to resubmit it in some different
way?
No, if you didn't get the confirmation link, then you haven't submitted
it. You can use `foghorn::cran_incoming()` to see what's in the CRAN
incoming queue.
Duncan Murdoch
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On 2024-06-02 7:39 p.m., Iris Simmons wrote:
To avoid the remapping of beta to Rf_beta, you should
define R_NO_REMAP_RMATH before you include Rmath:
#define R_NO_REMAP_RMATH
#include
... and then remember to include the "Rf_" prefix on the routines that
you do want to use.
Dunc
was detected at the end?
This problem has two sides.
The side that R CMD check is giving you NOTEs about is that _examples
and tests_ are requried to keep the global state of the system intact.
Only some parts of the global state: examples can create variables in
globalenv().
Duncan Murdoch
of their forums.
By the way, RStudio has project and global options that affect its
builds; the default uses devtools, but I generally deselect that, and go
straight to 1.
Duncan Murdoch
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a0
run_REngineRmainloop + 260
14 R 0x102d1a64c -[REngine runREPL]
+ 124
15 R 0x102d0dd90 main + 588
16 dyld 0x188fae0e0 start + 2360
Duncan Murdoch
_
hould
submit a patch containing it to bugs.r-project.org. Based on c.Date,
here's a first attempt:
c.hexmode <- function(...) as.hexmode(c(unlist(lapply(list(...),
function(e) unclass(as.hexmode(e))
If you want this to be incorporated into R, you should test
On 2024-05-23 11:49 a.m., Dirk Eddelbuettel wrote:
On 22 May 2024 at 14:03, Duncan Murdoch wrote:
| On 2024-05-22 10:18 a.m., Dirk Eddelbuettel wrote:
| >
| > On 22 May 2024 at 13:54, Nixon, Michelle Pistner wrote:
| > | Thank you both for your responses and help! Kurt-- your mess
On 2024-05-22 10:18 a.m., Dirk Eddelbuettel wrote:
On 22 May 2024 at 13:54, Nixon, Michelle Pistner wrote:
| Thank you both for your responses and help! Kurt-- your message makes a lot of
| sense. I'll try to debug soon and will reach out if I have more questions.
Interesting.
Kurt, is there
I've just upgraded to an M3 Mac laptop, and I'm working through getting
the right configure settings to build R.
The Installation and Administration manual says to have this in config.site:
FFLAGS="-g -O2 -mmacos-version-min=11.0"
FCFLAGS="-g -O2 -mmacos-version-min=11.0"
but those give an
I don't think that will ever happen. It only happens when a user tries
an "--as-cran" check, but doesn't have a current version of tidy
installed. CRAN does have the up-to-date versions installed, so they
won't see this.
Duncan Murdoch
On 2024-05-18 5:10 p.m., Richard M. Heibe
e required to be a hard dependency, but that
seems too strong: most package users don't need to rebuild vignettes.
Duncan Murdoch
The error from the additional "noSuggests" check
(<https://www.stats.ox.ac.uk/pub/bdr/noSuggests/README.txt>) shows it
cannot be rebuild if BiocStyle is
A criticism of your suggestion is that it is not backwards compatible.
Does that matter? I don't know, but probably not. The X11 version of
the viewer does what you suggest.
Duncan Murdoch
On 2024-05-15 2:20 a.m., Iago Giné Vázquez wrote:
About the decisions:
Actually, the same way
), but I could help with the design.
Duncan Murdoch
On 2024-05-14 5:25 a.m., Iago Giné Vázquez wrote:
Thanks again Duncan and Ivan,
I forward then the email to R-devel.
Summarizing, the dataedit options (in RGui preferences or RConsole) to
colouring the View output do not have effect
esn't matter that it's not on CRAN.
Have you tried submitting your package to CRAN? If so, could you show
us the error you received?
Duncan Murdoch
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uot;, etc.
Perhaps you turned off the aliasing?
