On 05/07/2013 12:29 PM, Barry Rowlingson wrote:
On Fri, Jul 5, 2013 at 12:57 PM, Duncan Murdoch
wrote:
> R itself doesn't make use of the text column, it's for display of code
> by highlighters etc. So if anyone does assume text is a function name,
> it's their bug,
e a run-time warning that some arguments were being
skipped (by testing length(list(...)) for example), but then NextMethod
might fail, in a case where an object has a complicated class vector.
This is basically a limitation of the S3 class system. The S4 system
can do much
computation and then use NextMethod. It should not need to know
that it is calling subset.data.frame next, so it will pass all of its
arguments along, possibly including some that subset.data.frame should
ignore.
Duncan Murdoch
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which is what I currently do)?
Are you calling them from inside the package? If so, you don't need the
:::.
If you're not calling them from inside the package, then why not export
them? I think you need to explain the context.
Duncan Murdoch
--j
--
Jonathan A. Greenberg
ent matching?
At a higher level, is pmatch intended to be the same as the argument
matching algorithm or is it just supposed to be "close"?
I would take that line in the documentation to say it is intended to be
the same except for empty strings.
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1, not 3.0.0) and R-patched, you should file a bug
report.
If it only occurs in R-patched or in R-devel, then a message to this
list is probably better.
If it only occurs in the release but not R-patched, then no report is
necessary: it has been fixed.
Duncan Murdoch
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2.15.3 Patched (2013-03-13 r62402) [Platform:
x86_64-w64-mingw32/x64 (64-bit)]
Can others reproduce this? If so, I'll submit a bug report. (On
Linux/OSX it does not crash/core dump.).
Following Duncan Murdoch's advice in a related message, I've filed bug
report PR#15406
[https://
x27;
A translation of the error message: The data in the reparse point buffer are
invalid.
It's hard to diagnose the cause of the error, but you can avoid the use
of junctions by setting the environment variable R_WIN_NO_JUNCTIONS to
some non-empty content, and that might avoid it.
D
r called" is to run Rprof on your test code,
and see which functions are not mentioned. I have a package under
construction with some students that can use this approach to identify
which lines are never seen while profiling the test code.
Duncan Murdoch
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it something, but not for a week or so: I am mostly
offline until then.
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note on the bug saying you're working on
it (which will push it to the top of the list in the default ordering),
along with a note saying when you expect to be done. That would stop me
from spending time on it until you submitted a patch, or your stated
d idea to write tricky code to subvert the tests. If
the tests are wrong, you can argue for changes (and in this case you
did, and changes were made), but if you can't give a convincing
argument, you should follow the good practices that the repository
policies enforce.
Duncan Murdoch
re. There are plenty
of other places (github, R-forge, etc.) where you can distribute it.
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ION file as well. It might be something like
Author: Duncan Murdoch, with code from others (see the man pages)
However, I just looked at rgl (a package I maintain), and I see we
didn't do that. We have a separate README file listing other credits.
Duncan Murdoch
Happy to learn more and
te it, then it harms their
reputation if it doesn't meet their standards.
Duncan Murdoch
Best,
Kasper
On Mon, Aug 26, 2013 at 11:38 AM, Hadley Wickham <mailto:h.wick...@gmail.com>> wrote:
> I would say that you should certainly state it in the man page,
and have
On 26/08/2013 11:20 AM, Benjamin Hofner wrote:
Dear Duncan,
thank you for the quick reply.
Am 26.08.2013 16:47, schrieb Duncan Murdoch:
> On 26/08/2013 8:51 AM, Benjamin Hofner wrote:
>> Hi,
>>
>> related to this important discussion I have several questions:
>>
>
y
chronological order, rather than categorized as NEWS is?
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can ask CRAN where such discussions should happen, but I
suspect the answer will be "nowhere public", because most public
discussions of CRAN policy devolve very quickly into ridiculous demands
on the volunteers who run it.
Duncan Murdoch
Dirk
[1] http://lists.debian.org
recent discussion, but no one answered the question "Is
there a preferred method to accomplish this?" (I suppose the answer is
that there is no other way, given that no one actually suggested
anything else.) Most of the on topic discussion in that thread was about
how to subvert the
you don't have control over the other package, because its author might
unwittingly change it in a way that causes me to get incorrect results.
