On 21/11/2009 7:44 PM, Guillaume Yziquel wrote:
Duncan Murdoch a écrit :
I believe I should. I'd like the OCaml / R binding to be closely knit
to R internals. One reason would be for speed, the other being that
I'd like to make use of camlp4 to write syntax extensions to mix OCaml
and R
2.0.2, but I don't know the best fix for this.
Duncan Murdoch
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On 11/24/2009 8:06 AM, Ulrike Groemping wrote:
Duncan Murdoch-2 wrote:
On 11/18/2009 8:01 AM, ml-it-r-de...@epigenomics.com wrote:
Ulrike Grömping wrote, On 11/18/09 13:28:
Duncan Murdoch schrieb:
Ulrike Groemping wrote:
Duncan Murdoch-2 wrote:
Ulrike Groemping wrote:
Dear
the source into one big file
and parses it all at once. The filename is stored internally in a
variable called outFile.
I don't know what would be causing this difference between Windows and
Linux. If you can send me a copy of the package offline I'll take a
look later today.
Duncan Murdoch
just
says that the rectangles being coloured by the z values are not square.
If you want to leave blanks, then put in NA values for z.
For example,
x - c(1:6, 100:105)
y - 1:10
z - matrix(rnorm(110), 11, 10)
z[6,] - NA
image(x,y,z)
Duncan Murdoch
browseURL() on that page.
If not, it does more or less what it does now, but
- it defaults address to the package maintainer.
- it adds a line in the intro to the message pointing to the URL field
if there was one.
Duncan Murdoch
Just an idea for a rainy morning...
Barry
On 26/11/2009 9:20 AM, Martin Maechler wrote:
DM == Duncan Murdoch murd...@stats.uwo.ca
on Thu, 26 Nov 2009 08:39:27 -0500 writes:
DM On 26/11/2009 7:09 AM, Barry Rowlingson wrote:
A lot of R packages are now effectively maintained by several people
and so use sites like R
On 26/11/2009 12:38 PM, Barry Rowlingson wrote:
On Thu, Nov 26, 2009 at 1:39 PM, Duncan Murdoch murd...@stats.uwo.ca wrote:
This sounds like a good idea, though I would add a package parameter to
the bug.report() function, rather than creating a new function.
I'm sure when I did help.search
in the second
sentence of your post.
Duncan Murdoch
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On 29/11/2009 11:50 AM, Peng Yu wrote:
On Sun, Nov 29, 2009 at 10:40 AM, Duncan Murdoch murd...@stats.uwo.ca wrote:
On 29/11/2009 10:58 AM, Peng Yu wrote:
Some lines are indented by tabs and some lines are indented by spaces,
in R source code. This might due to the fact that the source code
that be package's ?
Thanks, I'll fix these.
Duncan Murdoch
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encoding problems, so it's not readable. Could you put
the code online somewhere where we could download it in its original
form? I doubt if this is an R bug, but I can't point out the problem in
your code (or confirm that it really is an R bug) without an undamaged
copy of the code.
Duncan
.
Duncan Murdoch
Best regards,
Jean Couteau
Your message has encoding problems, so it's not readable. Could you
put the code online somewhere where we could download it in its
original form? I doubt if this is an R bug, but I can't point out the
problem in your code (or confirm
and package and you'll get the error.
Will fix.
Duncan Murdoch
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the HTML is coming from???
Duncan Murdoch
again, I don't see the down side of having static html help pages.
(Maybe there is one. But it certainly isn't disk space: all together
these take about as much of that as a couple of digital photos.)
Jon
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lack of experience. Please do not abuse the bug reporting
system.
Duncan Murdoch
MANY THANKS -- Franc Brglez
The function binS2binV returns what I consider a wrong value -- see the
terminal output
binS2binV = function(string=0001101, sep=)
# this procedure is expected to convert a binary
not show up in the
plots.
It's working for me in r50697 in Windows. Please post sessionInfo, etc.
Duncan Murdoch
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'. The
character does exist in both ISO 8859-1 and Windows-1252.
