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.
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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 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
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
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
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
.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.
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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.
Duncan Murdoch
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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
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
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
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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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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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
It would be much faster (but slightly less reliable) to use
list.files(.libPaths()) to get the names of all installed packages, and
then filter them to the known list of base and recommended packages,
which changes very rarely.
Duncan Murdoch
On 12/10/2023 8:34 a.m., Tony Wilkes wrote:
Dear
, in which case
I'd go one step further back, and write a function to create the source
package, rather than including it. For example, have a file
DESCRIPTION.txt which your test renames to DESCRIPTION, etc.
Duncan Murdoch
On 11/10/2023 3:06 a.m., Tony Wilkes wrote:
Dear all,
I'm trying
and the vignette
that generated the errors, something specific was passed as outdir. But
what? If it was getwd(), that's bound to fail -- you don't have
permission to write there. tempdir() should have worked, but Berry
pointed out some other things that might be problems.
Duncan Murdoch
What were you using as "outdir"?
On 09/10/2023 2:59 p.m., Keshav, Krishna wrote:
Hi,
I am developing an R package where I need to save Raster file with .tif
extension to the tempdir(). I am using terra::writeRaster for the same. While
it works through R CMD check in mac, it is failing in R
suggests that you
could explicitly make your functions visible even if they default to
invisible.
Duncan Murdoch
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s will use "Imports" instead. That triggers loading but
not attaching.
Duncan Murdoch
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, and it
doesn't.
Duncan Murdoch
On 21/09/2023 4:30 p.m., Michael L Friendly wrote:
I am an RStudio user, and I could see this as a plugin somewhere, but I don't
want to create a package just for this.
I'd rather that my code could be adopted somewhere in the framework of
devtools/usethis
ahead of the data definition.
Duncan Murdoch
On 21/09/2023 12:33 p.m., Michael L Friendly wrote:
I have many datasets in a some of my packages, and always used
`utils::promptData()` to generate the skeleton of a man/data.Rd file.
Now that I've switched to roxygen style, I have found no simple
rected at Roxygen; R checks will never
look at them. R will run tests based on what is in the my_func.Rd
examples section. I'd guess that's pretty similar to your second
version (except for the \dontrun part, which you shouldn't use, as Ivan
said).
Duncan M
Sorry, I missed the --as-cran option: you run
R CMD check --as-cran
Duncan Murdoch
On 19/09/2023 5:59 a.m., Duncan Murdoch wrote:
On 18/09/2023 10:10 a.m., Shu Fai Cheung wrote:
Hi All,
I know we should not use more than 2 cores in tests, vignettes, etc. I
encountered and solved
lder keeps the timings file when it runs
a check.
Duncan Murdoch
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. CRAN will do that for you.
Duncan Murdoch
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If you are on Ubuntu, my guess is likely not relevant (unless maybe the
server holding your files is running Windows).
Duncan Murdoch
On 30/08/2023 12:32 p.m., Emanuele Cordano wrote:
Thanks . I’m working on Linux Ubuntu 20.04. I’m seeing the url you sent.
Il giorno mer 30 ago 2023 alle 18
On 30/08/2023 12:03 p.m., Emanuele Cordano wrote:
Dear list,
I'm creating a package. At a first build, I found out the following error.
I parsed DESCRIPTION file and I did not find any possible causes for this
error. I searched on the web , but I found no clear explanation of this
error. Have
is that there are two stubborn groups opposing each
other: the data.table developers and the CRAN maintainers. The former
think users should by default dedicate their whole machine to
data.table. The latter think users should opt in to do that.
Duncan Murdoch
Toby
On Fri, Aug 25, 2023 at 6:46 AM
sion,
so presumably it could be done from "R -d valgrind -e":
tools:::.check_packages(c("pkg", "--option1", "--option2"))
A likely problem is that many of the check tests are run in separate
processes; I don't know if the
-name. Instead
document _PACKAGE to get all the defaults for package documentation, or
use @name to override the default file name."
Duncan Murdoch
On 19/08/2023 8:54 a.m., Daniel Kelley wrote:
# Preamble
This email is to tell other developers what I did to address an issue with
documen
for parsing
it eludes me.
Does anyone know if there are plans to use NEWS for some purpose in
the future i.e., to actually track changes beyond package maintainer's
comments?
NEWS has been used for a long time by the utils::news() function, which
in turn is used by the HTML help system.
Duncan
entSDI and PowerSDI
should be in single quotes. I am not sure whether that also applies to
your other non-English words.
Duncan Murdoch
Regarding note 2, I don't know what's wrong. Is it related to the time to run the
examples (>5s)? If is it so, it is not an error. There are so many cal
version of the package that you downloaded last
time, but you might not be able to download a version of the package
that works with the current version of R.
Duncan Murdoch
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changes,
commit any that were missed, then throw away the damaged one.
Duncan Murdoch
On 05/07/2023 4:44 a.m., Chris Evans wrote:
I hope this is a legitimate question here. I have a package of very
simple functions: https://github.com/cpsyctc/CECPfuns. For the forseeable
future it's really only
oesn't exist. The generic is now in the base package, at
<https://stat.ethz.ch/R-manual/R-patched/library/base/html/plot.html>.
