eck thinks that was
unintentional and wanted to point it out to you. It's legal, so it's
not an error, just a note.
If I look at the display of the help page ?aminoAcidFun, I think it's
right that something is wrong. The formatting near the end of the Value
section looks messed up.
ike something that would be transitory. If you are
working with random data it might be hard to reproduce, but still worth
worrying about. Or it could be transitory because some package you're
using was updated between the two runs, or some weird timing issue
caused some val
-Builder checks to see whether this prevents the
"invalid URLs" NOTE. And, even if the NOTE is prevented, i'm not sure
this is preferred.
Why not leave off the scheme, e.g. "www.r-project.org" instead of
"https://www.r-project.org";.
Duncan Murdoch
__
o arithmetic on bool
values, you might be surprised by the answer. For example
bool x = true + true;
results in x storing true, which is equivalent to 1 when used as an integer.
Duncan Murdoch
Thank you!
--
Jerome
On Mon, Mar 31, 2025 at 11:28 AM Duncan Murdoch
mailto:murdoch.dun...@gmai
er file or just those definitions?
The problem is that the definitions may vary from compiler to compiler,
and the error message you're getting only shows up some of them. Since
the compiler will supply stdbool.h, it's safer to use that than to try
to emu
27;t see that as the original source. My rgl
package includes a few thousand lines of Javascript code which is
minified when installed; the tarball contains the original source.
Duncan Murdoch
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On 2025-02-07 10:09 a.m., Dirk Eddelbuettel wrote:
On 7 February 2025 at 05:05, Richard M. Heiberger wrote:
| Michael and Brian.
|
| thank you
| exactly correct.
For completeness: this check is a fairly recent addition to r-devel and hence
a 'policy change'.
I don't think it's a policy chang
One question is when that file is produced. Do you produce it before
preparing the tarball, or is it produced as part of the installation
process?
Duncan Murdoch
On 2025-02-04 6:27 p.m., Josiah Parry wrote:
The file was written using writeLines() but it is just a normal R script
with normal
Without seeing your package, I don't think anyone could help you, other
than very generic help: "Find what is creating that file, and figure
out how to stop it."
If you submit your package to one of the online check services (e.g.
https://win-builder.r-project.org/) then you could post a link
suggesting that you require the user to explicitly ask for the
data. You don't want CRAN to install the data during testing and then
have it left behind at the end.
Duncan Murdoch
On Thu, 2 Jan 2025 at 22:42, Henrik Bengtsson
wrote:
As a first step, this sounds like something for the &
en your package is
unloaded.)
Duncan Murdoch
On 2025-01-02 4:29 p.m., Lluís Revilla wrote:
Dear Duncan,
Thank you for your answer. I checked again and made a mock package
that removes a file with .onDetach.
The file was not removed upon uninstalling the package.
Lluís
On Thu, 2 Jan 2025 a
hen the
namespace is unloaded (via a call to unloadNamespace, perhaps called by
detach(unload = TRUE)) with argument the full path to the installed
package’s directory. Functions .onUnload and .onDetach should be defined
in the namespace and not exported, but .Last.li
I think CRAN
would be reluctant to do even this, because it inconveniences anyone who
has used the plasma package.
Alternatively, point out these issues to the reviewers, and suggest that
confusion with blood plasma is unlikely given the context and full title
a2156/src/library/stats/R/glm.R#L687-L773
. You can copy that into your package, then modify it to work with
Matrix. You should list "The R Core Team" as a copyright holder on that
file if you do this so you're not violating the R license.
Duncan Murdoch
On 2024-12-22 4:26 p.m.
just going by the two mentions you quoted in your first
message.)
Duncan Murdoch
|We trade run-time and compile-time off in other ways so this should be a
run-time check, with e.g. Rf_error() or Rcpp::stop() returning to the R
prompt with an error message. If you feel you must program your C++
comp
remember that those
asserts were effectively just comments, not being acted on without some
trickery to enable them?
You'd be much safer if you used a different function specific to R that
triggered an R error if the assertion was false.
Duncan Murdoch
|
|So viewed from that an
Nice spotting!
Just for fun, I just asked chatgpt if there were any other problems in
that code. It spotted 3, but not the one you found. Two of them were
definitely bogus, but this one might not be:
On line 471 kmax is used, but it may not be initialized.