Duncan Murdoch
On 03/05/2024 11:17 a.m., Jarrod Hadfield wrote:
Hi,
I have an R library with C code in it. It has failed the CRAN checks for
Debian. The problem is with the error function being undefined. Section 6.2 of
the Writing R e
put as Jing Hua:
Input filename.csv:
Gene,SNP,prot,log10p
YWHAE,13:62129097_C_T,1433E,7.35
YWHAE,4:72617557_T_TA,1433E,7.73
Output:
> read.csv("filename.csv")
Gene SNP prot log10p
1 YWHAE 13:62129097_C_T 1433 7.35
2 YWHAE 4:72617557_T_TA 1433 7.73
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only sparingly.
I don't know why you didn't see this on the other platforms; maybe they
just haven't been rebuilt recently.
Duncan Murdoch
On 13/04/2024 5:35 a.m., Tony Wilkes wrote:
Hi everyone,
I am updating my R package (tinycodet), and I have checked my R-package in all
operating systems
sing around with the user's search list, which may have
been intentionally set to include only one of those.
So I'd suggest changing the docs to say
"[library and require] check and update the list of currently attached
packages and do not reload a namespace which is already loaded. If a
package is already attached, no change will be made."
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to \doi, but it only
takes one. I would have thought that would be fine, but apparently not.
So add a space after "\doi{10.2307/3071950}" and/or remove the braces
around "{Relevance of community structure in assessing indeterminacy of
ecological predictions}".
Dunc
Yes, definitely looks like a bug.
Are you able to submit it to bugs.r-project.org?
Duncan Murdoch
On 05/04/2024 8:15 a.m., June Choe wrote:
There seems to be a bug in out-of-bounds assignment of list objects to an
expression() vector. Tested on release and devel. (Many thanks to folks
over
On 02/04/2024 8:50 a.m., Dirk Eddelbuettel wrote:
On 2 April 2024 at 07:37, Dirk Eddelbuettel wrote:
|
| On 2 April 2024 at 08:21, Duncan Murdoch wrote:
| | I have just added R-4-4-branch to the feeds. I think I've also fixed
| | the \I issue, so today's news includes a long list of old
I have just added R-4-4-branch to the feeds. I think I've also fixed
the \I issue, so today's news includes a long list of old changes.
Duncan Murdoch
On 16/03/2024 8:47 a.m., Duncan Murdoch wrote:
I have now put the files online at https://github.com/dmurdoch/diffnews
. It seemed like too
operator: it was in magrittr
(and I think another package, but I forget the name) first, was widely
adopted, then a simpler version was brought into base R.
Duncan Murdoch
Le ven. 29 mars 2024 à 16:25, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> a écrit :
On 29/03/2024
could be made simple enough and bulletproof and were
widely adopted, maybe they'd be copied into one of the base packages,
but really the only need for that would be to support validation on
setting, rather than validation on retrieval.
Duncan Murdoch
I have now put the files online at https://github.com/dmurdoch/diffnews
. It seemed like too much trouble to include the SVN history, so this
is just a copy of the current version of the files.
Duncan Murdoch
On 15/03/2024 12:04 p.m., Lluís Revilla wrote:
Hi!
Thanks for this service
).
Duncan Murdoch
On 15/03/2024 12:04 p.m., Lluís Revilla wrote:
Hi!
Thanks for this service! It is very helpful to know what is being developed.
I distribute the content to other venues and I noticed some times that the
updates are duplicated.
For example, the sentence "‘is.R()’ is depre
.frame -> [ -> [.data.table -> [.data.frame
Execution halted
I'm pretty sure that import should not be made, but I don't know the
intention of this example, or what the correct fix would be.
Duncan Murdoch
On 14/03/2024 2:34 p.m., Michael Chirico wrote:
In an effort to streamline our
positive, but what it says is that your checks created a file called
metabolomics_data.csv some place where it shouldn't have created it.
You should only be writing in the temp directory, and you should clean
up afterwards.
Duncan Murdoch
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to open in the default browser on MacOS. See ?browseURL for
details of how to specify other browsers.
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y value.
The usual way to handle this is to include both x and y in all methods,
but document some of them to say that y is ignored.
Duncan Murdoch
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, but you could always write the code something like this:
if (Sys.getenv("RUN_SLOW_CHUNKS", 0)) {
... the slow code goes here ...
