On 13-12-12 3:22 PM, Duncan Murdoch wrote:
On 12/12/2013 2:08 PM, Karl Millar wrote:
According to
http://cran.r-project.org/doc/manuals/r-release/R-lang.html#Reserved-words
if else repeat while function for in next break
TRUE FALSE NULL Inf NaN
NA NA_integer_ NA_real_ NA_complex_
3
$ : symbol *
$ : num 2
$ : symbol x
Function definitions get srcrefs.
Second, what is the proper way to drop that 'srcref' element in
'exprA'? I can think of either
exprC <- exprA
exprC[[4L]] <- NULL
That should be best.
Duncan Murdoch
or
exprC <- parse(t
lways be. I would much
prefer that the compiler code were made smarter about detecting this
rather than adding exceptions to the language design.
Duncan Murdoch
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The equivalent of your example above would be
rgl:::subst("pi = %pi%, 2pi = %twopi%", pi = pi, twopi = 2*pi)
i.e. general expressions aren't supported, just specific named
substitutions.
Duncan Murdoch
Thanks
Henrik
PS. The following is on the borderline because it does not do
a
nd Administration
manual. In particular, *do not* run configure.
If you do choose to create a Cygwin build, please make sure it passes
the tests before you use it. I haven't seen one that does.
Duncan Murdoch
I am stuck at the moment, because the build process tries create symlink
= 10,
posthoc = "std.pearson.residuals.sign",
assoc = ifelse("univariate"
Notice how the line above differs from your source -- the % signs are
taken as comment markers. You need to escape them.
Duncan Murdoch
list(c("N", "alpha.X2", "uc.1
After initializing R, set it to 1.
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during the construction of the colorspaces
list, which calls make.rgb later in that same file. You could insert
print() or message() statements to localize the error, but it's not an
error that should have happened in a valid build.
Duncan Murdoch
I hope this is not too offtopic with the i
that is a little tricky, but should be doable.
First, work out whether R_FunTab is corrupted or not. If it is, then
set a hardware breakpoint to see when it happened. If not, then you
have to wait until the La_solve primitive is created, then set a
hardware breakpoint on it. Good luck
for a solution for Sweave.
You are running with the strip.white option set to TRUE. That strips
blank lines at then beginning and end of each output piece. Just set
strip.white=FALSE.
Duncan Murdoch
Cheers
Kirill
\documentclass{article}
\begin{document}
<>=
cat("a\n")
ca
On 14-01-02 7:53 PM, Kirill Müller wrote:
On 01/03/2014 01:45 AM, Duncan Murdoch wrote:
You are running with the strip.white option set to TRUE. That strips
blank lines at then beginning and end of each output piece. Just set
strip.white=FALSE.
Thanks, the code below works perfectly. I have
On 14-01-02 8:04 PM, Kirill Müller wrote:
On 01/03/2014 01:59 AM, Duncan Murdoch wrote:
But results=tex is not the default. Having defaults for one option
depend on the setting for another is confusing, so I think the current
setting is appropriate.
True. On the other hand, I cannot imagine
It's dishonest to quote me out of context.
Duncan Murdoch
On 14-01-03 3:40 AM, Kirill Müller wrote:
On 01/03/2014 02:34 AM, Duncan Murdoch wrote:
Carriage returns usually don't matter in LaTeX
I'd rather say they do. One is like a space, two or more end a paragraph
and star
On 14-01-03 4:57 AM, Martin Maechler wrote:
Kirill Müller
on Fri, 3 Jan 2014 02:04:06 +0100 writes:
> On 01/03/2014 01:59 AM, Duncan Murdoch wrote:
>> But results=tex is not the default. Having defaults for
>> one option depend on the setting
fault than "true", I think it would be more likely to cause trouble
than to solve it.
Duncan Murdoch
-Kirill
On 01/03/2014 11:39 AM, Duncan Murdoch wrote:
It's dishonest to quote me out of context.