If you want to use :::, go ahead, just don't put your package on CRAN,
where I get most of my packages. Then we'll both be happy.
Duncan
On 13-08-28 9:00 PM, Kasper Daniel Hansen wrote:
On Wed, Aug 28, 2013 at 3:22 PM, Duncan Murdoch
mailto:murdoch.dun...@gmail.com>> wrote:
On 28/08/2013 3:06 PM, Kasper Daniel Hansen wrote:
My point of view is that if you have a core package where you
need
ut to
depend on the inputs, so this looks hard: that's why those front ends
need work by hand.
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use it needs to set debugging information and produce
diagnostic messages.
Duncan Murdoch
On Friday, August 30, 2013, Duncan Murdoch wrote:
On 13-08-30 5:19 AM, Оботуров Артем wrote:
Hello.
One of my clients asked if it would be possible to have an IDE
which could
. :-)
There is no path requirement. Christian was incorrect in his diagnosis.
texi2pdf won't delete files that existed before it was run, whether or
not they were changed during the run. That's likely what Christian was
seeing.
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On 30/08/2013 3:21 PM, cstrato wrote:
Dear Duncan, dear Marc,
Thank you for your fast reply.
Can you please tell me:
If texi2pdf() won't delete files how are the files deleted when the
directory structure is Test/inst/doc/?
Is this done by Sweave()?
No.
Duncan Murdoch
Best re
t to r-devel [1].
Scott
[1] http://permalink.gmane.org/gmane.comp.lang.r.devel/33987
Thanks. I would not do the alphabetization; that makes it much harder
to track changes. But if tkcoords is unnecessarily duplicated, that
seems like a reasonable change.
On 13-09-01 3:53 PM, peter dalgaard wrote:
On Sep 1, 2013, at 20:08 , Duncan Murdoch wrote:
On 13-09-01 2:45 AM, Scott Kostyshak wrote:
'tkcoords' is defined twice (in the same way) in src/library/tcltk/R/Tk.R.
Attached is a patch against r63780 that removes the duplicate
defi
t.files}}.}
In the comparison phase, an object of class \code{"changedFiles"}. This
is a list containing
\item{added, deleted, changed, unchanged}{character vectors of filenames
from the before
and after snapshots, with obvious meanings}
\item{changes}{a logical matrix with a row for
On 13-09-04 8:02 PM, Karl Millar wrote:
Hi Duncan,
I think this functionality would be much easier to use and understand if
you split it up the functionality of taking snapshots and comparing them
into separate functions.
Yes, that's another possibility. Some more comment below...
On 13-09-04 11:36 PM, Scott Kostyshak wrote:
On Wed, Sep 4, 2013 at 1:53 PM, Duncan Murdoch wrote:
In a number of places internal to R, we need to know which files have
changed (e.g. after building a vignette). I've just written a general
purpose function "changedFiles" tha
On 05/09/2013 12:32 PM, Dr Gregory Jefferis wrote:
Dear Duncan,
This certainly looks useful. Might you consider adding the ability to
supply an alternative digest function? Details below.
Thanks, that's a good idea.
Duncan Murdoch
I often use a homemade "make" type function
On 13-09-06 2:46 AM, Karl Millar wrote:
Comments inline:
On Wed, Sep 4, 2013 at 6:10 PM, Duncan Murdoch wrote:
On 13-09-04 8:02 PM, Karl Millar wrote:
Hi Duncan,
I think this functionality would be much easier to use and understand if
you split it up the functionality of taking snapshots
u are importing it twice, e.g.
import(combinat)
importFrom(utils, combn)
?
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On 06/09/2013 2:20 PM, Duncan Murdoch wrote:
I have now put the code into a temporary package for testing; if anyone
is interested, for a few days it will be downloadable from
fisher.stats.uwo.ca/faculty/murdoch/temp/testpkg_1.0.tar.gz
Sorry, error in the URL. It should be
http
one snapshot to the current
file system
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longer
than the list of items to be excluded from an import.
This doesn't make sense to me. How could it be easier to maintain a
list over which you don't have control instead of one over which you do
have control?