Yes, I can reproduce this, and I know a likely cause. It will be fixed
in R-devel soon, but I think it will probably be too late to make it
into 2.10.1. It will go into 2.10.1 patched after release if that's the
case.
Duncan Murdoch
at the time you request it, and may contain dynamic content
(though there are very few examples of that as yet).
Duncan Murdoch
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On 10/12/2009 4:20 AM, k...@huftis.org wrote:
Full_Name: Karl Ove Hufthammer
Version: 2.10.0
OS: Windows XP
Submission from: (NULL) (93.124.134.66)
I have found a rather strange bug in R 2.10.0 on Windows, where the choice of
characters used in a string make R crash (i.e., Windows shows a
on Windows XP, but appeared on Windows 7 when the same
program is run.
That doesn't work on XP if program is an .exe, and I wouldn't expect it
to. The system() command on Windows doesn't process redirects. See the
documentation.
Duncan Murdoch
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and Documentation fixed.
Thanks. The problem is that the HTML converter doesn't escape the
question marks, which have special meaning in a URL, so they are
misinterpreted. I'll look into it.
Duncan Murdoch
Best regards,
Henrik Pärn
sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
This is now fixed in R-devel and R-patched as of r50774. It should
show up in Windows builds tomorrow. There were probably other special
characters besides ? that it handled incorrectly; thanks for noticing.
Duncan Murdoch
On 17/12/2009 4:05 AM, henrik.p...@bio.ntnu.no wrote:
Dear R
- lapply - FUN - .find.package
Execution halted
sessionInfo ()
R version 2.10.0 (2009-10-26)
Do you get the same message in 2.10.1?
Duncan Murdoch
x86_64-pc-linux-gnu
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8
[5
] TRUE
[[2]]
[1] FALSE
[[3]]
[1] TRUE
exprs[[2]]
A - this is code outside the function definitions
or
exprs[!unlist(lapply(exprs, isfundef))]
expression(A-this is code outside the function definitions)
Duncan Murdoch
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this message shows,
http://finzi.psych.upenn.edu/R/R-devel/2009-August/054319.html
there are several different encodings which are displayed as NA, and a
huge number (more than 2^50, I seem to recall) of different encodings
displayed as NaN.
Duncan Murdoch
the list as a whole.
Duncan Murdoch
HTH,
L.
Thanks,
Romain
[1]http://lists.r-forge.r-project.org/pipermail/rcpp-devel/
[2]
http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/pkg/src/RObject.cpp?rev=255root=rcppview=markup
-- Romain Francois Professional R Enthusiast +33(0) 6 28
Simon Urbanek wrote:
On Jan 2, 2010, at 12:17 PM, Laurent Gautier wrote:
On 1/2/10 5:56 PM, Duncan Murdoch wrote:
On 02/01/2010 11:36 AM, Laurent Gautier wrote:
[Disclaimer: what is below reflects my understanding from reading the
R source, others will correct where deemed
On 02/01/2010 6:35 PM, Laurent Gautier wrote:
On 1/2/10 11:41 PM, Romain Francois wrote:
On 01/02/2010 11:12 PM, Duncan Murdoch wrote:
On 02/01/2010 3:16 PM, Laurent Gautier wrote:
On 1/2/10 8:53 PM, Duncan Murdoch wrote:
Simon Urbanek wrote:
On Jan 2, 2010, at 12:17 PM, Laurent Gautier
bugs for such packages.
Duncan Murdoch
On 12/01/2010 10:15 AM, je...@cs.uni-magdeburg.de wrote:
Full_Name: Jens Elkner
Version: 2.10.1
OS: Solaris
Submission from: (NULL) (141.44.24.14)
The configure.ac is bogus, since it does not include additional library pathes
at the right place and thus
, with an offer to do the rest once the
style is accepted. Expect that there will be one or more rounds of
discussion about whether your style really is usable. Writing a style
guide would really help.
Sound like too much work? I agree.
Duncan Murdoch
For example, the logical arguments comes in seven
parser there, just a fallible pattern
matching approach.
A better solution is to say your package requires a recent version of R,
but maybe that's not feasible for you.