Duncan Murdoch
On 14-01-03 3:40 AM, Kirill Müller wrote:
On 01/03/2014 02:34
On 03/01/2014 7:32 AM, Kirill Müller wrote:
On 01/03/2014 01:06 PM, Duncan Murdoch wrote:
> On 14-01-03 5:47 AM, Kirill Müller wrote:
>> I'm sorry, I didn't mean to be rude. Do you prefer including the entire
>> original message when replying? Or perhaps I misunderst
.
Duncan Murdoch
I am trying to create a large array using:
d = c(1e+10,2)
a=array(0,d)
This results in the error:
Error in array(0, d) : negative length vectors are not allowed
In addition: Warning message:
In array(0, d) : NAs introduced by coercion
Note that I can create a vector of the same
On 14-01-06 4:12 PM, Boris Aronshtam wrote:
Jay, Duncan,
Thank you for your replies.
The confusing part for me is that vector allows large indices, while array does
not allow.
See section 12 of the R Internals manual for a discussion of the issues.
Also, is there an estimate when R would
just not
where you were looking. You can get them as follows:
f <- getMethod("initialize", "MyClass")
getSrcref(unRematchDefinition(f))
This should work for the other cases too, where unRematchDefinition does
nothing. I don't know if there are any cases where it will fail, but if
there are, please let me know.
Probably the getSrcref function should do this automatically when it
sees that f is a method definition, but I'll wait to hear if it's the
wrong approach.
Duncan Murdoch
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this a while, I decided that it's really a bug that
getSrcref didn't do this automatically. So now it does (in R-patched
and R-devel).
Duncan Murdoch
Thanks again
Markus
2014/1/8 Duncan Murdoch mailto:murdoch.dun...@gmail.com>>
On 14-01-07 2:40 PM, Markus Müller wro
s2i <- 1+2i
test <- function(a = Cplx_1plus2i){}
Less sneaky, but a tiny bit different due to scoping issues: if the
function happens to assign something to a local variable Cplx_1plus2i
before evaluating a, the local variable will be used rather than the
global
On 14-01-19 4:45 PM, Duncan Murdoch wrote:
On 14-01-19 4:16 PM, peter dalgaard wrote:
It's not formals() that is doing you in. Rather, it is a conspiration between
two things:
(a) R always displays complex constants as x+yi, even if x is zero and (b)
there really is no way to specify co
t use
mkCharCE instead of mkChar, as described in Writing R Extensions. If it
is in UTF-16 you might have more trouble because of possible embedded 0
bytes. Translate to UTF-8 first using C facilities like
WideCharToMultibyte.
Duncan Murdoch
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was the function that you *did* want to export and document.
multiply was the function you wanted to keep local.
So you should export timestwo, and not multiply. You will then need to
document timestwo, but you won't need to document multiply.
That will work.
Duncan Murdoch
Thanks ag
s is hugely incomplete. Please stop wasting everyone's time, and
post something reproducible.
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?SHLIB, and it will tell you
that -n will give you some diagnostic information. You can also try
R CMD SHLIB --help
to see a bit more.
One other thing you can do if you need to ask here again, is to post
system and version information printed by R by sessionInfo(). And
please don't p
On 14-01-26 9:34 AM, Axel Urbiz wrote:> Hi Duncan,
>
> My most sincere apologies. It's really not my intention to waste anyones
> time. More the opposite...for some reason I thought that the problem had
> to do with my call to options() and thought that would be enough
it's
not the way that the terms function works, so you'll need to do more
work yourself, including specifying what the evaluation rules should be
in case a variable occurs in more than one of those locations.
Duncan Murdoch
Thanks,
Axel.
#mycodefiles <- c("cmt.R&q
one in the namespace will take
precedence. In most cases users don't want that.
The problem is that in order to make the user one take precedence, you
could modify the parent of the environment of the formula, but that's
bad too (because it will have global effects since enviro
On 28/01/2014 2:43 PM, William Dunlap wrote:
[inline below]
Bill Dunlap
TIBCO Software
wdunlap tibco.com
> -Original Message-
> From: Duncan Murdoch [mailto:murdoch.dun...@gmail.com]
> Sent: Tuesday, January 28, 2014 10:45 AM
> To: William Dunlap; Axel Urbiz; Henrik Bengt
user defines a
tt function, will coxph use theirs, or yours?
