the standard one if there is such a thing.
Duncan Murdoch
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es and 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 Murdoc
es 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
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
the 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 Mur
e (I recently purchased 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&
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
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 Serguei's
in my package)
and I've verified by typing `gcc` in the Mac Terminal. I've also 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
t's going to
make debugging those 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
with 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 meth
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
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" is ha
possibility that one of them 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
met
will be invoked by the generic gen for class cl, so do not name
functions in this style unless they are intended to be methods."
So probably the best solution (even if inconvenient) is to rename
levels.no to something that doesn't look like an S3 method.
Duncan Murdoch
On 08/05/202
ght holders for your package and should also have
role = "cph" added so it doesn't give the impression that Posit owns
everything.
Duncan Murdoch
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rrent Seurat version.
Duncan Murdoch
and it uses conditional functions to check if those dependencies are
pre-installed.
"No, it is a requirement if the package is used but is not listed in
Depends or Imports.
If the package is in Depends or Imports it is a waste of time to make
the
e is used but is not listed in
Depends or Imports.
If the package is in Depends or Imports it is a waste of time to make
the check: it will always succeed.
I saw some packages still include it.
For example the Seurat package.
I don't understand your question here.
Duncan Murdoch
Un
re they exist on BioC and your code works with them.
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o you could use something
other than the current package name there.
Duncan Murdoch
[1]
https://github.com/klmr/box/blob/9f35bd28b26306fe94ade874c2b93a89ae3f3a61/NEWS.md
[2] https://www.gnu.org/prep/standards/standards.html#NEWS-File
Cheers,
Konrad
_
ction appears to be a false positive.
Duncan Murdoch
On 12/04/2023 4:05 a.m., Gianmarco Alberti wrote:
Dear All,
I trust this email finds you doing well.
I had planned to release a new version of my package, and everything was
checking perfectly on my machine and using the ‘devtools’ func
mily"
else "newfamily")
You should do some sort of manual comparison when those two reference
values are first created to make sure there are no other changes.
Duncan Murdoch
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w
exactly what devtools::check does, but it's probably your problem.
I'd suggest this: build the tarball, and check the tarball.
Duncan Murdoch
On 04/04/2023 9:41 a.m., Dennis Boos wrote:
Thanks so much to all of you. If you have time, I'm getting really
contradictory results
The error message seems pretty clear: "The function xfun::isFALSE()
will be deprecated in the future. Please consider using base::isFALSE(x)
or identical(x, FALSE) instead".
So don't use xfun::isFALSE().
Duncan Murdoch
On 31/03/2023 5:01 p.m., Deepankar Basu wrote:
Hell
reduction of PDFs
but I got the latest versions of R and Rstudio and was able to get
qpdf to install and loaded with library(qpdf), but Rstudio still gives
that message.
It sounds as though you're using Roxygen2 to generate your NAMESPACE
file. If so, you need @imports directives in th
te of the app changes.
Yihui Xie (knitr's author) may not accept the PR I submitted to knitr,
so I'll hold off sending the rgl changes to CRAN for a while.
Duncan Murdoch
On 18/03/2023 4:26 p.m., Duncan Murdoch wrote:
That's great news. Thanks for your rapid testing!
Regarding q
On 25/03/2023 9:09 a.m., Duncan Murdoch wrote:
The message says you shouldn't be using the string 'BT' in the .Fortran
call, you should be using the object that was produced by
R_registerRoutines. That's probably named BT (without any quotes),
though you can add a prefix in
our call should look like this:
res <- .Fortran(BT, as.double(Temp), as.double(y), as.integer(icode))
Duncan Murdoch
On 25/03/2023 9:01 a.m., Shawn Way wrote:
Sorry to kind of repeat this but I really didn't understand the issues with the
prior thread and how it relates to my issue.
I&#x
I found three such calls in a quick search. The first is here:
https://github.com/gdkrmr/coRanking/blob/3656bc0cd3032a650be8c8783414a1e62e419437/R/coranking_internals.R#L20
Duncan Murdoch
On 20/03/2023 12:43 p.m., Duncan Murdoch wrote:
It appears that you have some uses of .Call() where you
entry point registration. I'm not familiar with that, I use the
basic way described in Writing R Extensions, section 5.4 "Registering
native routines".