Duncan Murdoch
The R change log doesn't show anything obviously related to this, though
it has several references
:::startDynamicHelp for code that does
this for the variable httpdPort.
Duncan Murdoch
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order(a, -xtfrm(b), c, -xtfrm(d))
??
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xtfrm stands for?
No, I don't think I ever worked it out. :-)
Duncan Murdoch
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can't tell
you who is wrong.
Duncan Murdoch
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is better, but I don't know if it can
really be called the Canberra distance.
Duncan Murdoch
Christophe
On 06/02/2010 10:39 AM, Christophe Genolini wrote:
Hi the list,
According to what I know, the Canberra distance between X et Y is :
sum[ (|x_i - y_i|) / (|x_i|+|y_i|) ] (with | | denoting
this.
The translation sources are maintained by the translation teams, so
corrections should go directly to them. I've cc'd this message to
Detlef Steuer, but for future
reference the list is on
http://developer.r-project.org/TranslationTeams.html
Thanks!
Duncan Murdoch
(TRUE, FALSE)], but how can R know you meant
that?
Duncan Murdoch
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to your .Rprofile,
saying something like myOptionPackage::loadMyOptions(). This can do
whatever you want, it only needs to know how to parse the file that your
package wrote.
Duncan Murdoch
Or is it a dumb idea? I can see other ways of doing this, such as
saving the options() as an object and re
On 12/02/2010 3:50 AM, Barry Rowlingson wrote:
On Wed, Feb 10, 2010 at 3:06 PM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
But I agree that writing a saveable options package is the first step
- then making that a default in R is the second so people don't have
to edit profiles and
? Yeah, we have a parser and that's what all
the hipster web 3.0 kids are using these days
We have read.dcf() if you want human and machine readable.
Duncan Murdoch
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to take
shortcuts, and then you need to debug your edits, not just your code.
Duncan Murdoch
pj
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than ::, but
version - 1:10
base::version[1]
shows :: has higher priority. I'll take a look.
Duncan Murdoch
On Sat, Feb 20, 2010 at 6:57 AM, Barry Rowlingson
b.rowling...@lancaster.ac.uk wrote:
On Sat, Feb 20, 2010 at 9:52 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote
On 21/02/2010 12:44 PM, Duncan Murdoch wrote:
Gabor Grothendieck wrote:
I wasn't claiming there was an ambiguity but it does not perform
according to the operator precedence documented in ?Syntax . If it
performed as documented it would give an error.
There are a few other errors
functions.
I would normally use a mixture of styles 1 and 2. Use style 2 for
functions that really do need access to Foo locals, and use style 1 for
self-contained functions.
Duncan Murdoch
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as single stepping when we exited from
inner()), but debug() is certainly not the only possibility for
debugging. It's not even the best choice in a lot of situations where
it does work.
Duncan Murdoch
Functions can be nested in environments rather than in other functions
and this will allow
a
front end to trace, which has been in the base package for quite a long
time.
Duncan Murdoch
existed before. I also like Mark Kimpel's trick, which appeals to a
simple-minded person like me.
Either R needs to expand it's standard library, or there should be a
standard guide on what you really
additional ones I've used are R, Perl and
Tcl, all with add-on packages.
Duncan Murdoch
In
standard languages asking for b inside the p object gives you an
error, and no one complains. Even in R, we have this behavior:
z - 1
list(a=3)$z
NULL
(Actually I think the above should be an error
for that, but I'd prefer it if it
were more limited.)
Duncan Murdoch
since the former gives you everything you want and the distinction
seems pretty trivial given how easy it is to use one or the other. If
you used iolanguage or similar you would have to specify Object so
there is not even
are not tested a lot.
If declaring the encoding in DESCRIPTION doesn't solve the problem, I'd
be happy to take a look at the package.
Duncan Murdoch
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be able to make the error message in the package installer more
informative (e.g. giving the line number that failed). I'll look into that.
Duncan Murdoch
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not sure
if it would slow down processing of files that include no bad chars.
I'll take a look.
