ehow before it is executed? That would be unexpected at best.
That message comes from the compiler package, so presumbly you (or
Rscript) are trying to compile something. You can't have undefined
references in compiled code.
Duncan Murdoch
__
e process to do
its calculations.
Other packages can do other variations on parallel computations.
I can't help you with the rest of your question, I don't know what XPtr
objects are.
Duncan Murdoch
Similarly there is the RcppParallel package for RMatrix/RVector objects.
But none of
would be
better if vignettes were built in a separate process that was started
with an empty workspace.
There's an intention to clean up several vignette building issues, but
so far no action.
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ommand---while reading file sos.aux
Calls: -> texi2pdf -> texi2dvi
Execution halted
Don't know about that one.
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reads,
"<>=".
In RStudio, you are running knitr rather than Sweave, but your vignette
uses Sweave syntax. This is an option you can set in "Global options"
and "Project options"; the latter take precedence.
Duncan Murdoch
What can I do to get this
org/R/?group_id=235).
Is there a way to get "R CMD build" to work with a vignette with
output: word_document?
Not easily. Vignette outputs need to be HTML or PDF. You'll need to
add another step to the processing to convert the .docx file to one of
those.
Duncan Murd
unix 'd everything. Any thoughts?
We don't support Cygwin builds.
If you get this using one of our builds, put together a simple
reproducible instance of it and make it available. If it's only in
Cygwin, you should do the same, and send it to someone there.
Duncan Murdoch
_
w prefixed ones.
The second patch fixes a typo where CPPFLAGS is misspelt as CPPLAGS
which causes them to be forgotten about in the middle of configure.
Your patches were attached. I'll apply the second one, but I'll leave
the first one for someone who knows the issu
isn't
downloaded anywhere else.
You can make a Windows-only package that contains it, but it's quite
possible CRAN won't accept it. See their policy document statement on
portable code.
Duncan Murdoch
thanks for your help
Holger
[[alternative
on mac/linux with default utf-8 encoding)
I'm not sure what should happen here, but that's not a legal string in a
UTF-8 locale, so it's not too surprising that things go wonky.
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invalid UTF-8 was
found. That would echo back the input in this case. No idea if it
would cause other problems.
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ably means that line 85 of
R_HOME/src/gnuwin32/fixed/etc/Makeconf needs to be changed from:
TCL_VERSION = 85
to
TCL_VERSION = 86
That is the current setting in R-devel, and has been since revision
70701 on June 3. (It is 85 in the 3.3 branch.)
Dunc
you can open the vignette, and execute the code chunks one by one.
If they all succeed in that context, they still might not when you run
checks: it *won't* have your package loaded when it compiles a
vignette. You need to put an explicit
library(hexbin)
in one of the code chunks.
Du
me doesn't.
So, should I use .packageName or utils::packageName() for this?
You should use utils::packageName. It is documented; .packageName is not.
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rm(bigdf)
and it will be safe to remove bigdf after the loop. (I see that Bill
Dunlap has posted a different way of achieving the same sort of thing.)
Duncan Murdoch
In the case where the model exists in .GlobalEnv, everything is
peachy. So replicating whatever happens when saving the model
Linux also.
It sounds as though you're talking about RStudio on Windows, not the R
GUI. If so, you should use RStudio on Linux as well; it is very similar.
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On 03/08/2016 4:12 PM, Paul Johnson wrote:
I have a script that goes wrong because I assumed that seq.int would
return integers.
"int" means "internal", not "integer". Sometimes you should read the
documentation.
Duncan Murdoch
Below please see it does not
me type"-only {e.g., would also work for characters}
version.
I don't know what you mean by these.
Of course, an ifelse2() should also be more efficient than
ifelse() in typical "atomic" cases.
I don't think it is obvious how to make it more efficient. ifelse()
already skip
I please be whitelisted? Many thanks.
Sure, I'll whitelist hieb...@uvic.ca.
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,
i.e.
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16333, with a
promise to submit a patch. It hasn't arrived in 16 months. So please
don't promise a patch unless you intend to deliver.
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ing a change. But changing the default RNG definitely
introduces problems in reproducibility, so it's not obvious that we
would do it.