Duncan Murdoch
On 20/03/2023 11:36 a.m., Guido Kraemer wrote:
I am the maintainer of coRanking and got a message about an error
ork is
not yet complete.
Jonathan
-Original Message-
From: Duncan Murdoch
Sent: Sunday, 19 March 2023 7:39 am
To: Jonathan Godfrey ; R Package Development
Subject: Re: [R-pkg-devel] Screen reader help request
I've made another attempt at this now. I'm a bit more hopeful abo
ge the alt text in response to
user actions, but that's not possible yet. If there are any Shiny
experts reading this, I could use some help with that.
Duncan Murdoch
On 17/03/2023 7:59 p.m., Jonathan Godfrey wrote:
Hello again Duncan,
I could see the two successes were ... creatio
people in either
group, but I'm hoping to make the package useful to others, who would be
writing documents with different audiences.
Duncan Murdoch
On 17/03/2023 5:18 p.m., Jonathan Godfrey wrote:
Hello Duncan,
I guess a few people might expect me to contribute to your request. Fir
a
reasonable limitation?
Duncan Murdoch
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d. Uwe is an authority on CRAN, Martin is an authority on
BioConductor, and Ivan and I are experienced R users.
Duncan Murdoch
On 17/03/2023 8:29 a.m., Ruff, Sergej wrote:
Really.Whats a problem i have when all dependencies arent prei
installed. I thought the problem would be solved once my
note that package names are case sensitive.
Please do not start the description with "This package", "Functions
for", package name, title or similar.
---
Duncan Murdoch
Thats the source of my worries. Will the same error appear when CRAN
checks the examples of my
or not, so you
shouldn't worry about it.
Duncan Murdoch
with regards,
Sergej
Von: Martin Morgan
Gesendet: Donnerstag, 16. M�rz 2023 20:12:51
An: Ivan Krylov; Ruff, Sergej
Cc: r-package-devel@r-project.org
Betreff: Re: [R-pkg-devel] How to de
ain if you don't, but it does mean that it might start doing so if
it doesn't already.
Do you know of any examples of packages that use things like
graphics::abline without mentioning graphics in either the NAMESPACE or
DESCRIPTION file?
Duncan Murdoch
_
I'd test what
happens if a user runs pliman::object_edge( ... ) . (That function
isn't in the CRAN version, just the Github version, so I haven't tried
this.)
Duncan Murdoch
Both EBImage and BiocManager are listed as suggests <
https://github.com/TiagoOlivoto/pliman/blob
I think the Writing R Extensions manual is pretty clear about this:
yes, you should include "methods" in Imports or Depends if you are
calling methods::.
You say "some packages do so and some don't". Which ones don't? It's
helpful to be specific in your e
each dependency, which exports are supported?
- Are there other ways to get the same support with fewer
dependencies? E.g. if rgl used devtools::install_github, it could be
replaced with remotes::install_github.
Does a tool already exist that addresses these questions?
Duncan Murdoch
NOTE, or if not, is there some acceptable way to
suppress it?
Duncan Murdoch
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the code so it will work in newer standards, but if
that is not feasible, you need to write to CRAN and explain why you need
this older standard.
Duncan Murdoch
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n
On 2023-02-23 12:59 p.m., Duncan Murdoch wrote:
Hi Martin.
I think your calculations are way off. A one-tonne tree contains about
5000 kWh of energy. A typical computer server uses about 200 watts, and
can process many jobs simultaneously on different cores, but let's say
the whole se
r checking on 5 different platforms) we have .05 kWh. Let's say
we do this 300 times/year for a package, so 15 kWh. Hard to get 'tree
equivalents' from the EPA web site, but this is equivalent to 1.2
gallons of petrol/gasoline consumption (0.011 metric tonnes)
On 2023-02-23 12:59 p
would
consume 1 kWh in 5 hours, and would take about 10 days to consume 1% of
a tree.