I'd say the answers for situations like this should be "yes" and
"theirs", but that's not true of my tables package, where answers to the
corresponding questions would be "yes" and "mine"
g both updates seems to have fixed things.
Duncan Murodch
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lob, but the docs
don't make it clear to me that this also implies export of the generator
function.
So I'd add
export(Blob)
to your NAMESPACE. I just checked another package that exports a class,
and it separately exported the generator function, so I guess this is known.
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does use setRefClass. I don't think it uses
exportClass though...
Duncan Murdoch
>
> Thanks for your help.
>
> On 02 Feb, 2014,at 12:57 AM, Duncan Murdoch
> wrote:
>
>> On 14-01-31 10:14 PM, Imanuel Costigan wrote:> I am having an issue with
>> reference c
On 14-02-03 3:41 AM, Saptarshi Guha wrote:
Hello,
I was reading through serialize.c and i couldn't answer something.
In readItem, case CHARSXP, rules exists to adjust the read string for
string encoding.
This is described in the R Internals manual.
Duncan Murdoch
Q1. I couldn&#
lem, you should contact the maintainer of that
package.
If it's not just a devtools problem and you still need help, you need to
describe what you did in more detail. What is your PATH? What about
other environment variables? What version of R are you using? What
version of Rtools?
hat you mean by your functions, and
put them in a package, along with examples where they give more useful
results than the standard definitions. I think the current base package
functions match the mathematical definitions better.
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possible
non-missing value that would give anything else when added to NaN, but
the answer should not depend on the order of operands.)
However, I get the same as you in 64 bit 3.0.2. All calculations I've
shown are on 64 bit Windows 7.
Duncan Murdoch
The aggregate package is availa
easier; I don't know if that's
trivial or hard.
Duncan Murdoch
> hex(NA_real_)
[1] "7FF007A2"
> hex(NA_real_+1)
[1] "7FF807A2"
> hex(NaN)
[1] "7FF8"
This is with 64-bit R (on OS X Mavericks, R-devel r64910), as we
Similarly, the standard doesn't say which bit pattern propagates when
you do binary operations on two NaNs. That's why sometimes NA + NaN is
NA, and sometimes NaN.
Duncan Murdoch
On 32-bit R-2.15.3:
NA: 7ff807a2
NaN: 7ff8
On 64-bit version of R-2.15.3
NA: 7f
n his/her search list, maybe there's a reason for
that, and mypackage::foo shouldn't mess with it.
I think the real problem is that loading the mypackage namespace isn't
enough to get the functions within it to work.
Duncan Murdoch
In the following thread, it's stated th
haven't tried
that. But somehow you need to tell R where the knitr engine lives.
Also for what its worth Sweave'ing still fails to produce graphics output
Now that sounds unrelated.
Duncan Murdoch
https://stat.ethz.ch/pipermail/r-devel/2014-February/068414.html
$ R --versi
normal dataframe. Dataframe columns are
vectors all of a type. You want the first row to be a string, the
second row to be an integer. You can't do that with simple atomic
columns, and you probably don't want to mess with the alternative (which
, and
I'd recommend bumping the version number.
Duncan Murdoch
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.
Put the C code for the DLL in "src" (not "SRC"). R will compile it for
the platform where your package is being installed.
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in this, then post a simplified sample
package and someone else will be able to see if they have the same
problem as you, and perhaps fix it.
Duncan Murdoch
If (1) is not possible, any suggestions how to auto-generate a
crude generic bibtex .bib file from my existing document?
Bac
t may be duplicated and
the result after the change will be at a new location.
Duncan Murdoch
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ch to obtain packages.
The only objection I can see to this is that it requires extra work by
the third party, rather than extra work by the CRAN team. I don't think
the total amount of work required is much different. I'm very
unsympathetic to proposals to dump work on others.
Duncan
suggestion seems like an ideal solution to this problem.
Any CRAN mirror could implement it. If someone sets this up and commits
to maintaining it, I'd be happy to work on the necessary changes to the
install.packages/update.packages code to allow people to use it from
within R.
Duncan
[1]-1
paramChoice['xy']<-xy
}else{paramChoice['toDo'] <- ""}
},
"Down" = {
if(xy[1]
It can also return NULL, but to be sure, why not print the value?