Duncan Murdoch
Or have I overseen some obvious, easier way to ac
On 13-09-06 7:40 PM, Scott Kostyshak wrote:
On Fri, Sep 6, 2013 at 3:46 PM, Duncan Murdoch wrote:
On 06/09/2013 2:20 PM, Duncan Murdoch wrote:
I have now put the code into a temporary package for testing; if anyone
is interested, for a few days it will be downloadable from
On 13-09-06 9:21 PM, Karl Millar wrote:
Hi Duncan,
I like the interface of this version a lot better, but there's still a
bunch of implementation details that need fixing:
* As previously mentioned, there are important cases where the mtime
values change in ways that this code doesn
On 13-09-06 11:07 PM, Karl Millar wrote:
On Fri, Sep 6, 2013 at 7:03 PM, Duncan Murdoch wrote:
On 13-09-06 9:21 PM, Karl Millar wrote:
Hi Duncan,
I like the interface of this version a lot better, but there's still a
bunch of implementation details that need fixing:
* As previ
Thanks for everyone's comments on this. I have now committed a version
to R-devel. I don't plan to backport it to 3.0.2 (coming out in a
couple of weeks), but it should appear in 3.1.0 in the spring, and it's
conceivable it could make it into 3.0.3 (not yet scheduled).
#x27;t have the relevant \alias{}
defined correctly. If you do, please post the top of one or two of the
Rd files, and we can tell you what's missing. (I'd like to see at least
the \alias{} and \usage{} sections.)
Duncan Murdoch
If anyone has advice on how to pass R CMD c
prefix.
Attaching it first loads it, then modifies the user's search list so the
user can see it.
Loading is less intrusive, so it's preferred over attaching. Both
library() and require() would attach it.
Duncan Murdoch
In DESCRIPTION I have
Depends: R (>= 2.10), vcd, gnm (&g
On 13/09/2013 8:31 AM, Michael Friendly wrote:
On 9/12/2013 1:37 PM, Duncan Murdoch wrote:
>
> I think this one would be fine if you had library(MASS) or
> require(MASS) or (probably best) used MASS::loglm explicitly. It may
> be that in the past some other package put MASS on the
ssible to solve this before the upcoming release?
I don't see the error in 32 bits, but I do see it in 64 bits. I think
it's really unlikely this will be fixed before 3.0.2, unless you send a
well tested patch in the next few days. Code freeze is on Wednesday.
Duncan Murdoch
Th
On 13/09/2013 10:18 AM, Dirk Eddelbuettel wrote:
On 13 September 2013 at 09:51, Duncan Murdoch wrote:
| Changes are generally announced in the NEWS.Rd file long before release,
| but R-devel is an unreleased version, so you won't see the news until it
| is there. Announcing things that n
On 13/09/2013 10:37 AM, Prof Brian Ripley wrote:
On 13/09/2013 14:51, Duncan Murdoch wrote:
> On 13/09/2013 8:31 AM, Michael Friendly wrote:
>> On 9/12/2013 1:37 PM, Duncan Murdoch wrote:
>> >
>> > I think this one would be fine if you had library(MASS) or
>>
lot, but if they only did a little bit more work it would
help me even more."
I suspect they'd be more receptive to suggestions that had them doing
less work, not more.
Duncan Murdoch
| by users without them needing to specifically attach Rcpp. They are
| available with Depends bu
On 13-09-14 9:14 AM, Dirk Eddelbuettel wrote:
On 14 September 2013 at 09:04, Duncan Murdoch wrote:
| On 13-09-13 12:00 PM, Dirk Eddelbuettel wrote:
| > But the focus here should not be on my hobby package. The focus needs to be
| > on how four CRAN maintainers (who do a boatload of amazin
On 13-09-14 9:16 AM, Brian G. Peterson wrote:
On 09/14/2013 08:04 AM, Duncan Murdoch wrote:
>> On 13-09-13 12:00 PM, Dirk Eddelbuettel wrote:
But the focus here should not be on my hobby package. The focus
needs to be on how four CRAN maintainers (who do a boatload of
amazing work wh
On 13-09-14 12:19 PM, Paul Gilbert wrote:
On 13-09-14 09:04 AM, Duncan Murdoch wrote:
On 13-09-13 12:00 PM, Dirk Eddelbuettel wrote:
On 13 September 2013 at 11:42, Paul Gilbert wrote:
| On 13-09-13 11:02 AM, Dirk Eddelbuettel wrote:
| > It's not so much Rcpp itself or my 20-ish pack
AN is just asking you to do it
sooner, rather than later. However, I would guess that if you have an
urgent fix in the package you are uploading, and something is going to
stop you from fixing the newly identified problem, they'll be
sympathetic to the need to allow your package to fix t
out Windows binaries already built.
