).
Duncan Murdoch
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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 Sciences
University
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
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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 file
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 reporting
be fine later today or tomorrow.
Duncan Murdoch
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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
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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 X11
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).
Duncan
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] .GlobalEnvpackage:devtools package:stats
[4] package:graphics package:grDevices package:utils
[7] package:datasets package:methods
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 included from
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 such options. Or does that refer to the
installation
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)
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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 error, I
installed it a second time, then got
= =, - = {
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:
# create dummy NAMESPACE file with two bad / one good directives
cat
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]]),
lots of args omitted here,
stop(gettextf(unknown
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 an error
. (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 deelnemerslijst.tex
Processing code chunks ...
1 : echo term verbatim
:
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.
Duncan Murdoch
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, Australia
that the package 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
/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 that helps.
Duncan Murdoch
fixes are easy, and big additions to the base packages are not.)
Duncan Murdoch
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an outside package maintainer
would be.
Duncan Murdoch
John, thanks for raising an important issue.
Thanks Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology School of Medicine Johns
Hopkins
file, and there's a description in the R
Admin manual as well as the Writing R Extensions manual.
Duncan Murdoch
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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 extreme, one can
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
[[alternative HTML version deleted
In addition: Warning message:
In file(file, r) : cannot open: HTTP status was '404 Not Found'
is there a way to test where localization is an html page, or not ? and to
say that if localization does exist, then scan it ?
What's your definition of an html page? Testing for valid html is hard.
Duncan
(Error!)
Duncan Murdoch
2010/12/13 Duncan Murdoch murdoch.dun...@gmail.com
mailto:murdoch.dun...@gmail.com
On 13/12/2010 12:36 PM, Arthur Charpentier wrote:
I was wondering if there was a function like does connection
exists ?
See ?showConnections.
I am
/
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
friedrich.lei...@stat.uni
(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 expect a length 1 result from letters[TRUE], would you?
Duncan Murdoch
give an error or warning,
something like logical index of incorrect length. But I suspect
people rely on the recycling of logical vectors, so there'd be a lot of
complaints if we made that change.
Duncan Murdoch
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::.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 grDevices datasets
On 19/12/2010 7:01 AM, Gabor Grothendieck wrote:
On Sun, Dec 19, 2010 at 6:39 AM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 19/12/2010 6:06 AM, Gabor Grothendieck wrote:
On Sat, Dec 18, 2010 at 8:23 PM, Dominick Samperidjsamp...@gmail.com
wrote:
On Sat, Dec 18, 2010 at 5:24 PM
On 19/12/2010 3:09 PM, Gabor Grothendieck wrote:
On Sun, Dec 19, 2010 at 10:31 AM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 19/12/2010 10:04 AM, Gabor Grothendieck wrote:
On Sun, Dec 19, 2010 at 9:07 AM, Duncan Murdoch
murdoch.dun...@gmail.comwrote:
On 19/12/2010 7:01 AM
. (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 Mathematical Sciences Building (Building 27
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 1194,
John Dedman
\documentclass line.
Duncan Murdoch
In this example we embed parts of the examples from the
help page into a \ LaTeX {} document :
a=
y=2
y = y +1
@
which shows that the location parameter of the Ozone
distribution varies significantly from month to month . Finally we
include a boxplot of the data :
\end
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
- Original
.
But don't trust what I write as legal advice.
Duncan Murdoch
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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 Murdochmurdoch.dun...@gmail.com
To: carol whitewht_...@yahoo.com
Cc: r-devel@r-project.org
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 Murdochmurdoch.dun...@gmail.com
To: carol whitewht_...@yahoo.com
Cc: r-devel@r-project.org
Sent: Thu
- 1
creates or modifies a new local variable, while
beta - 1
goes looking for beta, and modifies the first one it finds. If it fails
to find one, it creates one in the global environment.
Duncan Murdoch
If you have ideas about packages that might be handy teaching
examples, please let me
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 Murdoch
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
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about the
problem on that page, and it should eventually be fixed.
Duncan Murdoch
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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
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, Simon Urbanek
). 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 question
+ 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
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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 4:31 PM, ken.willi
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)
writeBin(ttccggaa, con)
close(con
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'
\SweaveOpts{engine=R, keep.source
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
On 05/02/2011 1:18 PM, Duncan Murdoch wrote:
On 04/02/2011 3:34 PM, Kevin R. Coombes wrote:
This is probably the same underlying bug, but it is not caused by
semicolons.
Yes, it was the same bug. I think I have it fixed now, and will commit
after some more testing.
Now committed as r54232
Thanks, I'll take a look. The internal error message was intended to
catch this kind of problem.
Duncan Murdoch
On 07/02/2011 7:36 AM, Clément Calenge wrote:
Dear all,
There seems to be a problem with named chunks in Sweave with the version
of R under development (downloaded yesterday
This should be fixed as of r54259.