Duncan Murdoch
On 23/02/2023 11:29 a.m., Martin Maechler wrote:
Spencer Graves
on Tue, 21 Feb 2023 05:25:39 -0600 writes:
> On 2/21/23 2:34 AM, Vasileios Nikolaidis wrote:
>> Yes, w
your package is not attached, e.g.
through a function imported by a different package? If so, you should
use .onLoad(), not .onAttach().
Duncan Murdoch
++
Alex
On Thu, 9 Feb 2023 at 11:11, Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
On 09/02/2023 3:56 a.m., Ivan
7;s pdf viewer, nor when files are downloaded from CRAN and
opened with a local pdf viewer.
I don't see a problem in Firefox 109.0.1 on a Mac. Maybe the "0.1" is a
bug fix? Or maybe I looked in the wrong place. Could you be very
specific, i.e. URL, page, line.
Duncan M
ds for the check complaints are discussed here, among other
places: https://stackoverflow.com/a/75384338/2554330 .
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C++
is available, it will be C++11 or higher).
I think it wouldn't hurt to look through the available versions and pick
from them, but I don't think it's supposed to be necessary.
If it eventually turns out that your code is not compatible with some
later
On 06/02/2023 4:01 p.m., Duncan Murdoch wrote:
On 06/02/2023 3:46 p.m., Winston Chang wrote:
I recently submitted a package to CRAN with "SystemRequirements: C++11".
This raises the following NOTE on R-devel, and I was asked to fix and
resubmit:
* checking C++ specificatio
ard, which will fail.
2. Update it to "SystemRequirements: C++17". The problem here is that on
systems that don't have a C++17 compiler, the package won't build -- even
though the package only actually requires a C++11 compiler.
How should I deal with this?
Are you allowed
to step 2,
mention what steps you took to inform mvmesh users.
Duncan Murdoch
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ork on all systems, not just Unix-alikes. My goal is to
simplify rgl. Part of this means I'd like to minimize the system
dependence, since I no longer have easy access to a Windows machine for
testing.
Duncan
Cheers,
Simon
[1] - https://github.com/s-u/background
On Feb 3, 2023, at 1
thing, i.e. if
I want to evaluate an R expression nothing else can be running, or if I
want action while R code is running, I can't involve R at all.
Duncan Murdoch
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ntf(), but typed
Rprintf() out of habit.
Duncan Murdoch
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I think that is likely bad luck, in that your package was being
evaluated at the same time as the new minpack.lm, and CRAN/winbuilder
don't isolate the builds. If you resubmit unchanged (I'd do this on
winbuilder, not CRAN) you may get a more reasonable outcome.
Duncan Murdoch
On
On 20/01/2023 9:47 p.m., Spencer Graves wrote:
On 1/20/23 7:32 PM, Duncan Murdoch wrote:
On 20/01/2023 8:16 p.m., Spencer Graves wrote:
Hello, All:
My attempts to fix this problem exposed what seems to be a
completely
unrelated problem: All five GitHub Actions end now with:
Error
ch
C++ version adopted it, but it's available there too.
Duncan Murdoch
Best
Holger Hoefling
On Sat, Jan 21, 2023 at 11:27 AM Duncan Murdoch
mailto:murdoch.dun...@gmail.com>> wrote:
On 21/01/2023 5:15 a.m., Holger Hoefling wrote:
> Hi,
>
> In my recent re-sub
ers before the NUL at
the end, and avoids the possibility of a buffer overrun.
Duncan Murdoch
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export in the NAMESPACE file.
Duncan Murdoch
???
I have Bitdefender installed on this computer. A "Quick Scan"
produced nothing just now.
Thanks,
Spencer
On 1/20/23 5:08 PM, Duncan Murdoch wrote:
On 20/01/2023 6:02 p.m., Greg Hunt wrote
not at all the same as UTF-8. I don't know how to read UTF-16
in R. Uwe's advice was for UTF-8.
Duncan Murdoch
On Sat, 21 Jan 2023 at 05:09, Bill Dunlap wrote:
Setting the locale to "C" (or perhaps some other non-UTF-8 locale) will
show the BOM bytes. E.g., on Window
pply his two steps,
and commit it again. Your showNonASCIIfile() call was trying to work on
something else. Maybe your other commands were too?