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ckage S3 generic into an S4 generic. Clearly they
should not be creating separate generics, there's just one.
I don't know if there's something wrong with the way apcluster or
BiocGenerics are doing things, or something wrong with the way the
methods package is creating the generic,
or unequal strings, and users are likely
to get messed up by that, or to submit bogus bug reports. And it's not
impossible to work around: if you can collect the universe of strings to
compare in advance, then just use order() to convert them to integer
values, and compare those.
Dunc
cular
context.
So depending on what you are trying to accomplish, it may be fine to
just set up an environment. Why do you think that won't work?
Duncan Murdoch
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rgl.* function that set the lty property to dashed.
Duncan Murdoch
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gy) if you want the equivalent of
lines3d but with the persistant material properties.
I had forgotten that, because I never use the rgl.* functions. I would
say "neither should you", but there might be some good reason to do so.
Duncan Murdoch
I'm using R 3.1.0 alpha
On Mo
ave the functions in the package that it needs, so
they've already lost reproducibility.
Duncan Murdoch
$ R --version|head -n 3
R version 3.1.0 RC (2014-04-05 r65379) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (
pre-release versions.
Duncan Murdoch
Thanks again.
Regards,
Marc
On Apr 14, 2014, at 7:28 AM, Martin Maechler wrote:
Marc Schwartz
on Sun, 13 Apr 2014 10:22:55 -0500 writes:
[on the R-SIG-Mac mailing list] :
Hi all,
With R version 3.1.0 on OSX, using either the Snow
On 15/04/2014 8:12 AM, peter dalgaard wrote:
On 15 Apr 2014, at 13:14 , Duncan Murdoch wrote:
> On 14/04/2014, 10:23 AM, Marc Schwartz wrote:
>> Hi Martin,
>>
>> Thanks for your confirmation on this.
>>
>> I normally do not use R CMD Sweave, as I too ru
ate package with a
maintainer who is willing to take this on.
Duncan Murdoch
On 15/04/2014 1:48 PM, Arni Magnusson wrote:
Hi all,
I would like to propose the attached function ASCIIfy() to be added to the
'tools' package.
Non-ASCII characters in character vectors can be problematic f
e was announced there more than a year ago
(http://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2013/03/19),
and has shown up several times since as minor edits have been made to
the announcement.
Duncan Murdoch
Here's my use case: I have a function that pulls arbitrary financial data
On 17/04/2014 12:47 PM, Gregory R. Warnes wrote:
Hi Arni,
I’ll be glad to drop ASCIIfy into gtools. Let me know if this OK.
Thanks, that sounds like a great solution if Arni doesn't want his own
package.
Duncan Murdoch
-Greg
On Apr 17, 2014, at 9:46 AM, Duncan Murdoch
the
"model's z-axis" is parallel to the z axis in the box around the plot.
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uotes must
have no effect on the interpretation.
Duncan Murdoch
How about something like this:
- if it is quoted (and not specified otherwise in colClasses), then it is a
character/factor
- if it is not quoted (and not specified otherwise in colClasses), then the
type is automatically detected, ac
search (since r-patched builds aren't archived), and few
would test r-devel.
Duncan Murdoch
Thereby they would automatically be using the latest ("devel")
versions of base packages in the same way as they currently test their
script/project/package to work with the latest ("
dda6d84880c0
A link to your report would be more useful, if it included an example
where the bad regexp causes trouble.
Duncan Murdoch
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On 24/04/2014, 5:26 PM, Henrik Bengtsson wrote:
On Thu, Apr 24, 2014 at 1:42 PM, Duncan Murdoch
wrote:
On 24/04/2014, 1:11 PM, Yihui Xie wrote:
Hi,
I guess the backslash should not be used as the separator for
strsplit() in compareVersion(), because the period in [.] is no longer
a
get
missed again. If nobody else gets to it first I'll deal with it.
I don't see any value in fixing the compareVersion example, but if
someone submits a bug report about it, someone else might fix it.
