looks like a bug to me, probably related to the new error repo

Re: [Rd] Link to R 2.12.0 patched build for windows

2010-10-27 Thread Duncan Murdoch
. The files should be fine later today or tomorrow. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] on the usage of do.call

2010-11-02 Thread Duncan Murdoch
uld rarely want to use do.call from C. You should use eval(). See the examples in the Writing R Extensions manual, in the section "Evaluating R expressions from C". Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

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

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