Duncan Murdoch
On 30/08/2016 5:45 PM, Mark Roberts wrote:
Whomever,
I recently sent the "bug report" below tor-c...@r-project.org and have
just b
ementation of withAutoprint() may
need considerable more changes than just setting R_Visible to TRUE in one
place.
Have any efforts / experiments already happened towards providing such
functionality ?
I don't think the performance cost would matter. If you're printing
somethin
on Windows), you'll need to
translate the string to the local encoding. The Writing R Extensions
manual section 6.11 tells you how to do the re-encoding.
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ction.
This has the form ifelse(condition, a, b) and returns a vector of the length of
its longest argument, with elements a[i] if condition[i] is true, otherwise
b[i].
In fact, ifelse(condition, a, b) returns a vector of the length of 'condition',
even if 'a' or 'b
On 22/09/2016 7:43 AM, Mikko Korpela wrote:
In ?image (src/library/graphics/man/image.Rd), the text fragment "will
show though" should probably be "will show through".
Thanks, fixed.
Duncan Murdoch
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;ve also filed this on bugzilla, and have updated it there. See
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=1715
Thanks for an amazing piece of software!
Best,
Evan
P. S. I'm new to the mailing list, so I apologize in advance if I'm
violating any conventions I'm unaware of.
Presumably someone from Microsoft will respond to this.
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kg).
It would be possible to change, but would take time. Since we don't
need it for R's purposes, and you already have it, it seems like a low
priority.
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27;t say what platform you're working on, but I'd guess Windows,
because on Windows "inst/extdata/" (or "inst\extdata\") is not a valid
path. The dir() function works around this issue by removing trailing
slashes as appr
A))
Length Class Mode
2 character character
Here's a method and example using it:
> summary.character <- function (x, ...) { cat("this character vector
has", sum(is.na(x)), " NA value(s)\n")}
> summary(c
ot2' depends on package 'Rcpp', but 'Rcpp' was not found
might not be easy (which function knows both names?) However, if you
want to suggest a patch to implement this, I would take a look.
Duncan Murdoch
In other words, it might be helpful to avoid printing the
&
On 26/10/2016 5:52 AM, Martin Maechler wrote:
Duncan Murdoch
on Mon, 24 Oct 2016 14:54:16 -0400 writes:
> On 24/10/2016 1:51 PM, Kevin Ushey wrote:
>> Hi R-devel,
>>
>> One of the more common issues that new R users see, and become stumped
>
Those should be persistent.
If you have never posted to the bug list you will need to be manually
added to the list of people allowed to post. In that case, write to me
and I'll do it.
Duncan Murdoch
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On 27/10/2016 11:58 AM, Hervé Pagès wrote:
Hi Duncan,
On 10/27/2016 05:17 AM, Duncan Murdoch wrote:
[...]
> Could you please post it to the bug list as an enhancement request?
> Those should be persistent.
>
> If you have never posted to the bug list you will need to be manually
&g
ness", we all know that the value of a density at any
particular point is irrelevant. Only the integrals of densities have
any meaning.
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rror in b() : could not find function "b"
Notice the "Error in **b**() :" part. The original error message seems more
correct to me, although I can see how you can argue for either one.
I'm not seeing that in R-devel r71694. Cou
ause of abuse by spammers.)
Duncan Murdoch
On 06/12/2016 12:27 PM, frede...@ofb.net wrote:
Hi all,
Here's a more minimal version of my earlier bug report (thanks, Joshua
Ulrich):
d=as.POSIXlt(Sys.time()); d$zone=NULL; d$zone=""; d
I got some helpful, if glib, feedback from Joshu
es which export their
C-level entry points either guarantee them not to change or offer
(require?) version checks by user code. So dplyr should start out by
saying "I'm using Rcpp interface 0.12.8". If Rcpp has a new version
with a compatible interface, it replies "that&#x
On 16/12/2016 8:37 AM, Dirk Eddelbuettel wrote:
On 16 December 2016 at 08:20, Duncan Murdoch wrote:
| Perhaps the solution is to recommend that packages which export their
| C-level entry points either guarantee them not to change or offer
| (require?) version checks by user code. So dplyr
On 16/12/2016 10:40 AM, Dirk Eddelbuettel wrote:
On 16 December 2016 at 10:14, Duncan Murdoch wrote:
| On 16/12/2016 8:37 AM, Dirk Eddelbuettel wrote:
| >
| > On 16 December 2016 at 08:20, Duncan Murdoch wrote:
| > | Perhaps the solution is to recommend that packages which export thei
help with the general
compatibility problem, but nothing to help with this one.