Duncan Murdoch
Göran
winbuilder's R-devel seems to be built daily,
saving me the time. Since I don't have Windows it kills two birds with
one stone. It has caught many problems for me before submitting to CRAN
and I can't remember it ever
een stated many times. I don't expect that to change because
users on this list make stupid jokes about it.
Duncan Murdoch
CRAN is like a ghost in r-devel (or any other mailing
lists) -- everybody is discussing about it, and nobody has ever seen
it. Perhaps one day useRs will realiz
other formats. The standard location for these is
subdirectory inst/doc of a source package, the contents will be copied to
subdirectory docwhen the package is installed."
That statement should be correct, hence current behaviour is a bug.
Duncan Murdoch
However, it is also clear tha
he big vignette, but will consider it to be a
vignette. R-devel will not consider it to be a vignette. Both should
install it into inst/doc in the tarball.
Duncan Murdoch
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n the HTML help page under "User guides, package vignettes
and other documentation."
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R-patched after 3.0.2 is released next week.
Duncan Murdoch
p=parse(text='1i')
getParseData(p)
line1 col1 line2 col2 id parent token terminal text
1 11 12 1 2 NUM_CONST TRUE1
2 11 12 2 0 exprFALSE
sessionInfo()
R
utput? Or alternatively, is
there a way to make R pipe stdout and stderr from system2 in such a
way that they can be captured with sink or capture.output in the R
parent process?
See the recent thread
<https://mailman.stat.ethz.ch/pipermail/r-devel/2013-September/067552.html>
for an appro
On 13-09-23 6:34 PM, Simon Urbanek wrote:
Duncan,
On Sep 23, 2013, at 10:20 PM, Duncan Murdoch wrote:
On 13-09-23 2:17 PM, Jeroen Ooms wrote:
Is there any way to capture output (both stdout and stderr) from
install.packages? Solutions like sink and capture.output don't work
becaus
On 13-09-24 10:37 AM, Jeroen Ooms wrote:
On Mon, Sep 23, 2013 at 6:50 PM, Duncan Murdoch
wrote:
x <- system2("Rscript", "-e \"install.packages('MASS',
repos='http://probability.ca/cran')\"", stdout=TRUE, stderr=TRUE)
Thank you, this sugge
my code somehow got mixed up with the igraph code, so I really do
have a call out to igraph's Shape::~Shape instead of rgl's
Shape::~Shape, or is this just bad info being given to me by gdb?
- If I really do have calls to the wrong destructor in there,
d in other packages in the future?
Duncan Murdoch
On 02/10/2013 10:50 AM, Duncan Murdoch wrote:
I've had reports lately about segfaults in the rgl package. I've only
been able to reproduce these on Linux. I am not so familiar with C++
details, so I have a couple of questions way down b
with
extern "C" declarations; pointers to any readable tutorials would be
appreciated.
Duncan Murdoch
On 02/10/2013 11:52 AM, Dirk Eddelbuettel wrote:
On 2 October 2013 at 15:45, Martyn Plummer wrote:
| In C++, everything goes in the global namespace unless the programmer
| explicitly
On 02/10/2013 4:01 PM, Ross Boylan wrote:
On Wed, Oct 02, 2013 at 11:05:19AM -0400, Duncan Murdoch wrote:
>> Up to entry #4 this all looks normal. If I go into that stack frame, I
>> see this:
>>
>>
>> (gdb) up
>> #4 Shape::~Shape (this=0x15f8760, __in_
On 13-10-02 4:26 PM, Romain Francois wrote:
Le 02/10/13 22:15, Duncan Murdoch a écrit :
On 02/10/2013 4:01 PM, Ross Boylan wrote:
On Wed, Oct 02, 2013 at 11:05:19AM -0400, Duncan Murdoch wrote:
Up to entry #4 this all looks normal. If I go into that stack
frame, I
see this:
(gdb) up
On 13-10-02 4:37 PM, Ross Boylan wrote:
On Wed, 2013-10-02 at 16:15 -0400, Duncan Murdoch wrote:
On 02/10/2013 4:01 PM, Ross Boylan wrote:
On Wed, Oct 02, 2013 at 11:05:19AM -0400, Duncan Murdoch wrote:
Up to entry #4 this all looks normal. If I go into that stack frame, I
see this
n't say an "as" method
will be applied if colClasses is one of the atomic, factor, Date, or
POSIXct classes; but I can see how you might assume that, since all
the atomic, factor, Date, and POSIXct classes already have "as"
methods...
