Kurt Hornik wrote:
>>>>>>Duncan Murdoch writes:
>
>
>>>>>On Tue, 7 Jun 2005, Duncan Murdoch wrote:
>>>>>
>>>>>[...]
>>>>>
>>>>>
>>>>>
>>>>>>My proposal (modified
On 6/10/2005 8:00 AM, Gabor Grothendieck wrote:
> On 6/10/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> Kurt Hornik wrote:
>> >>>>>>Duncan Murdoch writes:
>> >
>> >
>> >>>>>On Tue, 7 Jun 2005, Duncan Murdoch wrote:
&g
On 6/10/2005 8:17 AM, Duncan Murdoch wrote:
> On 6/10/2005 8:00 AM, Gabor Grothendieck wrote:
>> It would be invoked like this:
>>
>>package?boot
>>
>> with the effect of giving help on boot-package.
>
> Okay, I get it. That's a good change.
Tobias Verbeke wrote:
> In the `See Also' section of ?lowess, I read
>
> 'loess'), a newer formula based version [...]
Fixed, thanks.
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ld be changed (what's the point of having ``pretty''
> breakpoints anyway?), but if not, the documentation should be
> clarified.
I like the pretty breakpoints. It is good to label the breakpoints, and
ugly to have labels at other than pretty points. I'd clarify by
changing "giving" to "suggesting".
> I'll be happy to provide a patch if these changes are considered reasonable.
Please do.
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Thanks, I've committed the change.
Duncan Murdoch
On 6/17/2005 10:30 AM, Deepayan Sarkar wrote:
> On 6/17/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> On 6/17/2005 8:58 AM, Deepayan Sarkar wrote:
>> > I think there are a couple of things in ?hist that are no
to control that
behaviour.
The retention I put in is entirely within an R session. Each download
just makes the same progress window visible where you last left it,
instead of creating a new one. This way if you're doing something like
installing all of CRAN, you can push the
NE (vor)
>
>
> Note that the files are listed as: [1] "A" "B" "a" "b"
>
> Now start an R session
>> list.files("~/FOO")
> [1] "a" "A" "b" "B"
>
> which differs in order from
On 6/23/2005 4:38 PM, Duncan Murdoch wrote:
> On 6/23/2005 4:18 PM, Vadim Ogranovich wrote:
>> Hi,
>>
>> The list.files() function seems to order its result vector differently
>> when is run during R CMD INSTALL. Here is an example:
>>
>> ~% mkdir ~/FOO
ular the
chapters on the R API (for access to the underlying computational
routines) and the one on linking GUIs or other front-ends (which sounds
more like what you want to do).
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les)
>> file.show(rdFiles[1])
>> file.remove(rdFiles)
>>
>> For me it crashes when it gets to the Rdoc$compile() line and Dr. Mingw
>> reports:
>>
>> Rterm.exe caused an Access Violation at location 7c911e58 in module
>> ntdll.dll Reading from location 52474f52.
I get a crash there too. I'll take a look.
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of an SEXP would also be
welcome, but I can probably figure that one out once I get this...)
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On 6/29/2005 2:06 PM, Luke Tierney wrote:
> On Wed, 29 Jun 2005, Duncan Murdoch wrote:
>
>> I'm trying to track down a bug in some experimental code, where an
>> object's attribute is getting messed up. This means I'd like to examine
>> R objects while
handling multiple shortcuts
with the same hotkey. I'd rather stay away from this.)
#4 is another case where you can put your libraries outside R_HOME.
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I build R-patched and R-devel which
> I update from SVN.
I haven't seen that error so far during an R build, but I believe you'll
get it if the directory is busy because it is the current directory for
some process. Did you have another window open that was looking at it?