Duncan Murdoch
Karl
On Fri, Dec 16, 2016 at 8:19 AM, Dirk Eddelbuettel wrote:
On 16 December 2016 at 11:00, Duncan Murdoch wrote:
| On 16/12/2016 10:40 AM, Dirk Eddelbuettel wrote:
| > On 16 December 2016 at 10:
hecks
for empty datasets.
Duncan Murdoch
The problem in other words:
I have a vector filled with missing numbers. I run the 'sum' function on
it, but instruct it to remove all missing values first. Consequently, the
sum function is left with an empty numeric vector. There is nothing to sum
ove
If it is recognized by the OSF or FSF or some other authority as a FOSS
license, then CRAN would probably also recognize it. If not, then CRAN
doesn't have the resources to evaluate it and so is unlikely to
recognize it.
Duncan Murdoch
_
don't have access to Windows, submit it to
win-builder.r-project.org for testing. Mac OS and Solaris are currently
harder to test without setting up your own local systems. Maybe someone
else will report on available test systems for those platforms.
Dunc
otherwise could be much simpler, such as using
deriv() or deriv3() to generate functions, for example to use as an nls model.
The nlsr package allows you to specify derivatives.
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I haven't tried any
of them in Windows.
The other choice is the old fashioned method: add lots of Rprintf()
statements to the source and recompile.
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be found, does "a %chr% %chr% b" mean "%chr%(a, %chr% b)", or is
it a syntax error (like typing "a %chr%(%chr%(b))" would be)?
Duncan Murdoch
On 16/03/2017 10:24 AM, Jim Hester wrote:
R has long supported user defined binary (infix) functions, defined
with
emantics won't break any of those uses?
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such a function and possibly missing some
desirable feature, I'd like to ask if anyone can point to an existing
one that is perfect (or nearly perfect, and point out what changes would
be desirable)?
Duncan Murdoch
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ave dependencies outside of it
Indeed, I'm looking for one that can be copied into base R. The author
can retain copyright, but we need to be able to offer it under our GPL
license.
ii) more importantly, Duncan asked for a good example of a "consistent" (as
in: predict
's better for the process to
always die than to sometimes silently produce incorrect results.
Frederick posted the way to do this in systems using systemd. We should
be putting that in place, or the equivalent on systems using other
tempfile cleanups. This looks to me like something that "make install"
should do, or perhaps it should be done by people putting together
packages for specific systems.
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like that idea, as long as checking for its existence doesn't
make some system think it is in use and therefore protected from deletion.
Duncan Murdoch
Tomas
On 04/26/2017 02:29 PM, Duncan Murdoch wrote:
On 26/04/2017 4:21 AM, Martin Maechler wrote:
on Tue, 25 Apr 2017 21:13:
c(a=TRUE,
b=FALSE) doesn't give the same thing as foo(c(a=TRUE, b=FALSE)).
Duncan Murdoch
Cheers,
H.
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.5-bioc/R/lib/l
mbedded nulls. Character vectors can't, because
internally, R is using 8 bit C strings, and the nulls are string
terminators.
I don't know how difficult it would be to fix the write.table problems.
Duncan Murdoch
On 29/04/2017 7:53 PM, Jack Kelley wrote:
"R version 3.4
On 30/04/2017 12:23 PM, Duncan Murdoch wrote:
No, I don't think anyone is working on this.
There's a fairly simple workaround for the UTF-16 and UTF-32 iconv
issues: don't attempt to produce character vectors, produce raw vectors
instead. (The "toRaw" argument to ic
because doing those would mean R
would have to handle the translation of LF itself, and I'm too lazy to
do that.
So far this is working for writes, but not reads. I still have to track
down what's going wrong there.
Duncan Murdoch
The default eol for write.csv (via write.table)
Now fixed in R-devel revision 72650.
Duncan Murdoch
On 02/05/2017 4:11 AM, Duncan Murdoch wrote:
On 01/05/2017 8:49 PM, Jack Kelley wrote:
Thanks for looking into this.