Duncan Murdoch
On 07/02/2011 7:36 AM, Clément Calenge wrote:
Dear all,
There seems to be a problem with named chunks in Sweave with the version
of R under development (downloaded yesterday). When I sweave the file
toto.Rnw described at the end of this mail
that there are precision differences coming from there. I
think we'd be interested in knowing what they are even if they are
beyond our control, so I would appreciate it if you could track down
where the difference arises.
Duncan Murdoch
BACKGROUND
A colleague was trying to replicate some
adding it with the next update.
Duncan Murdoch
sessionInfo()
R version 2.13.0 Under development (unstable) (2011-02-11 r54330)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United
(){
return(a=5)
}
This is a mistake: return() doesn't take named arguments. It is
lenient and lets you get away with this error (treating it the same as
return(5)), and returns the 5, visibly.
Duncan Murdoch
f2()
Kevin Wright
On Tue, Feb 15, 2011 at 3:55 PM, Geoff Jentrygeoffjen
packages without a prefix, so they won't clash.
Your package will be guaranteed to see its own functions first. A
user can still have a clash between your exported functions and some
other package's exports, but with fewer functions exported, that will
not be as much of a problem.
Duncan
disadvantageous in certain situations.
As far as I know there is no such effect. I suspect what you saw just
triggered a bug in the C code that had stayed hidden before.
Duncan Murdoch
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attached when the original is
attached, if the locale says to use that language?
Duncan Murdoch
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On 11/03/2011 1:37 PM, Michael Lawrence wrote:
Thanks for the suggestion, but I don't think that R finalizes all of its
objects when it quits. At least a simple test suggests that on Linux.
Did you use onexit=TRUE? On Windows that appears to work...
Duncan Murdoch
Michael
On Fri, Mar 11
On 11/03/2011 3:11 PM, Henrik Bengtsson wrote:
On Fri, Mar 11, 2011 at 11:07 AM, Prof Brian Ripley
rip...@stats.ox.ac.uk wrote:
On Fri, 11 Mar 2011, Duncan Murdoch wrote:
On 11/03/2011 1:37 PM, Michael Lawrence wrote:
Thanks for the suggestion, but I don't think that R finalizes all
of scope when you try to use it.
Duncan Murdoch
Best,
Matt
On 03/15/2011 05:37 AM, Andreas Borg wrote:
Hi all,
I use txtProgressBar to monitor progress of large computations. What I
miss is the ability to redirect the progress bar to a stream other than
stdout, specifically to the message
are concatenated into one big file which is sourced. You've
got an unclosed parenthesis/brace/bracket in this file, but some later
file closed it -- so that file probably has an extra closing one.
Duncan Murdoch
Thanks anyway,
Max
On Tue, Mar 15, 2011 at 9:48 PM, Max Kuhnmxk...@gmail.com
on
environments made me hurt.
Quoting Uwe Ligges, No.
Duncan Murdoch
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if it proves too difficult.
Thanks for considering this idea...
That sounds like a good idea. It would be easier to experiment with if
you provided the offending file. (Yes, the lack of a name makes it hard
to find that file, but it's easier for you than for almost anyone else.)
Duncan Murdoch
'Writing R
Extensions'.
Documentation object 'ellipse.glm' tells me the \name{} inside the .Rd
file, which is enough to uniquely identify the file. Are you not seeing
this part of the message?
Duncan Murdoch
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On 11-03-17 12:33 PM, Dan Tenenbaum wrote:
On Thu, Mar 17, 2011 at 2:36 AM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 16/03/2011 7:55 PM, Dan Tenenbaum wrote:
Hi,
I came across the following warning in R CMD check (it only occurred on
Windows):
The \usage entries for S3 methods
I think this is a good idea; I'll put it into r-devel and possibly r-alpha.
Duncan Murdoch
On 18/03/2011 1:54 PM, Dirk Eddelbuettel wrote:
The other day I was working on an example which used tempfile() to create
file for use by the graphics device. And while I love tempfile
available in input
How can I fix this?
Everything in the inst directory is moved up a level when it is
installed. So you shouldn't mention inst in its path.
Duncan Murdoch
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, but it is not part of R), so
suggestions should go to the maintainer. But you need to put together a
simple example to illustrate the problem. When I modify the first
example in example(boot.ci) to specify type=normal, I get an error
message.
Duncan Murdoch
is wrong, or how I can go about it?
I think you need to think of your program as a new front end for R, even
if you're only using a few R functions. See Chapter 8 in the Writing R
Extensions manual.
Duncan Murdoch
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variable DEBUG set to T to get the debugging information compiled into
it. Not sure if you need to do anything on the other systems.
Duncan Murdoch
Thanks for your time on my behalf!
dan
Ouput from R session with library swat and subroutine junk:
library.dynam(swat,EcoHydrology)
.Fortran
you get outside, examine the
environment variables PATH and TEX in both places (with
Sys.getenv(c(PATH, TEX)) in R) to look for differences, etc.