Duncan Murdoch
Felix
Am 26.02.2010 um 18:37 schrieb Duncan Murdoch:
On 26/02/2010 11:05 AM, Felix Schönbrodt wrote:
Hi Duncan,
I now declared the endcoding in the DESCRIPTION to UTF-8
literals it will look ugly but should be accepted. In
comments it will look ugly, but comments aren't normally saved, so they
won't really matter there.
Duncan Murdoch
Felix
Am 26.02.2010 um 18:37 schrieb Duncan Murdoch:
On 26/02/2010 11:05 AM, Felix Schönbrodt wrote:
Hi Duncan,
I now
know, ask a C expert.)
We might want to save the hash to disk. On restore, the pointer based
hash would be all wrong. (I don't know if we actually do ever save a
hash to disk. )
Duncan Murdoch
shash would look like a slightly modified version of ihash like this :
static int shash(SEXP x
in particular around lines 110 and 160.
Duncan Murdoch
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] 2
$z
[1] 4
Duncan Murdoch
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collection in
the middle of drawing it threw it away. I suppose it could happen with
any title that needed conversion, but the large size of this one made it
more likely that GC would happen. Soon to be fixed in R-devel and
R-patched.
Thanks for the report.
Duncan Murdoch
Also, R
use strncpy to avoid overflows.
If you are unsure of the length of the message that you want to return,
you can use R_alloc in C to allocate a buffer, and you don't need to
worry about disposing of it: it will be garbage collected.
Duncan Murdoch
.
Duncan Murdoch
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? As of revision 38781 the builds are
using the new toolset. This build should be available on CRAN within a
few hours, and on the mirrors sometime after that. Go to
http://cran.r-project.org/bin/windows/base/rpatched.html
and check that the page is dated 2006-08-03 or later.
Duncan Murdoch
the class yourself:
cl - class(dates)
sorteddates - sort(dates)
class(sorteddates) - cl
You could put this into your own sort.Date function, but it won't be
called automatically: sort is not a generic.
sort.Date - function(x) {
cl - class(x)
structure(sort(x), class=cl)
}
Duncan Murdoch
the end of the month each time, or truncate to the end of a short month,
you lose important arithmetic properties: x - y is not equal to
(x+1month) - (y+1month).
Duncan Murdoch
Sys.Date()
[1] 2006-08-03
Sys.Date()-3
[1] 2006-07-31
# WORKS OK on Aug. 1:
seq(Sys.Date()-2, len=5
it: there are slight differences between the tarballs
and svn working copies.
Duncan Murdoch
collect2: ld returned 1 exit status
make[5]: *** [lapack.dll] Error 1
make[4]: *** [all] Error 2
make[3]: *** [all] Error 1
make[2]: *** [rmodules] Error 2
make[1]: *** [rbuild] Error 2
make: *** [all] Error 2
of specifying TEXINPUTS through environment variables, and then
it would work with older R builds, or maybe you just never noticed the
2.2.0 change ;).
Duncan Murdoch
Hope this helps,
Andy
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= paste(a,1:7,sep=)))
in base/demo/is.things.R
which I find clearer as
is.ALL(structure(1:7, names = a + 1:7))
But then I'm used to using + for strings from Borland's Pascal
extensions; to a C-speaker the meaning may not be so obvious.
Duncan Murdoch
I wonder however, if we do this in C
On 8/25/2006 4:55 PM, Martin Maechler wrote:
Duncan == Duncan Murdoch [EMAIL PROTECTED]
on Fri, 25 Aug 2006 13:18:42 -0400 writes:
Duncan On 8/25/2006 12:31 PM, Martin Maechler wrote:
This thread remains me of an old recurring (last May!)
theme which maybe fits well
they are buried in data.frames.
I'd be happy to continue to have the warning in that case. paste() is
pretty flexible, so there would be a lot of cases where paste(x, y,
sep=) gave a result but x+y gave a warning or error.
Duncan Murdoch
consistency with other common languages is a stronger reason.
Other than that, I'd be perfectly happy with %+%.
Duncan Murdoch
2. Having said that, it's a reasonable hope that efficiency of
dispatch will not be a serious problem. There are a bunch of fixes, for
semantic correctness
).