A few notes regarding all the UTF encodings on Windows 10 ...
This all stems from the ancient bad decision by Microsoft
this instance, but a common cause of this sort of
difference is a different parametrization. If that's the case, then
predictions in the two systems would match, even if coefficients don't.
Duncan Murdoch
X1 and X2 are correlated about .75 (yes, yes, I know - this model wasn't
ed" is available any more.)
For your application, you may have to allow users to attach names to the
object. I don't know how you're creating those things, but part of the
work could save a name as an attribute "SOSname", and then the print
method would use that.
Dunc
ng as though Windows is running in a
UTF-8 locale until you actually need to write to a file. Other systems
tend to have UTF-8 locales in common use, so they're already fine.
You offered to spend time on this. I'd appreciate some checks of the
patch I'm developing for 16098,
On 09/05/2017 5:46 PM, Kirill Müller wrote:
On 09.05.2017 13:19, Duncan Murdoch wrote:
On 09/05/2017 3:42 AM, Kirill Müller wrote:
Hi
I'm having trouble sourcing or parsing a UTF-8 file that contains
characters that are not representable in the current locale ("foreign
chara
ly get a clash if you explicitly imported two
things with the same name. (You can do a rename when importing if you
really want to do that.)
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endation in the admin manual section 2.1. So it's possible
there's a bug triggered when you do that. Can you try building in a
separate directory?
Duncan Murdoch
This suggests to me that perhaps "make clean" is not working.
I'm happy to provide more detai
manual Writing R Extensions, this should still be
recognized. When I try to use it in the help pages of my own packages,
\bold{} is interpreted correctly.
You missed the part about \eqn.
Duncan Murdoch
No idea what is going wrong and it's not that important, but I found it
curious enoug
On 23/05/2017 11:47 AM, Sahil Kang wrote:
Hi Duncan,
Would you merge this patch?
I'm planning on sending larger patches in the next few days that fix other
macros I've seen, but I figured it'd be best to start with a smaller patch.
No, I generally try to leave the macro
irst case you are working in a
locale where that character is representable. In my locale it is not,
so x1 is converted to UTF-8, and everything compares equal.
An explicit conversion of x1 to UTF-8 should fix this, i.e. replace
x1 <- path.expand(paste0("~/", filename))
with
x1
On 24/05/2017 7:59 AM, Hiroyuki Kawakatsu wrote:
On 2017-05-24, Duncan Murdoch wrote:
I think the test is wrong because in the first case you are working in a
locale where that character is representable. In my locale it is not, so x1
is converted to UTF-8, and everything compares equal.
An
On 24/05/2017 9:59 AM, Hiroyuki Kawakatsu wrote:
On 2017-05-24, Duncan Murdoch wrote:
[...]
Okay, how about if we weaken the test?
[...]
try
stopifnot(path.expand(paste0("~/", filename)) ==
paste0(path.expand("~/"), filename))
Nope:
## p
that's not a bug. Or maybe
R is wrong.
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es should move to JIRA, you need to
explain why it is better than Github, R-forge, Bioconductor, etc, not
just better than the mailing lists. I think it will be hard to make the
argument, because all of those have R-specific features, as well as
existing communities
own version of R.
As far as I know, there's only one version of R currently being
developed. Microsoft doesn't offer anything different; they just offer
a build of a slightly older version of base R, and a few packages that
are not in the base version.
Dunc
On 10/06/2017 6:09 PM, Duncan Murdoch wrote:
On 10/06/2017 2:38 PM, Morgan wrote:
Hi,
I had a question that might not seem obvious to me.
I was wondering why there was no patnership between microsoft the R core
team and eventually other developpers to improve R in one unified version
instead
;,
"bbb")
? Surely the execution time of the paste0 call is negligible.
Duncan Murdoch
Currently, if a string literal spans multiple lines, there is no way to
inhibit the introduction of newline characters:
> "aaa
+ bbb"
[1] "aaa\nbbb"
If a line end
On 14/06/2017 6:45 AM, Andreas Kersting wrote:
On Wed, 14 Jun 2017 06:12:09 -0500, Duncan Murdoch
wrote:
On 14/06/2017 5:58 AM, Andreas Kersting wrote:
Hi,
I would really like to have a way to split long string literals across
multiple lines in R.