Duncan Murdoch
On 2024-12-17 5
I think that is coming from a package you are using, rather than from
your package NMRphasing. Maybe you can try working with the maintainer
of that package to work out whether the problem is in it or in the way
you are using it.
Duncan Murdoch
Thanks!
Aixiang
��ȡOutlook for Android<h
from DESCRIPTION Imports/Depends entries: ‘nloptr’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
And - admittedly - I have no idea about how to insert appropriate import
statements in NAMESPACE.
You shouldn't need to do that.
Duncan Murdoch
Best rega
way: In the `.onLoad` function of
your package, you would have code like
if (requireNamespace("pkg")) {
foo <- pkg::foo
bar <- pkg::bar
} else {
foo <- stub
bar <- stub
}
where `stub` is a function that says "you need `pkg` to use this function".
survey, and add some innocuous direct
reference to it to quiet the NOTE.
Duncan Murdoch
On 2024-12-02 3:38 p.m., Cohen, Aaron wrote:
Hello, thank you for getting back to me. I have a github with the code:
https://github.com/237triangle/surveynnet
<https://github.com/237triangle/surveyn
ncies in R code ... NOTE
Namespace in Imports field not imported from: ‘survey’
All declared Imports should be used.
How do I resolve this issue?
I'd remove the survey package on your system, and try running the
example that fails. If you get the same error, you can track it
I think I have a solution. Roxygen2 allows this option to be specified
in the DESCRIPTION file:
Roxygen: list(markdown = TRUE, load = "installed")
With the `load = "installed"` setting, it doesn't try to run the .R files.
Duncan Murdoch
On 2024-11-19 9:01 a.m.,
keDependency call so
that Roxygen ignores it. Is that possible?
4. I can write a Makevars file that runs makeDependency. That seems
like a pretty heavyweight solution, especially since I need to save the
result of the call so it is available later.
Does anyone else have this pr
re it does not need to be deleted. Just ignore it in the
build (i.e. list it in .Rbuildignore, so it doesn't end up in the
tarball, and each system installing the package recreates it).
Duncan Murdoch
The approach I have now is a cleanup script with only rm -rf src/Makevars.
This works *
with this note? Not all notes trigger a
rejection, some (like the maintainer note just above) are just for
information.
Duncan Murdoch
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in version 1.2.12. You can get 1.2.14 from
Github using this code: , or wait a couple of months until a later
version is released on CRAN". I dislike Hadley's x.y.z.9000 scheme.
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I don't think R will enforce a 3 part version just because you used it
once. You might have other reasons to try to maintain versioning
consistency.
Duncan Murdoch
On 2024-10-27 7:48 a.m., Gianmarco Alberti wrote:
Dear Duncan,
Thank you for the straightforward guidance.
My initial
cepted package, given that incrementing the
version number might seem a bit disproportionate?
Thank you for your time and assistance.
The simplest thing is to just update the version. Use 1.1.1 if you
don't want to go to 1.2.
Duncan Murdoch
_
package would be the CRAN request for
updates “no more than every 1–2 months".
I think the original package wouldn't have been archived unless it was
failing tests and the author didn't address the failures.
Duncan Murdoch
https://cran.r-project.org/web/packages/polici
. Were you running R from the command line when
aspell() worked?
Duncan Murdoch
On 2024-08-20 11:51 a.m., Kevin R. Coombes wrote:
Hi,
This is a follow-up to an earlier question where I asked about R CMD
check on Windows to be able to check R packages in a manner closer to
the checks on CRAN ma
also mess up on
sort_by( foo, bar, priority )
Duncan Murdoch
On 2024-08-03 7:13 a.m., Deepayan Sarkar wrote:
I haven't thought about this carefully, but shouldn't this mostly work?
sort_by.est_table <- function(x, y = c("op", "lhs", "rhs"),
obje
here if we
specified object explicitly?
if (!missing(object) {
if (!missing(x))
stop("both x and object specified!")
x <- object
}
# This one is more likely to do something:
if (!missing(by)) {
if (!missing(y))
stop("both y and by specified!"
f `dev.new()` or `pdf()` called anywhere
in the code.