This isn't a problem particular to the proposed string addition, in
general floating point addition isn't associative either, and in R, even
addition of integers isn't associative.
People who write a+b+c should be willing to accept either result.
Duncan Murdoch
-thomas
Thomas Lumley
On 8/27/2006 9:44 PM, Allen S. Rout wrote:
Duncan Murdoch [EMAIL PROTECTED] writes:
According to Wikipedia, the + operator is used for concatenation in
BASIC, Pascal, Delphi, Javascript, Java, Python, C++ and Ruby. These
are probably the most commonly used modern languages other than C
they are not available, check as
currently installed, require that they be available.)
Duncan Murdoch
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On 8/29/2006 11:58 AM, Seth Falcon wrote:
Duncan Murdoch [EMAIL PROTECTED] writes:
I think we need an option to R CMD check rather than a new field in the
DESCRIPTION. Currently a package could be mentioned for any of these
reasons:
1. To make functions, examples or vignettes work
2
On 8/29/2006 1:05 PM, Paul Gilbert wrote:
Duncan Murdoch wrote:
On 8/29/2006 10:12 AM, Martin Maechler wrote:
PaulG == Paul Gilbert [EMAIL PROTECTED]
on Tue, 29 Aug 2006 09:55:09 -0400 writes:
PaulG Martin Maechler wrote:
...
The idea was a field related
On 8/29/2006 2:24 PM, Paul Gilbert wrote:
Seth Falcon wrote:
Duncan Murdoch [EMAIL PROTECTED] writes:
On 8/29/2006 11:58 AM, Seth Falcon wrote:
I think there is an important distinction between a dependency needed
for the package to function and a dependency needed to demonstrate
said
On 8/29/2006 4:13 PM, Paul Gilbert wrote:
Duncan Murdoch wrote:
On 8/29/2006 2:24 PM, Paul Gilbert wrote:
Seth Falcon wrote:
Duncan Murdoch [EMAIL PROTECTED] writes:
On 8/29/2006 11:58 AM, Seth Falcon wrote:
I think there is an important distinction between a dependency needed
On 8/30/2006 3:21 AM, [EMAIL PROTECTED] wrote:
On 8/29/2006 4:13 PM, Paul Gilbert wrote:
Duncan Murdoch wrote:
[...]
This doesn't address the problem of someone who hasn't got the package
installed yet, though perhaps CRAN could put a version of that man page
(or all of them) online
, but I think it's 2004
or 2005.
Duncan Murdoch
Sometimes the R helpers spend a long time answering the wrong question,
which is why it always helps to give the real one.
If it matters to you, investigate the code your compiler creates. (The
ATLAS developers report very poor performance
On 8/30/2006 7:44 AM, Martin Becker wrote:
Duncan Murdoch schrieb:
McLeish published algorithms to simulate these directly in a recent
issue of CJS. I don't have the reference handy, but I think it's 2004
or 2005.
Duncan Murdoch
Thank you for this reference, I think it is the 2002
On 8/30/2006 4:44 AM, Martin Maechler wrote:
FrL == friedrich leisch [EMAIL PROTECTED]
on Wed, 30 Aug 2006 09:34:13 +0200 (MEST) writes:
Duncan Murdoch [EMAIL PROTECTED] writes:
I think we need an option to R CMD check rather than a new field in
the
DESCRIPTION
that declare a dependency on methods. There
may be cleaner techniques.
This does the same within R:
pkgs - installed.packages()
pkgs[grep(methods, pkgs[,Depends]),]
Duncan Murdoch
If
so, I could scan my already installed libraries and call
install.packages() on its S4 subset of packages
revision to the docs that describes it?
Duncan Murdoch
Dirk mentioned 'Enhances' --- something which I could also live
with instead of 'CanUse' -- I just to be generous
with myself (as package author) in my interpretation of
enhancing :-)
Those developers who cannot remember disambiguating
. There was a transient failure to connect to the server last
night; I'll change the script so that if this happens, the old log is
left online.
Duncan Murdoch
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No problem: let me know what to do.