} else
cat("This chunk takes several hours to compute. If you want to run
it, set the environment variable RUN_SLOW_CHUNKS to
don't have any idea if this is intentional or not.
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On 07/03/2024 4:16 a.m., Ivan Krylov wrote:
On Wed, 6 Mar 2024 13:46:55 -0500
Duncan Murdoch wrote:
is this just a more or less harmless error, thinking that
the dot needs escaping
I think it's this one. You are absolutely right that the dot doesn't
need escaping in either TRE (which
and about that suggestion (which is taken from
WRE, I'm not blaming Rich for it): why include the backslash in the
negated character class? Does R ever create variables starting with a
backslash, or is this just a more or less harmless error, thinking that
the dot needs escaping?
Duncan Murdo
, and it matches that variable.
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On 05/03/2024 2:26 p.m., Dirk Eddelbuettel wrote:
On 5 March 2024 at 13:28, Duncan Murdoch wrote:
| What I'm seeing is that the tags are ignored, and it is distributing the
| HEAD of the main branch. I don't think most users should be using that
| version: in my packages it won't have had
On 05/03/2024 1:04 p.m., Dirk Eddelbuettel wrote:
On 5 March 2024 at 11:56, Duncan Murdoch wrote:
| I have mixed feelings about r-universe. On the one hand, it is really
| nicely put together, and it offers the service described above. On the
| other, it's probably a bad idea to follow its
hor doesn't know it happened? I found
out about "my" site dmurdoch.r-universe.dev today, but it seems to have
existed for quite a while.
Duncan Murdoch
On Tue, Mar 5, 2024 at 11:56 AM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
On 05/03/2024 8:02 a.m., Dirk Edd
On 05/03/2024 8:02 a.m., Dirk Eddelbuettel wrote:
On 5 March 2024 at 06:25, Duncan Murdoch wrote:
| You could make a compatible version of `survivalmodels` available on a
| non-CRAN website, and refer to that website in the
| Additional_repositories field of DESCRIPTION.
Every r-universe sub
ed package.
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TRUE x2
9 1 12 1 13 9 10exprFALSE
The expressions produced are the same, but the parse data is different.
Duncan Murdoch
On 04/03/2024 11:51 a.m., Bill Dunlap wrote:
Maybe someone has already suggested this, but if your functions accepted
strings you could use sub o
operands reversed when it sees that token.
Duncan Murdoch
On 02/03/2024 6:06 a.m., Adrian Dușa wrote:
That would have been an elegant solution, but it doesn't seem to work:
`->` <- `+`
1 -> 3 # expecting 4
Error in 3 <- 1 : invalid (do_set) left-hand side to assignment
It is possi
On 01/03/2024 8:51 a.m., Dmitri Popavenko wrote:
On Fri, Mar 1, 2024 at 1:00 PM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
...
I was thinking more of you doing something like
parse(text = "A -> B", keep.source = TRUE)
I forge
On 01/03/2024 5:25 a.m., Dmitri Popavenko wrote:
Dear Duncan,
On Fri, Mar 1, 2024 at 11:30 AM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
...
If you parse it with srcrefs, you could look at the source. The parser
doesn't record whether it was A
I wonder if there is any possibility whatsoever to signal the use of ->
instead of <-
If you parse it with srcrefs, you could look at the source. The parser
doesn't record whether it was A -> B or B <- A anywhere else.
Duncan Murdoch
__
tools were not available.
Duncan Murdoch
On 26/02/2024 10:34 a.m., Christophe Dervieux wrote:
Hi,
I am trying to release a new version of the quarto R package. This new
version is adding support for a new vignette engine that will use quarto
CLI (https://quarto.org) when available. The vignettes
anyone provide insights or suggestions on how to resolve this warning?
What is in that file at those locations?
Duncan Murdoch
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. Another choice would be to work with the arrow developers to get
it to install on the systems where it fails now, but it's a big package,
so that would likely be a lot harder.