Not explicitly, but if you try to call a plot function with no device
active, the graphics system will call dev.new().
Duncan Murdoch
On Sun, Jul 28, 2024 at 3:44 PM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
On
ut will
be used in a non-interactive one.
Duncan Murdoch
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have done this in your submission
comments. I don't think a Fedora failure will cause a submission to be
automatically rejected, but the CRAN reviewers may want to know if you
have dealt with the error, and you should explain that this is what
you've done.
Duncan Murdoch
On 2024-
b.com/wch/r-source/blob/b64422334a8269535718efd9a1f969c94b103056/src/main/gram.y#L2577-L2705
I don't know how much of that you want to replicate, but I suppose
handling the weird cases (e.g. 0x1p1) the way R does will make it easier
for your users.
Duncan Murdoch
On 2024-07-18 4:29 p.m., Khue Tran
# the mathematical fraction 1/10
It seems like mpfr("0.1", 100) works pretty well. I'd assume it does
the parsing, rather than parse 0.1 to the closest double, and convert that.
Duncan Murdoch
## if you really want that, I'd also recommend truly exact f
nix/sys-std.c, but I'm not sure which comments.
rgl references it from this code:
https://github.com/dmurdoch/rgl/blob/fbedc326e291c3ec28a9ccac7d030f04b05edfa3/src/x11lib.cpp#L53-L72
Can anyone tell me whether I can fix this?
Duncan Murdoch
_
to
make a contribution to one of them, they are less likely to want to do it.
Duncan Murdoch
On 2024-07-01 6:04 p.m., Kevin R. Coombes wrote:
Hi,
I have been maintaining packages in R-Forge for many tears. Last week I
sent an email to r-fo...@r-project.org to report problems with the build
process.
I'd
fix the "create conditionally, evaluate unconditionally" bug.
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which needs compilation?
Updating RStudio wouldn't help, that needs an R update, but it seems
like a possibly useful suggestion. What would be your suggested
wording? Should it depend on R trying to figure out if the current
version is old?
Duncan Mu
On 2024-06-23 5:44 a.m., Agner Fog wrote:
On 23/06/2024 09.56, Duncan Murdoch wrote:
CRAN only builds Windows binaries for the devel version, the current
release, and the previous release, so nothing older than 4.3.0 will
get it.
Thank you. Updating R helped.
BTW, I don't think we ne
On 2024-06-23 2:18 a.m., Agner Fog wrote:
On 23/06/2024 00.15, Duncan Murdoch wrote:
As far as I know, CRAN doesn't push changes to the mirrors, the
mirrors pull changes from CRAN. So if you are seeing that message,
the problem is likely with the mirror you're using. Which mirr
irror you're using. Which mirror is that?
Duncan Murdoch
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;.
You should definitely mention each of the issues that led to archiving
in the note you submit with your package.
Duncan Murdoch
On 2024-06-11 6:27 a.m., Hervé Perdry wrote:
Hello,
I 'm new here! I'm the maintainer of a handful of packages and should have
subscribed long ago.
He
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
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
This
r question in one 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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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 messag
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 a
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., R
, it could be 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
x27;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?
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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
op
o pass two arguments 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 prediction
in xj[i] : invalid subscript type 'list'
Calls: join_inner -> data.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
lse
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
help to open in the default browser on MacOS. See ?browseURL for
details of how to specify other browsers.
Duncan Murdoch
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luded the 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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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
I don't understand 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
n for the names instead of
listing each one separately, and it matches that variable.
Duncan Murdoch
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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&
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 follo
uthor 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.
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
tely, and drop it as a Suggested package.
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because the
Quarto 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 avai
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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an
error. 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
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 not
recommend 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 sugges
ous submission 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
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 u
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 He
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.c
test of the
R version to skip code that won't run properly.
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e x.y.z has 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
wi
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
gested last week -- 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.
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nd supply a function to the user to retrieve it
from there. 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 ru
cy chains) when
> 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 f
e
nice 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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call it a
huge number 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!
ry\_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,
pository on github:
https://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 cr
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
or ERROR. 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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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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on number. It would need an exception to the usual "new
submissions need new version numbers" rule. Exceptions waste CRAN's time.
Duncan Murdoch
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tation. 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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gh changes 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 Mirazc
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