Another possibility is to roll back all your changes to that file until
you have a copy you can work with. I think comm
running it, and see if running that line in a different context still
triggers the error. Etc.
Duncan Murdoch
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bit
lost in how folks are supposed to handle slow tests; I'd not be happy to
report how many times I've done web searches to find out just what
\dontrun and \donttest do, and when I should use them or should do
something else.
Your method sounds good. You choose to run your tests, yo
ytest package has an "at_home" argument to some functions; when
testing a whole package, it defaults to FALSE, which is also the
considerate choice.
Duncan Murdoch
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w.env(parent = parent.frame())
envir$parse_args <- parse_args
eval(call, envir)
}
parse_args <- function(...) {
cat("args were ", names(list(...)), "\n")
stop("Error in parse_args")
}
f(a = 1, b = 2)
#> args were a b
#> Error in parse_args(a =
iggers the same problem). Even better, a
link to Github or elsewhere where people can browse your entire package.
Duncan Murdoch
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sion number slightly
higher than the one on CRAN.
So conceivably your problem is caused by a bug in the hoardr package,
and it looks like the authors of that package aren't going to deal with it.
Duncan Murdoch
On 10/12/2022 5:00 p.m., Roy Mendelssohn - NOAA Federal via
R-package-devel w
lled: https://github.com/cran/Greymodels/blob/master/R/app_ui.R
One warning: make sure you run install.packages('Greymodels', type =
'source') in a new session, not in a session that already has Greymodels
loaded.
Duncan Murdoch
_
Thanks Spencer. Yes, devtools does give good support for CRAN updates
these days.
Duncan Murdoch
On 27/11/2022 12:07 p.m., Spencer Graves wrote:
On 11/27/22 10:44 AM, Duncan Murdoch wrote:
On 27/11/2022 11:29 a.m., Jahajeeah, Havisha wrote:
Dear CRAN team,
The Greymodels package has
think), according
to the CRAN submission instructions here:
https://cran.r-project.org/web/packages/policies.html . The last
section tells you how to do an update, but don't skip the earlier ones.
Duncan Murdoch
I look forward to hearing from you.
Thanking you and sincerely
Havisha Jah
https://github.com/eddelbuettel/drat for instructions on setting up
the drat repository.
Duncan Murdoch
On Wed, 16 Nov 2022 at 15:35, Bernd.Gruber wrote:
Hi,
I have a package (dartR) that needs to be updated by CRAN (and got a time set
until a certain date). It depends on a package that is curre
still be a problem if Matrix completely dropped a method or
it migrated to a different package, but I think that's less frequent
than a change to the internal implementation.
Has any thought been given to making this change for R 4.3.0?
Duncan Murdoch
On 19/10/2022 3:39 a.m., Martin Mae
d buildmer.
Duncan Murdoch
On 18/10/2022 2:51 p.m., Carl Schwarz wrote:
I've run into a problem where if you install the lme4, Matrix, and buildmer
packages using the binaries from CRAN on a Mac, I get an error message
about a missing method, but if I install the same packages from SOURCE
behaviour of
internal functions that they use, because CRAN will object if your
change breaks their tests. That makes it harder to write those internal
functions, because you have to get them "right" the first time, or
support the bad behaviour if someo
problem will go away when
all involved machines finally install ggplot2 3.4.0, but before that, I
don't see anything you can do to fix it.
Duncan Murdoch
On 23/09/2022 2:59 a.m., Riko Kelter wrote:
Hello again,
thanks for the help. Here is a link to download the .tar.gz pack
t and kind regards,
Riko
Could you provide the source for the package? I can see the DESCRIPTION
file at win-builder, but can't install it myself since I don't use Windows.
Duncan Murdoch
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If the Bioconductor packages are unconditional requirements, maybe you
should submit your package to Bioconductor rather than CRAN. Just from
the name ("multiomicsR") it looks like it might be appropriate there.
Duncan Murdoch
On 19/09/2022 2:14 a.m., Das, Sarmistha wrote:
Hello
base packages don't document this is a deficiency in that
documentation, not an excuse for having a deficiency in your documentation.