Duncan Murdoch
On 21/02/2024 5:15 p.m., Park, Sung Jae wrote:
Hi,
I’m writing to seek assistance regarding an issue we’re
On 20/02/2024 8:03 a.m., Duncan Murdoch wrote:
I noticed the following odd behaviour today:
exprs <- expression( mean(a), mean(b), { a }, { b } )
exprs[[1]] == exprs[[2]]
#> [1] FALSE
exprs[[3]] == exprs[[4]]
#> [1] TRUE
Does it make sense to anyone that the
contained in braces doesn't?
Duncan Murdoch
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*only* way to limit tracing
to some copies of the function, and if "where" is omitted, trace()
should attempt to modify all copies?
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Removing (or moving to inst) the unrecognized file should be sufficient.
Duncan Murdoch
On 19/02/2024 7:27 a.m., Package Maintainer wrote:
Hello all:
Thank you both for your advice.
I attempted to upload the latest version to CRAN, and again received
the notification that the package did
using knitr for Rnw documents instead of
Sweave. It will require a few changes, but in general it's more
flexible and works a bit better.
Duncan Murdoch
On 17/02/2024 7:51 a.m., Package Maintainer wrote:
Dear Ivan:
Thank you for your help again.
Thanks for your suggestion to use cai
On 08/02/2024 7:58 p.m., Jiří Moravec wrote:
> This is a workaround, and could be the basis for a round.Date
improvement:
> date <- Sys.Date()
> as.Date(round(as.POSIXct(date), "years"))
> as.Date(round(as.POSIXct(Sys.Date() + 180), "years"))
This is a workaround, and could be the basis for a round.Date improvement:
date <- Sys.Date()
as.Date(round(as.POSIXct(date), "years"))
as.Date(round(as.POSIXct(Sys.Date() + 180), "years"))
Duncan Murdoch
On 08/02/2024 12:23 p.m., Henrik Bengtsson wrote:
Techni
ubmission could have happened.
Duncan Murdoch
If not, then can anyone suggest the best way to debug a revdep check on as
close a setup to the CRAN machines as possible?
Cheers,
David
Git tag for the last CRAN submission:
https://github.com/hughjonesd/huxtable/releases/tag/v5.5.4-rc3
Info from the C
nd here's what I get when I run it on rgl:
dupnames("rgl")
name first dup
1 fns knitr.R:12 knitr.R:165
2 fns knitr.R:12 pkgdown.R:14
3 fns knitr.R:12shiny.R:8
Those are okay; the fns object is a temporary that is later removed in
each case.
Duncan Murdoch
On 0
On 07/02/2024 8:36 a.m., luke-tier...@uiowa.edu wrote:
On Tue, 6 Feb 2024, Duncan Murdoch wrote:
The SO post https://stackoverflow.com/q/77943180 tried to call
globalCallingHandlers() from a function, and it failed with the error message
"should not be called with handlers on the
uplicated names in ", basename(f), ":\n")
cat(paste(allnames[dups], collapse = ", "), "\n")
}
}
It could be made more fancy to report the locations of both the original
and the dup if you feel motivated.
Duncan Murdoch
On 06/02/2024 8:09 p.m., Chris Bla
including non-global ones (like the one try() added in
the line above)?
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code isn't smart enough to follow every code path, so it gives
the note to warn you that you might have something wrong.
You still have the same issue with my workaround, but the check code
isn't smart enough to notice that.
Duncan Murdoch
H.
On 2/4/24 09:07, Duncan Murdoch wrote:
On 04/02
Hi John.
I don't think the 80 bit format was part of IEEE 754; I think it was an
Intel invention for the 8087 chip (which I believe preceded that
standard), and didn't make it into the standard.
The standard does talk about 64 bit and 128 bit floating point formats,
but not 80 bit.
Duncan
object in your function which can't be called unconditionally. The
workaround doesn't create such an object.
Recognizing that your function never tries to call fun requires global
inspection of toto(), and most of the checks are based on local inspection.
Duncan Murdoch
___
I've just been reading
https://developer.mozilla.org/en-US/docs/Web/HTTP/Authentication, and it
states that putting userid:password in the URL is deprecated, but it
does make sense that R should protect users who still use that scheme.
Duncan Murdoch
On 01/02/2024 11:28 a.m., Xinyi wrote
, but I think usually people would
want the behaviour of paste(readLines(f), collapse = "\n").
