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".
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 08/05/2023 5:50 a.m., Ulrike
ould also have
role = "cph" added so it doesn't give the impression that Posit owns
everything.
Duncan Murdoch
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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
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 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
Under U
ey exist on BioC and your code works with them.
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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
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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’ functions
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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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.
1. It first seemed
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:
Hello
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 the comments
(conventionally before the function that uses the import, but I think it
doesn't really matter where).
Duncan Murdoch
__
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 quarto: most of what
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 useDynLib() in your
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'm getting the error mess
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, the
-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 about this one,
but still not sure.
In the new
n 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 ... creations and that the
others w
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. First I'll assure
limitation?
Duncan Murdoch
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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 package
ive.
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 package? Or should I not be worried?
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 declare
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
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hat
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/master/DESCRIPTION#
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 examples.
Dunc
?
- For 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
at an ignorable NOTE, or if not, is there some acceptable way to
suppress it?
Duncan Murdoch
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d change 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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-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 server is dedicated
cking 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.m., Duncan Murdoch
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, with a
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
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 Murdoch
The issue was docum
ts are discussed here, among other
places: https://stackoverflow.com/a/75384338/2554330 .
Duncan Murdoch
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le, 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 standard, I'm sure CRAN will
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 say &qu
,
mention what steps you took to inform mvmesh users.
Duncan Murdoch
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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 10:53 AM, Duncan
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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rintf() 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 24/01/2023
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
++ 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-submission
the NUL at
the end, and avoids the possibility of a buffer overrun.
Duncan Murdoch
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an
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
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 Windows I get:
Sys.getlo
ASCIIfile() 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 commit ab455089 is probably
the bad one; Github shows invi
, and see if running that line in a different context still
triggers the error. Etc.
Duncan Murdoch
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sed 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, you don't force
anyone else to run them.
Dun
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 =
the same problem). Even better, a
link to Github or elsewhere where people can browse your entire package.
Duncan Murdoch
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r 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 wrote:
CRAN h
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
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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
), 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 Jahajeeah
om/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 currently showing errors
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 Maechler
.
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, the
code runs
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 someone relied
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 package:
https://uni-siegen.sciebo.de/s
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
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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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 Murdoch
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
e_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
oft.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 spinning and memory
,
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
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
rkflows/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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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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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 discussion (here
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
/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 Sun, Feb 13, 2022 at 2
ly 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 maybe
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.
Duncan Murdoch
On 26/12/2021 5:55 a.m., Duncan Murdoch wrote:
On 26/12/2021 12:07 a.m., Spencer Graves wrote:
Hello, All
doi.org/10.18128/D010.V8.0
You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as
Steven Ruggles, Sarah Flood, Ronald Goeken,
Josiah Grover, Erin Meyer, Jose Pacas, and
Matthew Sobek (2018)
IPUMS
USA: Version 8.0 [dataset]. Minne
vignettes (which is the recommended way to do things, but
isn't required) then you shouldn't have inst/doc in the source at all.
R CMD build will create it when it builds the tarball.
Duncan Murdoch
Eric.
On Fri, Dec 10, 2021 at 10:25 AM Duncan Murdoch
mailto:murdoch.dun...@gmail.com>>
Just delete the .html output from earlier runs before you run R CMD
build, and it will have no choice but to rebuild them.
Duncan Murdoch
On 10/12/2021 9:29 a.m., Eric Weine wrote:
Hello,
Sorry yes, I think that my initial post on stack overflow is a bit
misleading. I have checked the file
.
Duncan Murdoch
Cheers,
Simon
On Dec 10, 2021, at 10:52 AM, Eric Weine wrote:
Hello,
I'm having an issue where my vignette created using R CMD build does not
match the vignette created using devtools::build_vignettes or when I knit
with RStudio. I posted about this issue on stack overflow
.
To handle larger ones, you need to know what size blocks you are going
to receive with each read. If that varies unpredictably, I doubt if
there's much you can do other than reducing the timeout.
Duncan Murdoch
Ben Engbers
-
CreateSocket = function(host, port
and add other examples that execute quickly.
Even better might be to include only the ones that execute quickly:
just like CRAN, users don't want to wait a long time for examples to
finish.
Duncan Murdoch
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to initialize the default for c as it depends on one value
of "a" or the other?
That c=a*b only works with non-standard tidyverse evaluation. It causes
other problems, e.g. the inability to pass ... properly (see
https://github.com/tidyverse/glue/issues/231 for an example).
Dunc
this should have been made illegal when R was created, but I think
it's too late to outlaw now: I'm sure there are lots of people making
use of this.
Or am I missing something?
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ody(fn)
Duncan Murdoch
Building Matrix with --no-byte-compile reduces the size of R/Matrix.rdx
by more than half, from 2.7 MB to 1 MB.
-Bill
On Sat, Oct 30, 2021 at 12:00 AM Mosqueira Sanchez, Iago
mailto:iago.mosque...@wur.nl>> wrote:
As far as I can see only clas
azyLoadDBfetch() works and read one of them to see what's in
it, but I haven't done that.
Duncan Murdoch
Iago
On Fri, 2021-10-29 at 20:21 -0400, Duncan Murdoch wrote:
On 29/10/2021 4:23 p.m., Gábor Csárdi wrote:
You probably (accidentally?) put some large object into your
package,
e.g. a non-
included too.
Duncan Murdoch
Gabor
On Fri, Oct 29, 2021 at 10:07 PM Mosqueira Sanchez, Iago
wrote:
I am getting warnings in some packages about the size of the R folder
* checking installed package size ... NOTE
installed size is 20.5Mb
sub-directories of 1Mb or more:
data
to
the end.)
Rebuild the formula after sorting.
Duncan Murdoch
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, you called the bit::clone generic which never
received the registration, so dispatch to clone.ff never happened.
It makes sense: you don't want a generic in one package to interfere
with an unrelated generic in another package that happens to have the
same name.
Duncan Murdoch
Anyhow, remov
And there are other choices too: there are several packages
implementing object systems that allow objects to maintain persistent
data. I haven't used those, so this list may contain omissions and
errors: R6, R.oo, proto.
Duncan Murdoch
___
t.foo never has a different environment than the one it ends up with
(and I don't need to remember how evalq() works).
Duncan Murdoch
On Thu, Oct 21, 2021 at 12:29 AM Rolf Turner
wrote:
I have a plot method (say plot.foo()) that I want to be able to call so
that if argument "add&q
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