On Tue, 7 Jun 2005, Duncan Murdoch wrote:
[...]
My proposal (modified following the suggestions I've heard so far) is as
follows:
- to check that a couple of help topic aliases exist (pkg.package
and pkg)
- to recommend that pkg.package contain general information about
the package
extensions manuals tells you the filenames that mean something to
R. (See the Package Structure section.) All else is omitted unless
it's in the inst directory, in which case it should be copied up a level
upon installation.
Duncan Murdoch
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to me.
Duncan Murdoch
To follow up on Gabor's suggestion to add more R CMD check granuality
than errors and warnings. Using classes and the new exception
handling, one could introduce a warning class called Suggestion
(CranSuggestion), which gives suggestions to the user, but not enforce
them
Torsten Hothorn wrote:
On Tue, 7 Jun 2005, Duncan Murdoch wrote:
[...]
My proposal (modified following the suggestions I've heard so far) is as
follows:
- to check that a couple of help topic aliases exist (pkg.package
and pkg)
- to recommend that pkg.package contain general information
The following is a bug or mis-design in help(package=):
showhelp - function(packageName) help(package=packageName)
showhelp(utils)
Error in .find.package(pkgName, lib.loc, verbose = verbose) :
none of the packages were found
The problem is that it calls library(help=) with
, not just for NULL. Changing that so
it only accepts NULL fixes this bug.
This code has been in place since prehistoric times, so I'm going to
tread pretty carefully here before I commit a change.
Duncan Murdoch
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be perfectly acceptable for ?package to pop up a vignette for
the package. However, right now we have too many different types of
ways to display help, and not all of them are capable of displaying
vignettes.
Duncan Murdoch
Best wishes
Robert
Some packages have so much material that it's
On 6/7/2005 11:59 AM, Robert Gentleman wrote:
Duncan Murdoch wrote:
On 6/7/2005 11:12 AM, Robert Gentleman wrote:
Robin Hankin wrote:
My 0.02:
I use Misc.Rd for the purpose that Duncan suggests. I put things
like details and rationale for package
organization, pointers to the most
above doesn't achieve that, but it gets closer.
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to a standard help topic for the package, so I like the
original better, but this would be better than the status quo.
Duncan Murdoch
Just my $0.02...
Andy
From: Duncan Murdoch
Prof Brian Ripley wrote:
I share Robert's `pretty strenuous' objections.
Adding compulsory things for package
, it doesn't always happen:
new(foo, bar = expression(1+1))
An object of class foo
Slot bar:
expression(1 + 1)
x - expression(1+1)
x
expression(1 + 1)
eval(x)
[1] 2
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is in them.
Of course, with disk sizes as they are now, it's not unreasonable to
install all of the contributed CRAN packages on a PC. Then
help.search() *will* do searches through them all.
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(dead ~ dose, family = binomial(link = logit)))
Error in .Call(logit_link, mu) : cannot resolve native routine
Execution halted
I'm cc'ing this to R-bugs so we don't forget it, but I'm not going to be
able to fix it down myself.
Duncan Murdoch
; when
you're done, you can send me the files and I'll review and commit the
changes.
Duncan Murdoch
[EMAIL PROTECTED] wrote:
Full_Name: Gavin Simpson
Version: 2.1.0-patched (1-Jun-2005)
OS: Linux (Fedora Core 3)
Submission from: (NULL) (128.40.32.76)
axis.Date() insists on labelling tick marks
you're done, you can send me the files and I'll review and commit the
changes.
Duncan Murdoch
[EMAIL PROTECTED] wrote:
Full_Name: Gavin Simpson
Version: 2.1.0-patched (1-Jun-2005)
OS: Linux (Fedora Core 3)
Submission from: (NULL) (128.40.32.76)
axis.Date() insists on labelling tick
changes are now committed to
R-devel (which will become version 2.2.0). Thanks!
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this change after testing, but I hope Duncan TL has time to
look at it and make sure the logic is okay.