And this does sugges
didn't put those into the rgl namespace. So there are
still possibilities for clashes if anyone else uses those.
I'm still surprised that anything with plugins works on Unix-alike
systems with such bizarre linking rules. This is one of those few cases
where the Windows design seems
ant to accept
anything except what is in .GlobalEnv; in that case, use inherits =
FALSE in the call to get().
Duncan Murdoch
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t is usually very easy to hide everything except the registration
function. (One exception: if your package has its own configuration
script, it's a bit more work.)
Duncan Murdoch
Martyn
On Fri, 2013-10-04 at 15:05 -0400, Duncan Murdoch wrote:
> I have now got two "solutions&quo
drawn before objects in
front of them. If you put two surfaces into the same plot there will be
no way to guarantee that.
If you want two surfaces in the same plot (or other things in a surface
plot), you should probably use persp3d from the rgl package.
Duncan Murdoch
e "shade"
argument) is active, transparency is ignored. However, if
the first colour is transparent, lighting is turned off, so transparency
*will* be used. I'm not sure what the intention was behind the latter
behaviour.
Duncan Murdoch
2. It would be helpful if one could add a surfa
f you have filed a bug report on it that doesn't include instructions
to reproduce it, please add them. Intermittent non-reproducible bugs
are unlikely to be fixed.
Duncan Murdoch
It hasn't been a big problem, but it potentially could be, if a critical
package were to have this e
oing this, I'll have to track
down 91+ files to make use of it? This sounds like an argument why
someone else should do it. ;-)
Duncan Murdoch
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o throw it out there.
No, we certainly won't do that. We rely on being able to process the Rd
files in multiple ways.
Duncan Murdoch
/Henrik
Regards,
Yihui
--
Yihui Xie
Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On Wed, Oct
On 13-10-12 6:49 PM, R. Michael Weylandt wrote:
On Oct 9, 2013, at 21:18, Duncan Murdoch wrote:
On 13-10-09 7:54 PM, Henrik Bengtsson wrote:
On my related wishlist: A standardized mechanism to 'R CMD build' for
building man/*.Rd from any input format (e.g. roxygen and so on)
a
On 13-10-14 1:54 PM, Luis Rodríguez wrote:
Thanks Duncan (and othersin R-devel).
I clearly got away from this project, but I am still quite interested in
resolving this issue and getting these codes into the CRAN.
Some attempts to repair the documentation have occurred in the intervening
On 13-10-18 8:32 PM, Jonathan Greenberg wrote:
R-developers:
Duncan Murdoch suggested I move a post I started on r-help over here,
since it is more at the developer level. Here is my
question/challenge -- to my knowledge, there is not currently an
official way to store a *package*'s optio
AMESPACE
file; you can import everything from a package if you want, but the best
style is in fact to just import exactly what you need. This is more
robust than using Depends, and it doesn't add so much to the user's
search path, so it's less likely to br
On 13-10-20 4:54 PM, Jonathan Greenberg wrote:
Duncan:
Thanks -- learning something new today -- quick follow-up, will using
the import statements in the NAMESPACE, when a user goes to
install.packages(), auto-install the "dependent" packages the same way
Depends forces?
You need t
odify both the DESCRIPTION file as you say above, and
the NAMESPACE file to say what to import. Once you do that, those
functions will appear to your own package functions without any prefix
needed.
