> ... The extra apostrophe does not seem to have created an issue during all
> those tests, or since, under either Debian or Ubuntu.
I think that is because the system library '/usr/lib/R/library' is
always appended at the end of the library path, so that non-existing
to folder (the one with the
Looks like a mistake in R that was fixed in R-devel (rev 82308) less
than a day ago, cf.
https://github.com/wch/r-source/commit/60cc6ebd762d4199aa8e5addf08282e336138a4a
/Henrik
On Tue, May 3, 2022 at 10:54 AM J C Nash wrote:
>
> I've been asked to "fix" some NOTEs in two of my packages.
>
>
On MS Windows 10, the following works:
> Rscript --vanilla -e "\"abc\""
[1] "abc"
and also:
> Rterm --vanilla --no-echo -e "\"abc.txt\""
[1] "abc.txt"
whereas attempting the same with 'R' fails;
> R --vanilla --no-echo -e "\"abc.txt\""
Error: object 'abc' not found
Execution halted
I get
Simon's suggestion with withCallingHandlers() is the correct way.
Also, note that if you use tryCatch() to catch warnings, you're
*interrupting* the evaluation of the expression of interest, e.g.
> res <- tryCatch({ message("hey"); warning("boom"); message("there"); 42 },
> warning = function(w)
Hi,
in R 4.1.2 we have:
> x <- structure(as.list(1:2), dim = c(1,2))
> x
[,1] [,2]
[1,] 12
> as.vector(x, mode = "list")
[,1] [,2]
[1,] 12
whereas in recent versions of R-devel (4.2.0) we have:
> x <- structure(as.list(1:2), dim = c(1,2))
> x
[,1] [,2]
[1,] 12
>
Hi,
in R-devel (4.2.0), we now get:
> mapply(paste, "A", character(), USE.NAMES = TRUE)
named list()
Now, in ?mapply we have:
USE.NAMES: logical; use the names of the first ... argument, or if
that is an unnamed character vector, use that vector as the names.
This basically says we should
The easiest is to use withr::with_seed(), e.g.
> withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))
[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F" "#B15CD8" "#A2B9D5"
> withr::with_seed(seed = 42L, randomcoloR::distinctColorPalette(6))
[1] "#A0E1BC" "#B8E363" "#D686BE" "#DEA97F"
On Tue, Nov 23, 2021 at 12:06 PM Gábor Csárdi wrote:
>
> On Tue, Nov 23, 2021 at 8:49 PM Henrik Bengtsson
> wrote:
> >
> > > Is there any reliable way to let packages to know if they are on CRAN, so
> > > they can set omp cores to 2 by default?
> &
> Is there any reliable way to let packages to know if they are on CRAN, so
> they can set omp cores to 2 by default?
Instead of testing for "on CRAN" or not, you can test for 'R CMD
check' running or not. 'R CMD check' sets environment variable
_R_CHECK_LIMIT_CORES_=TRUE. You can use that to
Hi,
the following question sprung out of a package settings option warn=-1
to silence warnings, but those warnings were still caught by
withCallingHandlers(..., warning), which the package author did not
anticipate. The package has been updated to use suppressWarnings()
instead, but as I see a
I'm trying to reuse some of the translations available in base R by using:
gettext(msgid, domain="R")
This works great for most 'msgid's, e.g.
$ LANGUAGE=de Rscript -e 'gettext("cannot get working directory", domain="R")'
[1] "kann das Arbeitsverzeichnis nicht ermitteln"
However, it does not
the time (May 2020). See "Dependencies NOTE lost with
> --as-cran" (https://stat.ethz.ch/pipermail/r-package-devel/2020q2/005467.html)
>
> On Wed, Oct 20, 2021 at 11:55 PM Henrik Bengtsson
> wrote:
>>
>> ISSUE:
>>
>> Using 'R CMD check' with --as-cr
ER=[${R_LIBS_USER}]"
R_LIBS_USER=[C:\Users\foobar\AppData\Roaming\R-library]
/Henrik
On Sun, Oct 31, 2021 at 2:59 AM Tomas Kalibera wrote:
>
>
> On 10/31/21 2:55 AM, Henrik Bengtsson wrote:
> >> ... If one still needed backslashes,
> >> they could then be entered
> ... If one still needed backslashes,
> they could then be entered in single quotes, e.g. VAR='c:\users'.
I don't think it matters whether you use single or double quotes -
both will work. Here's a proof of concept on Linux with R 4.1.1:
$ cat ./.Renviron
A=C:\users
B='C:\users'
C="C:\users"
For CRAN packages it's easy. Packages on CRAN are eternal. They may be
archived, but they are never removed, so in a sense they're always
"currently on CRAN". Archived packages may still be installed, but only
with some efforts of the user. Some packages go in an out of "archived"
status depending
Two comments/suggestions:
1. What about recommending to always quote the value in Renviron
files, e.g. ABC="Hello world" and DEF="${APPDATA}/R-library"? This
should a practice that works on all platforms.