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Duncan Murdoch wrote:
Huntsinger, Reid wrote:
Sorry, I was looking at 2.0.1 when I meant to be looking at 2.1.0. The line
numbers for the latter are 161-179 and line 164 is the one with what I think
is a typo.
Reid Huntsinger
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL
Jon Stearley wrote:
On Jun 1, 2005, at 11:22 AM, Duncan Murdoch wrote:
These functions convert their first argument to a vector (or
array) of character strings which have a common format (as is done
by 'print'), fulfilling 'length(format*(x, *)) == length(x)'. The
trimming
devices the first text
drawn could be improperly sized. (PR#7860).
If not, please download a newer copy of R-patched, and see if you can
still reproduce the bug. I can't reproduce it in a recent build.
Duncan Murdoch
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on windows() and related devices the first text
drawn could be improperly sized. (PR#7860).
If not, please download a newer copy of R-patched, and see if you can
still reproduce the bug. I can't reproduce it in a recent build.
Duncan Murdoch
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(...) then it tries to evaluate the arguments and dies
(because foo doesn't exist). If I use args - substitute(...) then it
gives just 1+1, it doesn't keep the names or give the whole list.
Is this possible?
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Prof Brian Ripley wrote:
On Thu, 19 May 2005, Duncan Murdoch wrote:
I'd like a function to get an unevaluated copy of its argument list,
including ... . That is, I'd like
f - function(...) {
args - what goes here??
args
}
when called as
f(a = 1+1, b = foo)
to return something like list
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. This is fixed now in the patched version. It
should show up in the snapshot builds on CRAN by tomorrow.
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on CRAN, so that's what I'd expect in this case.
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This is fixed now, in R-patched and R-devel.
Duncan Murdoch
[EMAIL PROTECTED] wrote:
Bob O'hara wrote:
I'm a bit reluctant to call anything a bug: I know it's usually my
incompetence instead. In this case, I can't see what else it is,
although it may be a bug in Windows.
The problem comes from
-project.org/bin/windows/base/rpatched.html
Thanks!
Duncan Murdoch
From: [EMAIL PROTECTED]
Subject: png device plot on athlon 64 processor
Date: Fri, 25 Feb 2005 15:52:40 +0100 (CET)
Full_Name: Emiel Ver Loren van Themaat
Version: 2.0.1
OS: windows XP
Submission from: (NULL) (145.117.31.248)
On our
, but I'd like to hear from someone on a different
platform...
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[EMAIL PROTECTED] wrote:
Yes, you are correct. I had only checked one of my platforms. Linux
works as you suggest. But for me on Windows,=20
Certainly looks like a bug on Windows to me. I'm going offline for a
day very soon now, but I'll try to remember to look into it.
Duncan Murdoch
x - 1
y
a - read.table('datafile2.txt',header=T)
a
scores - edit(data.frame(a))
After that i try to move with my third click on my mouse and
big bug and i'm ejected
I think this has been fixed. Could you please try the R-patched
version, available on CRAN mirrors, to confirm?
Duncan Murdoch
Prof Brian Ripley wrote:
On Mon, 9 May 2005 [EMAIL PROTECTED] wrote:
[Alexander Stoddard]
Subject: Re: [Rd] How to understand packages, namespaces, environments
Does saying the following load package 'foo' into its own
environment ?
library(foo)
[Duncan Murdoch]
This loads some of the (name
there are no syntax
errors, committing, possibly porting the change to the patch branch), so
batching them is efficient.
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Peter Dalgaard wrote:
[EMAIL PROTECTED] writes:
Full_Name: Michael Hoffman
Version: 2.1.0
OS: Linux (Fedora Core 3, kernel 2.6.11-1.14_FC3)
Submission from: (NULL) (193.62.199.8)
help(arrows) says:
arrows(x0, y0, x1, y1, length = 0.25, angle = 30, code = 2,
col = par(fg), lty =
Peter Dalgaard wrote:
[EMAIL PROTECTED] writes:
Full_Name: Michael Hoffman
Version: 2.1.0
OS: Linux (Fedora Core 3, kernel 2.6.11-1.14_FC3)
Submission from: (NULL) (193.62.199.8)
help(arrows) says:
arrows(x0, y0, x1, y1, length = 0.25, angle = 30, code = 2,
col = par(fg),
), but not in the
sense that it is the method that should be called.