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On 7/4/2005 1:01 PM, Bo Peng wrote:
> Dear list,
>
> I have developed a forward-time population genetics simulation
> environment simuPOP, which is a set of C++ (template)
> classes/functions wrapped by SWIG as Python libraries. R is used
> extensively as plotting and statistical analysis engine t
;
>>
>>It was claimed its portable and that is true in the strictest sense that it
>>works on both UNIX and Windows but it would be even more
>>desirable if it were not just portable but also worked the way the target
>>system worked rather than just acting like a UNIX u
;[1] "A"
>>>[1] "B"
>>>Error in .C("K_MEANSC", xrows = as.integer(xrows), xcols =
>>>as.integer(xcols), :
>>> "C" function name not in load table
>>>Everything that is printed on the screen is correct,
the functionality, but is guaranteed to produce a legal file
of the type it claims to produce. I don't see anything wrong with it.
Duncan Murdoch
>
> On 7/7/05, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
>> This topic already came up about a week ago on R-devel
>>
y sees R calls, it doesn't know what
goes on within functions. .Call() is an R call which internally calls
some C function, but the profiler just sees the call to .Call.
Duncan Murdoch
>
> Many thanks,
>
> Gav
>
>
>>summaryRprof(filename = "Rprof.out"
call, but they should be
fine where you have them. (The advantage of putting them immediately
after Sweave is that you don't need to think about the next line. If it
created a temp file and you wanted to keep it, you'd need the extra
lines first. But it doesn't, so it doesn&#x
you really have additional information to add to the bug report.
We're planning (or in the process of?) changing the bug reporting
system, so this is only a temporary inconvenience.
Duncan Murdoch
On 7/8/2005 9:36 AM, [EMAIL PROTECTED] wrote:
> This is great. Thank you for your help, but let
On 7/8/2005 8:52 AM, Olaf Mersmann wrote:
> Hi Duncan,
>
> On 7/8/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> Olaf Mersmann wrote:
> *snip*
>> > Looking at the source for pairs() suggests, that this is the case
>> > because col is part of t
ook serious enough to
make it onto my list of things to do myself.
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way to write a wrapper to convert the variable so
that Cygwin's perl understands it, or a configuration flag, but I'd say
it's easier to use the ActiveState perl.
Rgui is a Windows program, not a Cygwin one.
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It sounds like developing an R package to act as a wrapper would be the
best approach. I didn't see documentation for their API (the exports of
their DLL), but I didn't spend long looking.
Duncan Mu
5-07-15) also got this problem (although it won't crash on
> the below example). I previously reported this
> (https://stat.ethz.ch/pipermail/r-devel/2005-June/033772.html) and
> Duncan Murdoch kindly offered to look into the problem, but it is
> tricky. Now I would like to t
For a graphics display, I'd like a high resolution timer, something like
Sys.time(), but it is only accurate to a second. Is there a clock in R
that gives a finer value?
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On 8/1/2005 9:09 AM, Martin Maechler wrote:
>>>>>> "Duncan" == Duncan Murdoch <[EMAIL PROTECTED]>
>>>>>> on Mon, 01 Aug 2005 08:48:39 -0400 writes:
>
> Duncan> For a graphics display, I'd like a high resolution
>
y work on some Windows
platforms, but I'd rather not do that until we're not officially saying
that R runs on Win9x.
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the write harmless? I suspect this may be the bug I fixed on
July 16, since it had to do with character classes including ranges
(like Charlie's "[a-pr-z]").
Charlie, have you tried a recent version of R-patched?
Duncan Murdoch
>
> On an un-optimized build of R I am unable t
e name parameter of the .Fortran function,
> "wrapper", "kmeans3", "wrapper_" or "kmeans3_"
>
> I always get the same error call telling me that the fonction
> "Fortran" is not in the allocation table
That message could be more
ny odd naming
conventions of your compiler from causing trouble, and you'll only have
to worry about odd parameter passing conventions (and how to create the
C language registration function).
Duncan Murdoch
>
> Sebastien
>
>
>
>
>>You want to just say:
>>
f baggage!), with
no attempt to say anything about the external thing they point to.