Duncan Murdoch
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where, there should be information on the line
number at which the user code blew up. It's there in 2.12, but not in
2.13, from what I can see.
That's not intentional. I'll see what went wrong...
Duncan Murdoch
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On 11-03-27 7:42 AM, Duncan Murdoch wrote:
On 11-03-26 7:41 PM, Norm Matloff wrote:
The pattern (I can make a simple example if needed):
source(x.R)
options(error=recover)
x- ...
f(x) # f() from x.R
(subscript bounds error, now in recover
, not just its
home directory.
Duncan Murdoch
NULL
no matter what I do.
This is with:
sessionInfo()
R version 2.13.0 alpha (2011-03-27 r55077)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8LC_COLLATE
),
function(nm) {
c(gettextf(Rd files with duplicated name
'%s':,
nm),
.pretty_format(bad[[nm]]))
}))
Cheers,
H.
Thanks, will fix.
Duncan
) is zero. A C-level sanity check seems more
efficient and more helpful to me.
Seems to me that the S-PLUS solution (output=double) would be a lot
more useful. I'd commit that if you write it; I don't think I'd commit
the warning.
Duncan Murdoch
Pretending that it's really only four bytes because
configuration file or so ?
Why not just keep two PATH variables, and put one in place before R
builds, the other in place the rest of the time?
Duncan Murdoch
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it).
Duncan Murdoch
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=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Do you have pdflatex? It's not part of Rtools, it's part of LaTeX, as
described in Rtools.txt.
Duncan Murdoch
original suggestion to
monitor changes to the web page. I'll see if there's a way to
automatically include the revision number in the filename.
Duncan Murdoch
It might be more clear if there
instead the sections would be 'Changes in Rtools213', 'Changes in
Rtools212' and so on, and within
.
Duncan Murdoch
Using strings on unins000.dat did not reveal anything although there
was so much text it would be easy to miss.
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, if there isn't a simple implementation I missed.
Duncan Murdoch
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need
to be able to get rid of them when you are done. close(con) is the way
to do that. If you want to re-open it, you need to remember the filename
(or extract it before calling close()), and issue another call to file().
Duncan Murdoch
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, the search
could stop before it got to globalenv(). But it seems unlikely that
your students are writing packages with namespaces.)
Duncan Murdoch
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are up to date). There's also a VERSION.txt file that
contains the version number, which is likely to maintain its format more
consistently, so if you want an automatic check, you should look at that
file. It's also on the web site.
Duncan Murdoch
.
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On 11-04-09 9:22 PM, Spencer Graves wrote:
On 4/9/2011 6:12 PM, Duncan Murdoch wrote:
On 11-04-09 7:02 PM, Spencer Graves wrote:
On 4/9/2011 2:31 PM, Hadley Wickham wrote:
On Sat, Apr 9, 2011 at 2:51 PM, Paul Johnsonpauljoh...@gmail.com
wrote:
Years ago, I did lots of Perl programming. Perl
a look at src/main/deparse.c. The operators
that are labelled as PP_BINARY2 get no spaces. Looking in
src/main/names.c, we see those are /, ^, %%, %/% and :.
But clearly this is by design, and I think it's unlikely to change.
Duncan Murdoch
deparse(expression(1/1))
[1] expression(1/1
+, - and *.
I looked it up, and it has been like that since revision 2 when this
code was first committed to our repository in 1997. I imagine whoever
wrote it was following the pattern of some other language (maybe S), or
maybe just their own personal taste.
Duncan Murdoch
Regards,
Yihui
fix this in R-devel, and backport it to 2.13.0-patched.
Duncan Murdoch
x- structure(1:3, class=unrecognizedClass)
y- sort.int(x)
t- 1:3
identical(y, t) # expect TRUE
[1] FALSE
identical(as.vector(y), as.vector(t)) # expect TRUE
[1] FALSE
dput(y)
1:3
On 08/04/2011 11:39 AM, Joshua Ulrich wrote:
On Fri, Apr 8, 2011 at 10:15 AM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
On 08/04/2011 11:08 AM, Joshua Ulrich wrote:
How about:
y- rep(NA,length(x))
y[duplicated(x)]- match(x[duplicated(x)] ,x)
That's a nice solution for vectors
On 11/04/2011 1:10 PM, William Dunlap wrote:
If x has an S3 class then sort.int(x) returns a value
without an S3 class but which has the is.object flag set,
which, I think, causes identical() give a false/misleading
report:
Fixed in R-devel as of r55409.
Duncan Murdoch
x- structure(1
it be possible to have something akin to lint comment directives
to allow specific errors to be ignored by codetools?
Of course it would. Codetools is GPL licensed, so just do it.
Duncan Murdoch
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R-devel@r-project.org mailing list
https
meant that the process is somewhat fragile and hard to debug, and I'd
like to switch to pure R code (or at least self-contained code in a
package).
Does anyone know of an R package that provides text differencing and
display in HTML?
Duncan Murdoch
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