I don't understand why you requir
not convinced of that), then
shouldn't it be solved by the compiler applying constant folding to
paste0()?
(Some syntax like r"xyz" to make it easier to type strings containing
backslashes and quotes would actually be useful, but that's a different
issue.)
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sh_Australia.1252 does that's different from what
I use (English_Canada.1252), but the Chinese locale setting could cause
trouble. Could you try setting this (presumably in the Windows control
panel) to be consistent? You're using a much simpler setting on Linux.
Duncan Murdoch
at
On 17/06/2017 9:13 AM, Ben Marwick wrote:
Hi Duncan,
Thanks for your reply. Yes, it does seem to be specific to the CTYPE
setting to Chinese on Windows. If I set it to English using
Sys.setlocale() there is no problem, then back to Chinese and the
authors disappear:
Sys.setlocale("L
On 18/06/2017 5:57 AM, Andrie de Vries wrote:
Hi, Duncan
i have forwarded this thread to Nathan, who promised to look into it.
Any progress on this?
Duncan Murdoch
Andrie
On 17 Jun 2017 17:26, "Duncan Murdoch" mailto:murdoch.dun...@gmail.com>> wrote:
On 17/06/2
he sense that it gives much more information to see
"J?reskog" instead NA.
I'm considering updating packageDescription() to try these in
case it first returns NA. This would make the citation() hack
unnecessary.
I agree with the general sentiment (fix the underlying problem).
lossy). I think old code should behave as it did in the past,
but there will be a way to say that the incoming string is in UTF-8.
Duncan Murdoch
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the developers) if you are working in unusual
conditions.
R states quite clearly in the welcome message every time it starts: "R
is free software and comes with ABSOLUTELY NO WARRANTY." This is
essentially the same lack of warranty that you get with commercial
software, thoug
27;s a bug, I'm just saying that it is a difficult
one to test automatically (so we probably won't add a regression test
once it's fixed), and it's not one that has been reported often. I
didn't know there were any reports before yours.
Duncan Murdoch
JLL
--
looks as though the
write succeeded, when it didn't.
Duncan Murdoch
-Original Message-
From: R-devel [mailto:r-devel-boun...@r-project.org] On Behalf Of Lipatz
Jean-Luc
Sent: Tuesday, July 4, 2017 5:40 AM
To: Duncan Murdoch
Cc: r-devel@r-project.org
Subject: Re: [Rd] write.cs
testing this is to create and mount a
loop device [2] with a small file.
[1]: https://en.wikipedia.org/wiki//dev/full
[2]: https://stackoverflow.com/a/16044420/2055486
Loop devices sound ideal, but seem to be Linux-only (at least with that
recipe).
Duncan
On Tue, Jul 4, 2017 at 3:38 PM, D
when it came through (or did and forgot).
I'll probably move the error check to a lower level (in the Rconn_printf
function), if tests show that works.
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that whatever system you're on doesn't signal an
error when the write fails.
Duncan Murdoch
Cheers,
j.
On 4 July 2017 at 21:37, Duncan Murdoch mailto:murdoch.dun...@gmail.com>> wrote:
On 04/07/2017 11:50 AM, Jean-Sébastien Bevilacqua wrote:
Hello,
You ca
we need to do something, but
if packages are using it, things need to be changed carefully. I can't
just change it to raise an error instead.
Duncan Murdoch
Le 05/07/2017 à 15:33, Serguei Sokol a écrit :
Le 05/07/2017 à 14:46, Serguei Sokol a écrit :
Le 05/07/2017 à 13:09, Duncan Mu
On 06/07/2017 6:44 PM, Sokol Serguei wrote:
Duncan Murdoch has written at Thu, 6 Jul 2017 13:58:10 -0400
On 06/07/2017 5:21 AM, Serguei Sokol wrote:
I propose the following patch against the current
R-devel/src/main/connection.c (cf. attached file).