Duncan Murdoch
> -roger
>
> Martin Maechler wrote:
>>>>>>>"Paul" == Paul Roebuck <[EMAIL PROTECTED]>
>>>>>>>on Thu, 4 Aug 2005 00:29:03
get the same error message if a try the command "make
> pkg-test".
You need to make sure the tools directory (wherever you put it) is on
your path. Type PATH at a command prompt to see the current path; type
PATH= blah blah blah
to set a new one. See the R Admin manual for advice
> ff[[2]]
x
> ff[[2]] <- as.name("weights")
> ff
weights ~ g * h
If you know that ff is a formula with an expression on the left that you
want to replace with "weights", then ff[[2]] <- as.name("weights")
will
fferent name that still describes the function), but will often fail,
in which case I'd use the prefix/suffix decoration. Changing only
capitalization makes it nearly impossible to talk about your function
without confusion.
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tories to search. MikTex
doesn't, and it causes lots of trouble for people. This is the main
reason I haven't recommended MikTex over fptex even though I use it;
MikTex seems less stable about its interface.
Duncan Murdoch
>
> Various R docs recommend fptex or MikTex implement
ot (a ~ b)
> Error in list(a, b) : invalid 'envir' argument
>
> When we do exactly the same on another machine (Win2000) it works correctly.
> Any suggestions?
You probably have overwritten boxplot() or something with your own
object. This works fine for me in 2.1.0 (but yo
e of such systems.
No, there are no 64 bit Windows versions yet. You'll need to install
some 64 bit version of Linux on those machines to take full advantage of
the chips.
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27;ll need someone with a
64 bit Windows machine to handle builds there.
Duncan Murdoch
> Thanks in advance.
>
> Milton F. López
> IT Guy
> Inter-American Tuna Commission (IATTC)
> 8604 La Jolla Shores Drive
> La Jolla, CA 92037
> Tel: (858) 546-7041, Fax: (858) 546-713
documenting it), I'd be willing to take a look at your code
and commit it when it looked okay.
The deadline for this to make it into 2.2.0 is that I'd want to commit
it by Sept 6, so there's not a lot of time left.
Duncan Murdoch
>
> I think that just about sums it up.
[EMAIL PROTECTED] wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>
>>I would implement it differently from the way you did. I'd call it
>>a rawConnection, taking a raw variable (or converting something else
>>using as.raw) as the input, and provi
[EMAIL PROTECTED] wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>>>Having a rawConnection() entry point is simple enough. Seeking also
>>>seems straightforward. I'm not so sure about using as.raw(). I
>>>wondered about that, but also thought t
[EMAIL PROTECTED] wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>
>>I think the cost of duplicating as.raw is worse than the cost of using
>>extra memory. If the lack of symmetry bothers you, a solution is to
>>require a raw object as input.
>
>
bit Linux is much larger, but I don't know exactly
what.
Duncan Murdoch
>
> Thanks again for your prompt responses.
>
>
> M.
>
> -Original Message-
> From: Luke Tierney [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, August 31, 2005 6:04 PM
> To:
build the setTeXenv.sh script--but what
should it contain? Alternatively, can GNU make export environtment
variables directly, and skip creating this new script?
Advice from shell hackers is welcomed!
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On 9/6/2005 10:56 AM, Duncan Murdoch wrote:
> I'd like to make MikTeX the default TeX package in 2.2.0, but we still
I forgot to say "in Windows". Sorry.
> need to let people use other packages. The problem is that MikTeX wants
> a command line option --include-direc
ase that a side-effect of building a binary package
> is having that package be installed? My understanding is that R CMD
> INSTALL --build is the way to get zips on Windows, but maybe this
> changed?
There are two ways: R CMD INSTALL --build, and R CMD build --binary.
The latter do
load your dll by attaching the package,
then click on Misc | Break to debugger.
This assumes you have debugging symbols in your DLL, and have gdb set up
properly; see
http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR
for more details.