Duncan Murdoch
On Fri, Jan 26, 2024 at 2:05 PM luke-tierney--- via R-devel
wrote:
On Fri, 26 Jan 2024, Michael Chirico wrote:
I am curious why readLines() has a default (n=-1L) to read the fu
On 25/01/2024 12:38 p.m., Henrik Bengtsson wrote:
On Thu, Jan 25, 2024 at 8:27 AM Duncan Murdoch wrote:
On 25/01/2024 11:18 a.m., Henrik Bengtsson wrote:
On Thu, Jan 25, 2024 at 7:48 AM Duncan Murdoch wrote:
On 25/01/2024 10:27 a.m., Josiah Parry wrote:
Hey all,
I've encountered use
On 25/01/2024 11:44 a.m., Josiah Parry wrote:
The package of course passes R CMD check otherwise it wouldn’t be on
CRAN! (:
CRAN doesn't run checks using R 3.6.0. The package claims it works
there, and maybe it will, but it won't pass R CMD check.
Duncan Murdoch
Thank you Henrik! Good
On 25/01/2024 11:18 a.m., Henrik Bengtsson wrote:
On Thu, Jan 25, 2024 at 7:48 AM Duncan Murdoch wrote:
On 25/01/2024 10:27 a.m., Josiah Parry wrote:
Hey all,
I've encountered use of the native pipe operator in the examples for
'httr2' e.g.
request("http://example.com;) |> req
t run properly.
Duncan Murdoch
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s the
recent fix.
Duncan Murdoch
On 12/01/2024 1:09 p.m., Serge wrote:
I'm the mainteneur of the package MixAll.
This package has a dependency to the package rtkore (whom I'm the mainteneur
too).
I updated the package rtkore one month ago, fixing a compilation problem on
windows devel platform
en pages in
Hosting Data Packages via drat: A Case Study with Hurricane Exposure Data
at
https://journal.r-project.org/archive/2017/RJ-2017-026/index.html
And for the impatient, see the drat "Quick Start" instructions at
https://github.com/eddelbuettel/drat
They work
- but this time make sure to use a properly
formatted repository, not just a web site with some binary builds. The
"drat" package makes building one of those really easy.
Duncan Murdoch
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re. The user can choose where to assign the result of that
function.
So instead of:
user says to save to "myvar"
you save to myvar
user uses myvar
you would have
user says to save value
you save it privately
user runs myvar <- savedvalue()
If your app requires users to b
they practically never do that.
>
> Life would be much simpler if the Suggests packages would not be
> (automatically) installed, or if CRAN provided a way to include static
> Vignettes to avoid the heavy dependencies of building them.
>
Users aren't forced to install "Su
ce to include an Additional_repositories field so they can find the
package. This needs to be organized as an actual repository; the drat
package is a very convenient way to set one up.
Duncan Murdoch
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ent."
That text has been unchanged in the help page for 13 years.
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I'm really confused. Steve's example wasn't a scalar x, it was a
vector. Your zapsmall() proposal wouldn't zap it to zero, and I don't
see why summary() would if it was using your proposal.
Duncan Murdoch
On 17/12/2023 8:43 a.m., Gregory R. Warnes wrote:
Isn’t that the correct outcome
benefit for you if you are really interested in working with this kind
of thing.
Duncan Murdoch
On 13/12/2023 4:19 a.m., Iago Giné Vázquez wrote:
Dear all,
This is a request to get language objects more documented in the R Language Definition
document (CRAN version<https://cran.r-project.
I don't know what the warning looks like, but the ?tar help page
discusses the issues.
Duncan Murdoch
On 12/12/2023 3:10 p.m., Ben Bolker wrote:
FWIW the R-windows FAQ says:
Yet another complication is a 260 character limit on the length of the
entire path name imposed by Windows
the results until
a button is pressed to display them.
Duncan Murdoch
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of times, so the overhead adds up.
Duncan Murdoch
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On 14/11/2023 9:38 a.m., Tomas Kalibera wrote:
I would definitely look for a work-around. In the end we want to give
users software that works, rather than something that doesn't, but
telling them, possibly with good evidence, that it is not our fault.