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to make an
example using the import work, either during Rcmd CHECK or in the
console. It makes the import available from within your package, but
examples are run in the global environment.
Duncan Murdoch
Regards,
Florian
Here is my NAMESPACE file:
export(analysePlate, as.all
, but I don't think it exists now.
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the environment), but S4
methods aren't self-contained, they need to be registered with the
system. You could probably write a function to load them and
register them all at once, but I don't think it exists now.
Duncan Murdoch
(1) What is the difference between loading and registering objects in R
can be gigantic).
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to access its state. Each object exposes an
interface that specifies how other objects may interact with it.
Neither of these properties holds in S4.
Duncan Murdoch
But the hindrances faced by our friend Ali are
common, and even in packages maintained by experienced
R developers, S4 is implemented
Seth Falcon wrote:
Duncan Murdoch [EMAIL PROTECTED] writes:
What S4 is missing is encapsulation. Wikipedia's article on
object-oriented programming gives a good definition:
Encapsulation - Ensures that users of an object cannot change the
internal state of the object in unexpected ways; only
off.
So far this function is only in R-devel, but I'll commit it to R-patched
the next chance I get.
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it, I think the 0x prefix is fine.
We should provide a way to use other bases on input and output. This
could be through format specifiers, but it would be enough to have a pair
of dedicated functions to do the conversions.
Duncan Murdoch
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of the same
text. I didn't read it all, so might have missed something new hidden in
there.
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to write such a thing, in that R and C++ are
more different than Java and C++ are.
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must be used in S-PLUS and R to
detect and process the arguments of a function that can have empty
arguments matched to '...'.
Can you give an example where it's useful to do this, i.e. to have a
call like f(1,2,)? I've never used that construction as far as I can
recall.
Duncan Murdoch
the files, but not where to put them.)
Good suggestion; I've just done it. I think the only reason I didn't do
it before was laziness.
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them.
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After the release, I think this should go into R-patched. Do we have
tools to tell the translators all the new strings that need translating,
or should they be explicitly informed about such a thing?
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Prof Brian Ripley wrote:
On Wed, 13 Apr 2005, Duncan Murdoch wrote:
Prof Brian Ripley wrote:
On Tue, 12 Apr 2005, Liaw, Andy wrote:
Please consider adding the following to the next R release (I
understand
that it's too late for R-2.1.0). It adds the menu item `Search R
Site' in
the `Help' menu
this is not an unreasonable request considering that there is
menu item to select repositories to include BioConductor in R-2.1.0beta.
I think this would make more sense as an enhancement to
search.r-project.org (the site where RSiteSearch sends the search
request) than to Rgui.
Duncan Murdoch
.
The easiest thing is to write C routines to be called from R, but you
can also call some R functions or R itself from a C program.
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of Welch (1951) is used, which
generalizes the commonly known 2-sample Welch test to the case of
arbitrarily many samples.
I guess preformed should read performed
Thanks, I'll fix it.
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the
prediction and a new observation) rather than the standard error
(i.e. the stddev of the prediction).
Duncan Murdoch
Marek Ancukiewicz
n - 10
x - 1:n
y - x
y[c(2,4,6)] - y[c(2,4,6)] + 0.1
y[c(3,5,7)] - y[c(3,5,7)] - 0.1
a - lm(y~x)
rms - sqrt(sum(a$residuals^2)/(n-2))
s - covmat(a)*rms^2
Murdoch
cheers
dave
--please do not edit the information below--
Version:
platform = i386-pc-linux-gnu
arch = i386
os = linux-gnu
system = i386, linux-gnu
status =
major = 2
minor = 0.1
year = 2004
month = 11
day = 15
language = R
Search Path:
.GlobalEnv, package:methods
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and to the 2.0.1 patch version.