Duncan Murdoch
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es or
errors. If you use the a) code in a different project, it would do the
same, but report the errors in whatever way is natural in that context.
This is my first time writing into mailing list, hopefully I am doing
everything ok.
Looks fine to me!
Duncan Mu
On 07/07/2022 3:41 a.m., Tomas Kalibera wrote:
On 7/5/22 16:11, Ivan Krylov wrote:
On Tue, 5 Jul 2022 09:35:05 -0400
Duncan Murdoch wrote:
I see the -O0 option that I added, but afterwards -O2 coming from
somewhere in R.
It seems to come from the CXXFLAGS macro defined in /etc/R/Makeconf
Run debug(remotes::dev_package_deps), and run just that one command,
tracing through until you can isolate the issue.
There probably is, but I don't know how to find the right manual to
read nor any better place to ask for help with that than here.
Duncan Murdoch
___
On 13/06/2022 7:01 p.m., Spencer Graves wrote:
On 6/13/22 5:05 PM, Duncan Murdoch wrote:
On 13/06/2022 5:11 p.m., Spencer Graves wrote:
On 6/13/22 1:26 PM, Duncan Murdoch wrote:
On 13/06/2022 12:12 p.m., Spencer Graves wrote:
Hello, All:
How do I fix "Rd cross-refer
www.microsoft.com/en-us/download/details.aspx?id=48234 .
Duncan Murdoch
On Sat, Jun 11, 2022 at 6:33 AM Joseph Park wrote:
Apologies for the pages of minutia. I endeavored to post reproduceable
example. I'm unable to show the failure since it simply hangs at the prompt
with CPU spinn
e chunk option `eval = requireNamespace("plm",
quietly = TRUE)`. I'd put a comment in the code chunk too, saying it
won't be evaluated if plm is not available, but this is not a
requirement, just being nice to the reader.
Duncan Murdoch
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On 29/03/2022 8:58 p.m., Ben Bolker wrote:
After a rather painful remote debugging process, I've figured out
(I think) that the 'macos-m1-bigsur-release' platform on r-hub doesn't
have pandoc, and doesn't have it in a way that breaks
rmarkdown::pandoc_available(), so that trying to build an
rs that platform for running Github actions, but I imagine there's
one somewhere or other.
Duncan Murdoch
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On 25/04/2022 8:24 p.m., Duncan Murdoch wrote:
...
\value{
These functions return either a standard \code{fRegress} fit object or
or a model specification:
\item{The \code{fRegress} fit object case:}{
Aha, in a \value{} section, bare \items are supposed to mark components
of the
dmurdoch/rgl/blob/master/.github/workflows/R-CMD-check.yaml
Can anyone spot what I'm doing wrong, or is it just a matter of waiting
until something else is updated on Github?
Duncan Murdoch
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ckage" packages out there.
If you do include it in base R, please at least allow the CSS to be
customized.
Duncan Murdoch
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could even be implemented by a
pharmaceutical company: rename the file to include its SHA when you
download it, and keep a copy and a record of the new name as part of any
document that is produced with it.
There, it's solved.
Duncan Murdoch
Related to this, there's also been disc
fore the
old email goes away.
If the old address disappears before you have a chance to change the
package it creates extra work for everyone, because it makes it hard for
CRAN to verify that you aren't trying to hijack someone else's package.
Duncan Murdoch
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ct.org/web/checks/check_results_hardhat.html
I do recommend testing on Windows R-devel on one of the other platforms
I listed before submitting to CRAN. I don't think auto-rejects waste a
lot of their time, but it's better to get accepted on the first try.
Duncan Murdoch
On Su
quot;), ";C:\\Miktex\\bin")
but this will only last for the current session. To add it permanently,
you'll need to use some Windows configuration tools.
Duncan Murdoch
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before CRAN submission.
It is offline until at least Monday -- there's a message about this on
the R-sig-mac list.
Duncan Murdoch
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On 26/12/2021 8:03 a.m., Duncan Murdoch wrote:
I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.
And this patch was committed to the trunk by Kurt Hornik, so it should
appear in R 4.2.0 or
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