Duncan Murdoch
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this happens:
substitute(function(a=a) 1, list(a=quote(foo)))
function(a = a) 1
I would have expected to get function(a = foo) 1.
Duncan Murdoch
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On 9/14/2006 3:49 PM, Robert Gentleman wrote:
Duncan Murdoch wrote:
On 9/14/2006 3:01 PM, Seth Falcon wrote:
Hi,
Can someone help me understand why
substitute(function(a) a + 1, list(a=quote(foo)))
gives
function(a) foo + 1
and not
function(foo) foo + 1
The man page leads
).
The problem with S3 methods is that it's pretty difficult for R to know
that a particular object is an S3 generic. The only sign is that it has
a call to UseMethod() in it. I think this is one of the motivations for S4.
Duncan Murdoch
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to the current behaviour?
I'd say the long term solution is to get rid of S3 dispatch, so this
isn't an issue. There are improvements to S4 dispatch in 2.4.0, but I
think there are very high barriers preventing people from using S4, so
S3 will be around for a long time.
Duncan Murdoch
, or made API calls
with bad parameters: it was very useful. However, I don't think it
exists any more, and it almost certainly never did for the MinGW
compiler we use. I don't think there's any equivalent product for MinGW.
Duncan Murdoch
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it. Thanks!
Duncan Murdoch
For example:
dt1 - as.Date(2004-12-31)
dt2 - as.Date(2005-12-31)
seq.Date(dt1, dt2, length.out =3D NULL, by =3D month)
Error in seq.Date(dt1, dt2, length.out =3D NULL, by =3D day) :=20
'length.out' must be of length 1
This might be an issue if I want to wrap
on
validObject tests everywhere would slow things down a lot. Isn't it
easier to just sprinkle a few more validObject() calls into your code?
Duncan Murdoch
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for
matching help. I think working out the signature in the case above
would require it to call lm(...). So there's a precedent for what I
called a huge mistake: maybe it's not so huge...
Duncan Murdoch
Do you have an actual suggestion for a change to the current behaviour?
One obvious
functions where the
evaluator does almost nothing automatically, and handling R_Visible was
just overlooked.
Duncan Murdoch
Similar things happen in many similar circumstances.
Herve I need to use parenthesis to see the expected result:
a[[(t-'b')]]
Herve [1] 5
, but / is
accepted in R. There are a large number of inconsistencies between
Windows and other systems, and R mostly follows the GNU conventions;
it's a GNU project, after all.
Duncan Murdoch
On 10/1/06, Duncan Murdoch [EMAIL PROTECTED] wrote:
On 9/30/2006 10:54 PM, Gabor Grothendieck wrote:
I
prefer if R were case-insensitive in all
respects. However, it's not, so consistency pulls me to case-sensitivity.
Duncan Murdoch
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y=1, you're setting something in the ... part of the arg list. If you
say x=1, you're setting the first arg, but because a[[x=1]] is the same
as [[(a, x=1), it is going to evaluate it as [[(x=1, i=a) and try to
index 1 by a instead of a by 1.
Duncan Murdoch
see it, you need to use assignInNamespace().
Duncan Murdoch
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
on my system. I'll commit
the change to R-devel and R-patched.
Duncan Murdoch
2006/10/5, [EMAIL PROTECTED] [EMAIL PROTECTED]:
I've tracked down where this is occurring, but I don't know how to fix
it. Here's a summary:
If the language in Windows is set to simplified Chinese (i.e. Chinese
for the
report, and the detailed script to reproduce the bug.
Duncan Murdoch
for (n in 58950:58970) {
cat(n=, n, \n, sep=);
# Clean up first
rm(names, x, y); gc();
# Create a named vector of length n
# Try with format %5d and it works
names - sprintf(%05d, 1:n);
x - seq
in 2.4.0, but
you'll need the package source for that. As far as I could see (in a
very cursory examination) this is not available on his web site.
Duncan Murdoch
=20
which works perfectly in Rv2.2.0; after installing from a local zip and
loading I find:
=20
USING R version 2.2.0
=20
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