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diagnosis is right, because I was just trying to
manually duplicate bits of the CHECK script, and I might have missed a
setwd somewhere.
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saving the new preferences
first. As a result, I did not have an Rconsole file in My Documents.
This might be the reason why the problem was not reproducible by the
development team.
I think there's still something else: I don't see it when I follow
your instructions above.
Duncan Murdoch
saving the new preferences
first. As a result, I did not have an Rconsole file in My Documents.
This might be the reason why the problem was not reproducible by the
development team.
I think there's still something else: I don't see it when I follow
your instructions above.
Duncan Murdoch
then you won't have any files installed which
shouldn't be there.
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= nx, nx - 1, trunc(lx))
ifelse(ly = ny, ny - 1, trunc(ly))
would probably be a better fix, but I'd really like to see an example
of this in action. Could you email me a dataset where you see it?
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today's arithmetic.c with no error,
using
$ gcc --version
gcc.exe (GCC) 3.4.2 (mingw-special)
Copyright (C) 2004 Free Software Foundation, Inc.
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be to use the R menu item
Misc|Break to debugger to break out of R once it is running, and set
your breakpoints then, but I don't know that it will make any
difference.
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the reasons for the write barrier, see
http://www.stat.uiowa.edu/~luke/R/barrier.html
Duncan Murdoch
Did anyone come across such a problem?
version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system
as the environment for a function, you should
use
environment(f) - NULL
for now.
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using it in
the long term.
Sorry for any inconvenience that this causes.
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I've now added a function called alarm() to ring a bell. It's
documented to work on some platforms, but not all.
If it truly is easy to support this, you might as well, but I can't
see this as a high priority.
Duncan Murdoch
On Mon, 7 Mar 2005 21:12:17 +0100, stefano iacus
[EMAIL PROTECTED
(environment(NULL))
+ }
env - h( function(x) x^2 )
env$H
function(x) x^2
env$H(1)
[1] 1
Is this a bug, or just the way things are?
I get the same results in both R-patched and R-devel.
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promise: 0118A148
h - function( H ) {
+ H - H
+ return(environment())
+ }
env - h( 3 )
env$H
[1] 3
Duncan Murdoch
On Tue, 8 Mar 2005, Duncan Murdoch wrote:
I'm working on a function that does adaptive sampling, and I thought
it would be handy to return the function's environment
-function
H - env$H
H(1)
[1] 1
So the oddity is that I can evaluate H within f() without any problem,
but outside of f() I need extra work before I can do it.
Duncan Murdoch
On Tue, 08 Mar 2005 18:00:10 +, Duncan Murdoch
[EMAIL PROTECTED] wrote :
On Tue, 8 Mar 2005 17:44:41 + (GMT), Prof
installed 2.1-8 and ran your code
in R-2.0.1 with no problem.
In any case, this looks more like an mclust problem than an R problem;
if you're using the current version, you should follow up with the
maintainer, Ron Wehrens [EMAIL PROTECTED].
Duncan Murdoch
Under GUIs other than Windows (Mac OS X, ESS, etc.) does
cat(\a)
still make a bell (or some other) sound? If so, I'll add a bell()
function to utils.
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the wait parameter that bug.report()
currently has on Windows.
Rather than adding wait to file.edit(), I'd rather remove it from
bug.report(). Will anyone object if I do this?
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month02
day 24
language R
Could someone else please deal with this? I have trouble with test
builds right now.
Duncan Murdoch
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in quantile().)
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On Tue, 22 Feb 2005 21:36:20 +, Duncan Murdoch
[EMAIL PROTECTED] wrote :
On Tue, 22 Feb 2005 13:43:47 -0700, Tony Plate
[EMAIL PROTECTED] wrote :
Is it a bug that quantile() can return a lower sample quantile for a higher
probability?
