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.
Duncan Murdoch
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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I think the original package wouldn't have been archived unless it was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.
Duncan Murdoch
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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?
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
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.
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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.
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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.
Duncan Murdoch
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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.
Duncan Murdoch
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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
rod()’ 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_
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 co
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
pur
uot; field in DESCRIPTION, 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 addres
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: 'ionChannelD
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 da
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
lain about that, 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
e test 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.
D
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 h
f WRE suggests that you
could explicitly make your functions visible even if they default to
invisible.
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ckages will use "Imports" instead. That triggers loading but
not attaching.
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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
d
n skeleton
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
input2)
#' }
The @examplesIf comments are directed 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 \
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 this
winbuilder keeps the timings file when it runs
a check.
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d to make a manual at all. 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 y
em 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
valent from a regular session,
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
proces
That seems like a bug that should be reported to the Roxygen authors.
Duncan Murdoch
On 20/08/2023 8:22 a.m., Thomas Rusch wrote:
Dear list,
I'd like to add that it looks like if the package has the same name as a
function in the package, the default aliasing using the "_PACKAGE
cally adds -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 wi
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