Duncan Murdoch
>
> I'm using R 2.1.
e
R's stack, because in almost all other situations, writing that much
data to the stack is a sign of an infinite recursion.
Duncan Murdoch
>
>
> Details of the configurations on which I perfo
nfig
files (or set an environment variable).
I'd appreciate hearing of any problems during the alpha or beta test period.
A binary build containing the changes should be on CRAN tomorrow or the
next day. Look for revision 35546 or higher.
Duncan Murdoch
can Murdoch
>
> On 9/9/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>>I've just committed some changes to allow R to be built and to use
>>MikTeX without needing the Rd.sty files to be installed to localtexmf.
>>Unfortunately, the changes are not compatible wi
Gabor Grothendieck wrote:
> On 9/9/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>>I've just committed some changes to allow R to be built and to use
>>MikTeX without needing the Rd.sty files to be installed to localtexmf.
>>Unfortunately, the changes are not
've bookmarked the pages you
> sent me.
>
> Seth - Thanks for suggesting valgrind. I tried it out, and it correctly
> told me that memory leakage was not the problem (although I didn't believe
> it at first).
Is there a version of valgrind that works in Windows now, or di
Gabor Grothendieck wrote:
> On 9/10/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>>Gabor Grothendieck wrote:
>>
>>>On 9/9/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>>>
>>>
>>>>I've just committed some changes to all
Simone Giannerini wrote:
> Dear Duncan and Simon,
>
> many thanks for your helpful reply.
>
>
>>Duncan Murdoch wrote:
>>It looks as though your Fortran compiler is allocating the new matrix on
>>the stack. R doesn't give you a huge stack, and that's
On 9/9/2005 10:11 PM, Gabor Grothendieck wrote:
> On 9/9/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> I've just committed some changes to allow R to be built and to use
>> MikTeX without needing the Rd.sty files to be installed to localtexmf.
>> Unfortunately
-). Putting
together a simple package that does this would be nice, and would be
available sooner than 2.3.0.
Duncan Murdoch
> By the way I did find a tool, sigcheck.exe, on sysinternals.com
> that will find the file and product versions and running it on RGui.exe
> it does work.
; installing DLL
> installing R files
> installing inst files
> FIND: Parameter format not correct
Looks like a path problem. There's a find command in the R tools, and a
completely different one in Windows. You need to set your path to find
the R one first.
Duncan Murdoch
On 9/15/2005 7:51 PM, [EMAIL PROTECTED] wrote:
> First of all, thanks to those who've set up R to work so smoothly with
> Miktex-- even a total Latex bunny like me got it to work instantly, so
> that for the first time I'm able to run my Rd files through the Latex
> side of RCMD CHECK.
>
> Now the
On 9/16/2005 4:16 PM, Prof Brian Ripley wrote:
> There are two instances of this. If I add 'go' to both it works for me.
> I guess you only had the first one (the second is used here).
Yes, that's it. Thanks!
Duncan Murdoch
>
> On Fri, 16 Sep 2005, Duncan Murdoch
;
> Instead of the former argument
>
>panel = points
>
> I use the new ones
>
>panel = if(add.smooth) panel.smooth else points,
>
> add.smooth = isTRUE(getOption("plot.add.smooth")),
>
> - - -
>
> Now I even propo
have missed too much of the earlier
> discussion under some other subject.)
This was going to affect only plot.lm, as far as I know.
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> the clipboard, not just the text.
This looks like something someone should write a package to do. It
needs lots of support (e.g. what do all the possible clipboard format
constants mean, what binary format corresponds to each, etc.), but it
would only be useful on the
s easy for package
writers to write connections. Then a package writer could write
clipboard(), and it would fit into the rest of the R machinery.
Duncan Murdoch
>
> On 9/22/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> On 9/22/2005 11:13 AM, Gabor Grothendieck wrote:
>&g
On 9/22/2005 2:50 PM, Gabor Grothendieck wrote:
> On 9/22/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>> On 9/22/2005 1:12 PM, Gabor Grothendieck wrote:
>> > There is an open source clipboard extender CLCL that handles all
>> > clipboard formats. I think this co
urrently be a good way to do what he wants other than pattern matching
on the output.