# quantile returns decreasing results
-0.0009041968 -0.0009041968 -0.0009041968 -0.0009041968
20%
-0.0009041968
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/TranslationTeams.html
listing the current languages I know about and the contacts for each.
To offer your help with one of these, contact a team on the list. To
list your own translation project there, contact me or another member
of R-core with the details.
Duncan Murdoch
On Thu, 17 Feb 2005 20:37:36 +0100 (CET), [EMAIL PROTECTED]
wrote :
There's a harmless typo in screen.Rd where coner should be corner.
Nitpicking to the extreme, ie. should be i.e. in plotformula.Rd and
screen.Rd.
I'll fix these in R-devel.
Duncan Murdoch
is supposed to do this. If you're on Windows: I
have a copy of iconv for Windows on www.murdoch-sutherland.com/Rtools,
but you might not need it. Lots of editors (e.g. Windows notepad) can
also do this conversion.
Duncan Murdoch
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On 09 Feb 2005 00:29:37 +0100, Peter Dalgaard
[EMAIL PROTECTED] wrote :
Duncan Murdoch [EMAIL PROTECTED] writes:
(a) efficiency. Is it expensive no longer to have the base functions
bound directly to their symbol? (My gut feeling is that with suitable
hashing and cacheing, the penalty
of the varimax topic.
You only need the [] to disambiguate crossreferences, or to refer to
packages that might not yet be installed, which does not apply to [stats].
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On Tue, 8 Feb 2005 12:21:05 + (GMT), Prof Brian Ripley
[EMAIL PROTECTED] wrote :
On Tue, 8 Feb 2005, Duncan Murdoch wrote:
On Tue, 8 Feb 2005 07:18:28 + (GMT), Prof Brian Ripley
[EMAIL PROTECTED] wrote :
On Mon, 7 Feb 2005, Paul Gilbert wrote:
In some documentation for a package I
of situation?
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is missing this time).
It is in the list mentioned in INSTALL, which is worth checking
I accidentally put cal in instead of cat; it was fixed just
yesterday.
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notice.
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were unaware of these builds, they are available at your
favourite CRAN mirror (list here:
http://cran.r-project.org/mirrors.html) in the bin/windows/base
directory. Follow the link to the r-devel release or the r-patched
release.
Duncan Murdoch
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search
the archives.
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- read.table(filename)
Uwe Ligges
Good suggestions. I'll make the changes in R-patched.
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languages care quite a bit about the storage
mode, and give bizarre and hard to debug errors when it is wrong. If
you did this, you wouldn't care that seq(length=n) returns mode
double.
It might waste a few cpu cycles, but programmer debugging cycles are
much more expensive.
Duncan Murdoch
, but I think it's pretty straightforward.
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fix these (if they haven't been fixed already).
Duncan Murdoch
-mike
Page 4, first paragraph of 2.1.4: 'objects which they contain' - 'objects
which contain'
Page 5, second paragraph of 2.1.10 'environment can be accesses' -
'environment
can be accessed'
Page 13, second paragraph of 3.3.4
On Wed, 01 Dec 2004 10:32:57 +1300, Paul Murrell
[EMAIL PROTECTED] wrote :
Hi
Duncan Murdoch wrote:
On Wed, 01 Dec 2004 08:55:27 +1300, Paul Murrell
[EMAIL PROTECTED] wrote :
This sounds like the general problem of being able to capture keyboard
input on a graphics device (a key-stroke
On Sat, 04 Dec 2004 20:13:01 +0100, Uwe Ligges
[EMAIL PROTECTED] wrote :
Duncan,
I'm a bit late on this topic, but I'd like to bring up two points that I
find inconvenient / buggy in the current behaviour of R-devel:
1) I'm never looking at the windows()'s title, hence I don't see that I
the CRAN mirrors.
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posting to R-help or
R-devel. I've cc'd the Rcmdr and rgl maintainers on this. You can
see the maintainer listed by using
library(help=Rcmdr)
library(help=rgl)
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