Duncan Murdoch
On 30/06/2023 11:37 a.m., Ben Bolker wrote:
Nice! (I like "A longer description will go here eventually.")
It would be cute/ha
eone wants to see
changes across versions, so doing that should take extra work.
Duncan Murdoch
David
On Fri, 30 Jun 2023 at 09:55, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
Why store them? Download the source on demand, and convert it. Seems
pretty
one if there is such a thing.
Duncan Murdoch
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d converts them all to git branches. For example, here's the
help for Rd2HTML from R 2.9.0:
https://github.com/wch/r-source/blob/tags/R-2-9-0/src/library/tools/man/Rd2HTML.Rd
Duncan Murdoch
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Why store them? Download the source on demand, and convert it. Seems
pretty simple.
Duncan Murdoch
On 30/06/2023 1:19 a.m., David Hugh-Jones wrote:
This is for the rcheology package. I run a Shiny web app which lets you
examine changes to functions across R versions:
https
time, but I'd guess current R
could render old Rd pages reasonably well, back to when Prof Ripley and
I wrote Rd2HTML in R 2.9.0. Before that, it was done by a Perl script,
and the Rd syntax had more differences; I think the parser would likely
die on those very old files.
Duncan Murdoch
as they arise in CRAN checks. It
usually doesn't require much expertise: if an issue arises that you
don't understand, then people on this mailing list are likely to be
helpful in fixing it. Of course, if you are maintainer you can do much
more than that, but it's your choice.
Duncan Murdoch
On 06
On 23/05/2023 6:53 a.m., Martin Maechler wrote:
Duncan Murdoch
on Mon, 22 May 2023 15:38:10 -0400 writes:
> On 22/05/2023 3:07 p.m., Ivan Krylov wrote:
>> I fed your vignette to R CMD Sweave, and here's the
>> relevant fragment from the resul
escapes,
I think he should change
"{\tt \Sexpr{gFunc6}}"
to
"{\tt \Sexpr{sub("_", "_", gFunc6)}}
Even better would be to write a little function "sanitizeForLatex" that
did this and any other necessary changes, and call that.
Duncan Murdoch
a new MacBook Pro)..
I'll investigate.
Thanks!
On Tue, May 16, 2023 at 2:09 PM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
I don't know what the issue would be. I just tried
remotes::install_github("jphill01/HACSim.R")
and it worked fine,
I don't know what the issue would be. I just tried
remotes::install_github("jphill01/HACSim.R")
and it worked fine, but I think that's not the same version that you are
working with.
Duncan Murdoch
On 16/05/2023 2:01 p.m., Jarrett Phillips wrote:
On Tue, May 16, 2023
On 16/05/2023 1:14 p.m., Jarrett Phillips wrote:
Installing from the URL you provide, as well as doing R CMD build HACSim
as suggested by @JeffNewmiller fails.
When trying the latter solution, I get the same error as the one
provided in my original post.
Any thoughts?
Did you try
installed
`Homebrew` and `gfortran`, verifying via typing in the Terminal.
Any idea on what's going on how to fix the issue(s)?
You don't say how you installed gfortran, but it sounds as though you
installed Homebrew's build of it. You should install the tools as
available from https://mac.r-pr
hose packages much more confusing. And if they have a
class which inherits from Gam and want to call the inherited method,
they won't get it.
So I think in this case the NOTE is something you should fix.
Duncan Murdoch
On 10/05/2023 10:49 p.m., Lenth, Russell V wrote:
Dear R package developers
My
th an
imported copy of the generic.
Duncan
Cheers,
Simon
On May 9, 2023, at 11:23 AM, Duncan Murdoch wrote:
On 08/05/2023 6:58 p.m., Simon Urbanek wrote:
On 8/05/2023, at 11:58 PM, Duncan Murdoch wrote:
There really isn't such a thing as "a function that looks like an S3 method, but
isn't&
If anyone wants to try my demo, they can install the test package using
remotes::install_github("dmurdoch/testpkg")
and see the demonstration by running
library(testpkg)
example(f)
Duncan Murdoch
On 08/05/2023 7:23 p.m., Duncan Murdoch wrote:
On 08/05/2023 6:58 p.m., Sim
On 08/05/2023 6:58 p.m., Simon Urbanek wrote:
On 8/05/2023, at 11:58 PM, Duncan Murdoch wrote:
There really isn't such a thing as "a function that looks like an S3 method, but
isn't". If it looks like an S3 method, then in the proper circumstances, it will be
called as
On 08/05/2023 12:10 p.m., Ulrike Groemping wrote:
Am 08.05.2023 um 15:48 schrieb Duncan Murdoch:
On 08/05/2023 8:28 a.m., Ulrike Groemping wrote:
Thanks, Duncan. I appreciate the view that levels.no acts as an S3
method for the generic levels, if an object of class "no"
will
have that "no" class for a completely unrelated reason, and then there
will be trouble.
Duncan Murdoch
Best, Ulrike
Am 08.05.2023 um 13:58 schrieb Duncan Murdoch:
There really isn't such a thing as "a function that looks like an S3
method, but isn't".
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