It would probably be a good idea to deprecate warning.expression in the
next release, rather than beefing it up. If we don't have a good method
to do what Thomas wants, we should add it, but warning.expres
s the above:
> x <- NULL
> x[[1]] <- numeric(0)
> x
[1] 4.250083e-314
It looks like we're trying to be too clever with handling assignments to
components of NULL. Wouldn't it make more sense for those to generate
an error?
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On 9/26/2005 10:29 AM, Peter Dalgaard wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>
>> After foo<-list(), foo$bar is NULL, so we can simplify this.
>>
>> Here's a simpler version:
>>
>> # These work, which is a bit of a surprise, but
not an error in your
own code. If you need to use simulated data, call set.seed() first so
we can reproduce the results.
Thursday is code freeze; if you can post the relevant information enough
before that there's a good chance this could be fi
ted and you have the disk space
for both, perhaps both trunk and the current patch branch could be
listed, but I expect the statistics will be very similar.)
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) both die for lack of memory.
Any suggestions on how to do what I want, without using SAS?
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On 9/30/2005 1:41 PM, Peter Dalgaard wrote:
> Duncan Murdoch <[EMAIL PROTECTED]> writes:
>
>> I want to calculate a statistic on a number of subgroups of a dataframe,
>> then put the results into a dataframe. (What SAS PROC MEANS does, I
>> think, though i
, function(data) tapply(data$value, data$gp2,
> mean))
> data.frame.by(dataset, "gp1", function(data) lm(gp2 ~ value, data)) #
> doesn't print, but everything is there ok
>
> (note that the results column will be a list if necessary - this may
> be a serious abuse of data f
hat do
> those do exactly, and how do they relate to the REPL and R_Parse1()?
>
> Finally, are there any docs describing the design and implementation
> of the R internals? Should I be looking anywhere other than the R
> developer page here?:
The source code is sometimes the best place for low level details like
this. The R Language manual sometimes gives low level details, but is
is uneven in its coverage; I forget if it covers this.
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ow collected in the
Installation and Administration manual. Try following the setup
instructions there and see if it still fails.
Duncan Murdoch
>
> On 1.7.1 I built a packge with this command:
>
>Rcmd build --force --binary iL04
>
> On 2.2.0 this fails. First I had to copy sh.
NA
Shouldn't the second entry in the result be 2, with name "NA"? It seems
the string "NA" has been converted to here.
Duncan Murdoch
Prof Brian Ripley wrote:
> On Thu, 6 Oct 2005, "Jens Oehlschlägel" wrote:
>
>
>>Dear Thomas,
>>
&g
Peter Kleiweg wrote:
> Prof Brian Ripley schreef op de 7e dag van de wijnmaand van het jaar 2005:
>
>
>>On Fri, 7 Oct 2005, Peter Kleiweg wrote:
>>
>>
>>>Duncan Murdoch schreef op de 6e dag van de wijnmaand van het jaar 2005:
>>>
&g
ve ended up
with some fairly tricky Makefile programming to get what we want into
the R banner.
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Gabor Grothendieck wrote:
> On 10/7/05, Duncan Murdoch <[EMAIL PROTECTED]> wrote:
>
>>Gabor Grothendieck wrote:
>>
>>>Is there some way of automatically including the svn version number
>>>of a package in the DESCRIPTION file or otherwise so that one
&g
from, and seeing at that
point what is causing it.
I have some instructions for debugging R packages in Windows on
http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/.
Duncan Murdoch
>
>> library("bpkg")
> .onLoad: running R_g95_init
>> data(yij)
>> o =
me subtle change in the tools.
You may not have the latest versions of the MinGW tools. Check the
Admin and installation manual, or http://www.murdoch-sutherland.com/Rtools/.