Duncan Murdoch
On Apr 24, 2014, at 10:15 PM, Yihui Xie wrote:
You are right
needless to say, is disruptive for us. (Actually, it was downright
shocking.)
It wouldn't have been a shock if you had tested pre-release versions.
Commercial users of R should be contributing to its development, and
that's a really easy way to do so.
Duncan Murdoch
+1 f
revent it from being
expanded. After a bit more testing, I'll re-commit the fixes.
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On 26/04/2014, 12:28 PM, Tom Kraljevic wrote:
Hi Duncan,
Please allow me to add a bit more context, which I probably should have
added to my original message.
We actually did see this in an R 3.1 beta which was pulled by an apt-get
and thought it had been released
accidentally. From my user
tation; can you confirm that your Java code reads it and
writes the same string? This is about 1% bigger than the limit at which
type.convert switches to strings or factors.
Duncan Murdoch
Below is the R output from adding one row at a time to “bad.csv”.
The last attempt results in a facto
On 26/04/2014, 6:40 PM, Tom Kraljevic wrote:
Hi Duncan,
This program and output should answer your question regarding java behavior.
Basically the character toHexString() representation is shown to be
lossless for this
example (in Java).
Please let me know if there is any way I can help
d to a number should
be converted to a factor.
Yes, that's a bad default, but some people rely on it.
Duncan Murdoch
Hadley
On Saturday, April 26, 2014, Martin Maechler
wrote:
Simon Urbanek >
on Sat, 19 Apr 2014 13:06:15 -0400 writes:
> On Apr 19, 2014, at 9
tions("warning.expression"), but I
don't see how...
Duncan Murdohc
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isn't R terminology. Could you give an example of one call
that passes a parse tree, and one that doesn't?
Duncan Murdoch
Currently, I do various rather ad hoc eval()+substitute() tricks for
this that most likely only work under certain circumstances. Ideally,
I'm looking for a
?
Looks like something has a "finalizer", but it doesn't work.
To be more specific, I'd have to see it, i.e. you'd have to give us
instructions to reproduce.
Duncan Murdoch
#13 0x2afd612f in Rf_eval (e=0x1448d68, rho=0x16c6780) at eval.c:399
#14 0x2a
are higher precedence in R.
The other assignment operators are ordered as <<-, ->, (<-, _) in the
blue book (where parens indicate equal precedence), but in R they are
(->, ->>), (<-, <<-), =.
Also surprising:
> quote(!2+!2)
!2 + (!2)
where it is somewhat p
.
Is there a language where "- 2^2" gives a different answer than "-2^2"?
(Substitute ** or any other exponentiation operator for ^ if you
like.) This is important, because I'd like to avoid ever attempting any
important calculation in that language.
Duncan Murdo
to the environment using
as.environment("org:variables"), and access it within that. For example,
assign("test", 24, pos="org:variables")
or
e <- as.environment("org:variables")
e$test <- 24
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e what you want to do is to save the code and
data that produced each plot. Then at least if functions change you can
edit your saved copy and still get a plot.
Duncan Murdoch
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you can convince him that giving you access
is worth the trouble of exposing some of it to user-level code, then
he'll export a function for you. (I think it's unlikely to be
.win32consoleCompletion, but who knows.)
Duncan Murdoch
(full quote because of the age of the tread)
Kin
ws a warning with an incompatible pointer type,
because pointers should be integers of course).
I've looked at all SEXPTYPEs in the R internals, and the only one specific
to integer vectors is INTSXP. Can this be used for vectors of length larger
than 32-bit?
Yes, see the section on "Long Ve
caping) while others
treat it as text (i.e., need escaping). Personally, I would hence avoid
the problem and only use the DOI URL here as this will be robust across
BibTeX styles.
Nevertheless it is not ideal that there is a discrepancy between the
different printing styles. I think currently this c
27;t try to
call formals() to work it out at run-time.
Another way is to have an argument like "control" in optim(), and ask
the user to pass one set of options via that, and the other via ... .
You'd use do.call() again to construct that call.
Duncan Murdoch
On 02/06/2014, 1:41 PM, Carl Boettiger wrote:
Thanks both for the replies.