It gives (on my linux box):
> fc=f
On 07/07/2017 9:54 AM, Serguei Sokol wrote:
Le 07/07/2017 à 01:09, Duncan Murdoch a écrit :
On 06/07/2017 6:44 PM, Sokol Serguei wrote:
Duncan Murdoch has written at Thu, 6 Jul 2017 13:58:10 -0400
On 06/07/2017 5:21 AM, Serguei Sokol wrote:
I propose the following patch against the current
On 07/07/2017 11:13 AM, Serguei Sokol wrote:
Le 07/07/2017 à 16:52, Duncan Murdoch a écrit :
On 07/07/2017 9:54 AM, Serguei Sokol wrote:
Le 07/07/2017 à 01:09, Duncan Murdoch a écrit :
On 06/07/2017 6:44 PM, Sokol Serguei wrote:
Duncan Murdoch has written at Thu, 6 Jul 2017 13:58:10 -0400
rbage collection.
I will wait a while before porting these to R-patched, because there may
still be some problems to clean up.
Duncan Murdoch
On 07/07/2017 11:42 AM, Duncan Murdoch wrote:
On 07/07/2017 11:13 AM, Serguei Sokol wrote:
Le 07/07/2017 à 16:52, Duncan Murdoch a écrit :
On 07/07
On 10/07/2017 4:54 AM, Serguei Sokol wrote:
Le 08/07/2017 à 00:54, Duncan Murdoch a écrit :
I have now committed changes to R-devel (rev 72898) that seem to catch large
and small errors. They only give a warning if the error happens when the
connection is closed, because that can happen
On 10/07/2017 5:34 AM, Serguei Sokol wrote:
Le 10/07/2017 à 11:19, Duncan Murdoch a écrit :
On 10/07/2017 4:54 AM, Serguei Sokol wrote:
Le 08/07/2017 à 00:54, Duncan Murdoch a écrit :
I have now committed changes to R-devel (rev 72898) that seem to catch large
and small errors. They only
On 10/07/2017 9:00 AM, Serguei Sokol wrote:
Le 10/07/2017 à 13:13, Duncan Murdoch a écrit :
On 10/07/2017 5:34 AM, Serguei Sokol wrote:
Le 10/07/2017 à 11:19, Duncan Murdoch a écrit :
On 10/07/2017 4:54 AM, Serguei Sokol wrote:
Le 08/07/2017 à 00:54, Duncan Murdoch a écrit :
I have now
he value. "person" and "utils::person" are both expressions that give
a character string, but "utils::person" is not the name of a function.
It's similar to this:
as.numeric(1)
as.numeric("1")
as.numeric(0+1)
as.numeric("0+1")
The 4th expression
monly such things are
user errors.
To get R core to look at this, you'll need to simplify it to something
self contained that doesn't make use of non-base packages.
Duncan Murdoch
Bug manifested itself while testing a shiny app in both the R console
and in Rstudio. I've tried a
whole thread in detail, but it appears there's a bug
somewhere, in the report or in the poly() code or in the plsr() code.
That bug should be reported on the bug list if it turns out to be in
base R, and to the package maintainer if it is in plsr().
Duncan Murdoch
_
On 13/07/2017 4:37 PM, Marc Schwartz wrote:
On Jul 13, 2017, at 3:22 PM, Duncan Murdoch wrote:
On 13/07/2017 4:08 PM, Marc Schwartz wrote:
Hi All,
As per the discussion today on R-Help:
https://stat.ethz.ch/pipermail/r-help/2017-July/448132.html
I am attaching a proposed patch for
; 14 Jul 2017 16:30:50 +0200 writes:
>>
>>>>>>> Marc Schwartz on Fri, 14 Jul
>>>>>>> 2017 06:57:26 -0500 writes:
>>
>>>>> On Jul 13, 2017, at 5:07 PM, Marc Schwartz
>>>>> wrote
On 17/07/2017 2:57 AM, Martin Maechler wrote:
Duncan Murdoch
on Sat, 15 Jul 2017 19:27:57 -0400 writes:
> On 15/07/2017 11:37 AM, Martin Maechler wrote:
>>>>>>> Marc Schwartz
>>>>>>> on Fri, 14 Jul 2017 11:01:03 -0500 writes:
s
likely to be assigned a low priority. The sad truth is that very few
members of R Core are currently actively fixing bugs.
Duncan Murdoch
On 20/07/2017 5:02 PM, Steve Grubb wrote:
Hello,
There appears to be a break missing in the switch/case for the LISTSXP case.
If this is supposed to fall
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