Fortune nomination!
_codes\_V202201"
(and similar). That's not legal Rd syntax. You could use
"\code{country_codes_V202201}" or some other verbatim wrapper.
I see a 4th note, about files Combined_Results.csv and
Combined_Results.xlsx. If those files are produced by an example or
test, they should be
://github.com/Klona9/r-perARMA.git
gh repo clone Klona9/r-perARMA
I will be very glad for any help.
Your examples for `parma_ident` appear to create a directory named
"PARMA21del1_ident" below the current directory. You can't create files
there, you need to create them in tempdir().
Dunc
I have volunteered to take over maintenance of plotrix. I should be
submitting a version without the "orphaned" designation soon.
(If anyone else would rather be maintainer, please get in touch with me
offline.)
Duncan Murdoch
On 09/11/2023 9:47 a.m., Liam J. Revell wrote:
PkgB, and PkgB suggests PkgA?".
Duncan Murdoch
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biomet
. I'd use the grDevices::win.metafile for now, but wouldn't be
surprised if the NOTE turns up again later when #2 gets fixed.
Duncan Murdoch
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like a bug in the check code which has been fixed. Do you
have a function named pkgs() with an argument also named pkgs?
Duncan Murdoch
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.
My idea of politeness, and I think also Prof. Ripley's, is that you
don't discuss private discussions in public without agreement from all
parties.
Duncan Murdoch
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ld need an exception to the usual "new
submissions need new version numbers" rule. Exceptions waste CRAN's time.
Duncan Murdoch
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. A possibly faster alternative would
be to remove the dependence on MEIGOR, and resubmit once that is done
and the package is working again.
Duncan Murdoch
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executable name would make a lot of
sense, wouldn't it? I'm pretty sure all supported versions of Windows
can handle long filenames.
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I forget whether it was just hard or
actually impossible.
I am slowly working towards having rgl use newer OpenGL versions, but I
don't expect this to be done for quite a while.
Duncan Murdoch
Cheers,
Simon
Several Linux distributions have long defaulted to it, so we already should
have
in R might break it).
So if you did a binary build on R 4.4.x and tested it on R 4.3.1, it's
not at all surprising that it failed. If you did a source build on R
4.4.x and it failed on R 4.3.1, that's more surprising.
Duncan Murdoch
On 26/10/2023 9:43 a.m., Plamen Mirazchiyski wrote:
Thank
sprod()’ and ‘tcrossprod()’
are now also primitive and S3 generic, as ‘%*%’ had become in R 4.3.0."
Duncan Murdoch
On 25/10/2023 3:02 p.m., Plamen Mirazchiyski wrote:
Dear All,
Today I was preparing a new version for the RALSA package. I have built
a Windows package using "devtools::check_win_d
On 19/10/2023 8:17 p.m., Rolf Turner wrote:
In a package that I maintain, there are examples, in the *.Rd files,
that take an excruciatingly long time to run. This makes package
checking extremely tedious. There is no question of errors being
thrown from these examples, they are simply time
And if the vignette claims to help the users, but contains errors? Then
it's not very helpful at all. That's what the testing is there to detect.
Duncan Murdoch
On 17/10/2023 6:30 p.m., John Harrold wrote:
I ask myself the question: Who is the vignette for? It does server two
purposes. One
ESCRIPTION, but its
use is discouraged, and I don't think it allows you to ask CRAN to build
some vignettes but not all.
Duncan Murdoch
Best,
John
Cheers,
Simon
On 18/10/2023, at 3:02 AM, John Fox wrote:
Hello Dirk,
Thank you (and Kevin and John) for addressing my questions.
No on
Whoops, I just read the next line. Sorry!
On 15/10/2023 9:34 p.m., Rolf Turner wrote:
I have submitted a new package to CRAN, and this package has been
knocked back on the basis of a NOTE:
* checking package dependencies ... NOTE
Package suggested but not available for checking:
On 15/10/2023 9:34 p.m., Rolf Turner wrote:
I have submitted a new package to CRAN, and this package has been
knocked back on the basis of a NOTE:
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'ionChannelData'
This suggested package consists of
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