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open a new file when the window demo window is
> active.
> the error can be reproduce easly.
Not reproducible for me in 2.2.0. Things worked just as I'd expect.
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t;record 7 subtype 13, which is where the long variable names live.
>>
>
> What about using the SPSS input dll for those R users which would like to use
> their old SPSS files.
If you have that file, then presumably you have SPSS, and can ask it to
output a documented file format.
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gt;>dlapack0.f:203: warning: 'ipv' might be used uninitialized in this
>>>function
>>>dlapack0.f:203: warning: 'jpv' might be used uninitialized in this
>>>function
>>>dlapack0.f:204: warning: 'smin' might be used uninitial
structions on how to do
translations are on the web page
<http://developer.r-project.org/Translations.html>. If you want to
organize a Spanish translation team, I could list your name and contact
information on <http://developer.r-project.org/Transla
fic differences.
You don't need an OOP language to write a GUI (the Windows Rgui is
written in C, for example), but it makes things easier.
You can write R in that style, but it's not the standard style to use,
so it's not particularly easy.
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regular output, warnings, and errors)
would tie us down too much in the internal details.
Duncan Murdoch
Thomas Friedrichsmeier wrote:
>>I second the point about not having made a case, and also that (from the
>>part deleted below) about needing to understand the internals
the same output as
you did. Which version are you comparing to?
Duncan Murdoch
In my opinion, this
> leads to an inconsistency when indexing one-row matrices.
> Take
>
>>(mat <- matrix(1:9, nrow = 3, dimnames = list(paste("r", 1:3, sep = ""),
>
> paste(&
On 10/18/2005 8:51 AM, Thomas Friedrichsmeier wrote:
>> I'll volunteer to do your testing on Windows, provided nobody suggests a
>> way to do what you want without your patches. That is, if there's a way
>> for a custom front-end to separate the streams of text coming to
>> ptr_R_WriteConsole thro
mn name for that [1,1] element?
What should it do with the expression
mat[1,1 , drop = FALSE][1]
?
If you are really concerned about the names, you should use matrix
indexing in both places with drop = FALSE:
> mat[1, , drop = FALSE][1,1,drop=FALSE]
c1
r1 1
Duncan Murdoch
>
&g
ly want to
work with things as binary objects you'll need lower level access. It's
not that bad if you just want to write a function that gets passed R
objects. I don't think it be called "simple" if you want to do away
with the cons
need of a replacement and not an
> indication of a problem with the web sites.
No, that was my error. It's fixed now, and my md5sum agrees with yours.
Duncan Murdoch
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at the fix should be. There's a
>>test in image.default
>>
>>if (any(!is.finite(zlim)) || diff(zlim) < 0)
>>stop("invalid z limits")
>>
>>
>>that is throwing the error. We want the error if a user specifies
>>diff
on as the binary. If one is tampered with, the other
> one could be too. For the main release, I always send the md5sums via
> the mailing lists.
Well, the bad file was online for two weeks before anyone noticed, so
I'm not sure everyone is being diligent in checking it.
Duncan Murdoch
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2.0pat-win32.exe
http://cran.us.r-project.org/bin/windows/base/R-2.3.0dev-win32.exe
Duncan Murdoch
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d.html is currently looking like
> this:
See the thread on this with subject "Re: [Rd] download problem: Windows
binaries - patched/devel versions". We know about it and are working on
it. It's caused by the mirroring software being a little too helpful.
Duncan Murdo
haviour for floating point values,
discussed in the FAQ item on "7.31 Why doesn't R think these numbers are
equal?"
Duncan Murdoch
>
> To reproduce:
>
> expected:
>> typeof(3)
> [1] "double"
>
>> as.integer(3)
> [1] 3
>
> stra
ngs
like "eval", "substitute", etc. So I'd say that you don't want anything
special there, as long as you make sure that FUN is always evaluated in
its original environment.
Generally I don't like the look of that manipulation of the body of your
result; it lo
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