Duncan, I'm sorry if I wasn't clear. I am indeed writing a vignette using
Sweave (knitr actually), and I want it to be a vignette. I'm well aware
that I can dodge these tests as you suggest, or through
one in the
vignette. That's a useful thing to be able to do.
Duncan Murdoch
Regards,
Yihui
--
Yihui Xie
Web: http://yihui.name
On Mon, Jun 2, 2014 at 10:19 AM, Paul Gilbert wrote:
On 06/02/2014 12:16 AM, Gabriel Becker wrote:
Carl,
I don't really have a horse in this race ot
On 03/06/2014, 4:12 AM, Gavin Simpson wrote:
On 2 June 2014 11:44, Duncan Murdoch mailto:murdoch.dun...@gmail.com>> wrote:
On 03/06/2014, 12:58 AM, Yihui Xie wrote:
Please also note that I do not expect R core or CRAN maintainers
to do
any extra work: p
proper use of
inline expressions.
The latter.
I do not think it is trivial to improve the tangle function so that it
can generate an R script that fully reproduce what was done in weave.
Now you are being nitpicky.
Duncan Murdoch
Inline expressions are not the only thing that need improveme
).
rgl has no support for pinch gestures, so your OS is translating the
message into something else, which rgl is acting on. I'd guess it's the
scroll wheel.
So I guess you should see if you can configure it to translate to the
opposite direction of rotation.
Dunc
sider the issue closed.
Duncan Murdoch
(adjectives on personal pronouns instead of nouns
in a discussion is a sign for me to quit in my eyes). I'm fine with
optional tangling, and I believe one should not expect to reproduce
results generated by weave using a different approach, namely
there for most of a
year before being reported. Please people, test pre-release versions.
Duncan Murdoch
>
> For reference, with R-3.0.2:
>
>> getParseData(parse(text = "{1}", keep.source = TRUE))
> line1 col1 line2 col2 id parent token terminal text
> 7
h BiocStyle that would need its suggestions. However, I don't think
it's worth complicating the check code to support this. If you need
knitr to be present to build your vignettes, why not just declare it
explicitly?
Duncan Murdoch
>
> This is only with a recent R. In detai
also worth mentioning that there is something similar to test for
changes to vignettes:
If there is a target output file .Rout.save in the vignette source
directory, the output from running the code in that vignette is
compared with the target output file and any differences are reported
fficient
> and not a best way to maintain. Did I miss anything in the R-exts
> manual?
Only that you can have a link to the help page in the other package, e.g.
\code{\link[emdbook]{curve3d}}
You'll still need to copy the required parts, but you can link to the
original for the rest
gt; my make output is here:
> https://www.dropbox.com/s/q7ylkw00re7riaf/make
> and my config.log is here:
> https://www.dropbox.com/s/0w09zhds9q6253n/config.log
Just a missed commit, now fixed.
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It's hardly fair to call these "unfixed bugs". Most of them are better
described as "unreported bugs", or, after this posting, "bugs reported
with insufficient detail". We can't fix them if we don't know what they
are, and it's not easy to d
On 24/06/2014, 1:40 PM, Radford Neal wrote:
> On Tue, Jun 24, 2014 at 09:20:30AM +0200, Duncan Murdoch wrote:
>> It's hardly fair to call these "unfixed bugs". Most of them are better
>> described as "unreported bugs", or, after this posting, "bugs rep
On 24/06/2014, 10:26 PM, Radford Neal wrote:
>> Duncan Murdoch:
>>
>> No, I don't think it's reasonable to expect you to write a patch, but
>> reporting the bugs in the R bug reporting system isn't that hard to do,
>> and does lead to fixes pret
> exportFrom(utils, help)
>
> Then:
>
>> getNamespaceInfo("ReexportingPackage", "exports")$help
> [1] "help"
> attr(,"origin")
> [1] "utils"
>
> Comments?
I don't see why this is needed. What does it gain over documenting tha
ld an R installer and I seem to be stuck...
I have seen this, but I don't see it on every machine. One one where I
do see it is the Windows builder machine in Dortmund. The following is
inserted into the script after building the 32 bit build
cacls %name32% /T /E /G VORDEFINIERT\Benut
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