Duncan Murdoch
--j
On Sun, Oct 20, 2013 at 5:34 PM, Dirk Eddelbuettel wrote:
On 20 Oc
k to being updated. (There
were hardware changes on developer.r-project.org, and this didn't get
transferred until now.)
Duncan Murdoch
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t try() doesn't catch user
interrupts, so it never gets undone.
Shouldn't be too hard to fix...
Duncan Murdoch
Cheers, MIke.
## 1)
## this code creates a temporary file to run Sweave
## interrupt this code before Sweave() finishes
txt <- c("\\documentclass[a4paper]{ar
On 13-10-22 10:45 PM, Duncan Murdoch wrote:
On 13-10-22 9:45 PM, Michael Sumner wrote:
Hello, if I interrupt Sweave while it's processing a file it seemingly
leaves an open sink connection that hides printed output.
Can this be changed to reset the sink on exit? I've been baffled b
be a high priority to fix, but feel free to submit
it as a bug report, and someone will likely deal with it eventually.
Please attach a tiny package that illustrates the error to your bug
report (e.g. pkg with just about everything taken out).
Duncan Murdoch
Z:\R\source\effects>R
l <- sub("^\\* building '", "", tarball)
tarball <- sub("'$", "", tarball)
system(paste("R CMD INSTALL", tarball))
}
}
I haven't tested this much, and it doesn't offer options to the build or
install steps, but it could
.1 with or without compiling? Or were you comparing to some other
version?
Duncan Murdoch
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cases where you really do need something to happen.
Duncan Murdoch
Thank you.
Bests,
Renaud
###
Sys.info()
sysname release
version
"Linux"
"3.11.0-12-generic" &qu
tive encoding would be UTF-8, and the problem would go away.
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On 13-11-09 6:58 PM, Ben Bolker wrote:
Duncan Murdoch gmail.com> writes:
On 13-11-09 12:07 PM, Sverre Stausland wrote:
As recently discussed on Stack Overflow, R for Mac OS and Ubuntu (so
probably all Unix systems) can correctly write files with UTF-8
encoding, but R for Windows can
hat would make R look like "a software
program in 2013", since it would be so much work, and there's such an
easy workaround.
Duncan Murdoch
But this is just guesswork.
PS. A related issue:
http://stackoverflow.com/questions/19881553/using-unicode-inside-rs-expression-comma
e UTF-16 as its internal encoding
because at the time it was written, Unix systems didn't properly support
it. They generally used 8 bit encodings, and because of its roots, that
made sense for R too.
Duncan Murdoch
Sverre
On Sun, Nov 10, 2013 at 1:49 PM, Duncan Murdoch
wrote:
O
do it on a Windows machine, and copy the
files over.)
Duncan Murdoch
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e C
locale, and non-ascii characters are messed up.
Is there a way to declare that I am in a "generic" UTF-8 locale? It is
like the C locale in other respects, but it knows about UTF-8 characters.
Duncan Murdoch
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hat the
result of exportR will be a function that looks like exporter.
You should not include an assignment in your usage section. I think it
is being seen as a call to the "<-" function, so you get the warning
about documenting something that is not an alias. (I might be wrong
about
cc.Kindly
provide your suggestions whether it is good idea to use Intel compilers.
Thanks for your kind attention and time.
Can't help you with your final question, I have no experience with them.
Duncan Murdoch
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On 13-12-02 5:25 PM, Peder Axensten wrote:
Duncan,
As soon as I read your letter I realized the logic. I followed your advice and
the warnings are gone. I don’t know how long it would have taken me to see it
myself, but probably quite some time – thank you!
I do think it’s a pity, in this
For example,
#define INDEX(i,j) (i) + rows*(j)
Then mPtr[INDEX(i,j)] will do R-style indexing (except it will be
0-based, not 1-based. You could fix that too if you wanted.)
Duncan Murdoch
Thanks a lot in advance!
Cheers
Larissa
Here's the C main function showing that the C code itself
don't know a simple workaround for someone who depends on a data-only
package that they did not author.
Duncan Murdoch
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lly there's little or no code
that does.
It would have those benefits, but it would be harder to prototype
changes by actually replacing the `if` function. Implementations that
want to optimize the calls have other ways to do it, e.g. the sorts of
things t
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