2. What about having readRenviron() escapes strings it imports via
environment variables?
ISSUE:
Using 'R CMD check' with --as-cran,
set_R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_=TRUE, whereas the
default is FALSE, which you get if you don't add --as-cran.
I would expect --as-cran to check more things and more be conservative
than without. So, is this behavior a mistake? Could it
If you're willing to depend on R (>= 4.0.0), then tools::R_user_dir() can
replace the 'rappdirs' package.
/Henrik
On Mon, Oct 18, 2021, 09:05 Shraddha Pai wrote:
> Hi all,
> Despite moving rarely-used packages to Suggests and eliminating some (e.g.
> TCGAutils), the number of dependencies is
In addition to checking with Valgrind, the ASan/UBsan and rchk
platforms on R-Hub (https://builder.r-hub.io/) can probably also be
useful;
> rhub::check(platform = "linux-x86_64-rocker-gcc-san")
> rhub::check(platform = "ubuntu-rchk")
/Henrik
On Tue, Oct 12, 2021 at 4:54 PM Martin Morgan
if this is a property we should
all strive for for other types of objects?
/Henrik
On Thu, Sep 23, 2021 at 12:46 AM Martin Maechler
wrote:
>
> >>>>> Henrik Bengtsson
> >>>>> on Wed, 22 Sep 2021 20:48:05 -0700 writes:
>
> > The update in rev 80946
&g
The update in rev 80946
(https://github.com/wch/r-source/commit/d970867722e14811e8ba6b0ba8e0f478ff482f5e)
caused as.character() on hexmode objects to no longer pads with zeros.
Before:
> x <- structure(as.integer(c(0,8,16,24,32)), class="hexmode")
> x
[1] "00" "08" "10" "18" "20"
>
gt; > runif(1)
> [1] 0.3842704
>
> > sum(.Random.seed)
> [1] -13435151647
>
> # So let's make things really random, by using the new seed as a seed:
> > set.seed(.Random.seed)
> > sum(.Random.seed)
> [1] 24428993419
>
> # Back to the original!
>
>
warning or error with set.seed().
>
> Validating inputs and emitting errors early is a good practice.
>
> Just my 2 cents.
>
> Sincerely.
> Andre GILLIBERT
>
> -Message d'origine-
> De : R-devel [mailto:r-devel-boun...@r-project.org] De la part de Avraham
> Adler
&
Hi,
according to help("set.seed"), argument 'seed' to set.seed() should be:
a single value, interpreted as an integer, or NULL (see ‘Details’).
>From code inspection (src/main/RNG.c) and testing, it turns out that
if you pass a 'seed' with length greater than one, it silently uses
seed[1],
> Dana Farber Cancer Institute
>
> > On Aug 19, 2021, at 8:08 AM, Henrik Bengtsson
> > wrote:
> >
> > Hi,
> >
> > I seem to have "lost" write access to several Bioconductor git
> > repositories that I had git push access for before;
> &g
Hi,
I seem to have "lost" write access to several Bioconductor git
repositories that I had git push access for before;
$ ssh -T g...@git.bioconductor.org | grep -E
"(affxparser|aroma.light|illuminaio|QDNAseq)$"
X11 forwarding request failed on channel 0
R packages/QDNAseq
R
Thank you Simon, this is helpful. I take this is specific to quit(),
so it's a poor choice for emulating crashed parallel workers, and
Sys.kill() is much better for that.
I was focusing on that odd extra execution/output, but as you say,
there are lots of other things that is done by quit()
The following smells like a bug in R to me, because it puts the main R
session into an unstable state. Consider the following R script:
a <- 42
message("a=", a)
cl <- parallel::makeCluster(1L, type="FORK")
try(parallel::clusterEvalQ(cl, quit(save="no")))
message("parallel:::isChild()=",
$ grep -L -F "\value{" man/*.Rd
/Henrik
On Wed, Jun 23, 2021 at 10:58 AM Alex Chubaty wrote:
>
> During a recent package submission process, a CRAN maintainer showed one of
> their checks found missing \value{} documentation in some package Rd files,
> and asked us to ensure all exported
On Thu, Jun 17, 2021 at 2:32 AM wrote:
>
> Dear colleagues,
>
> It seems to me that, starting with the latest BioC devel branch (3.14), the
> build systems have become more pedantic about logical vectors of length > 1
> in conditions. Two of the packages I am maintaining, 'kebabs' and 'procoil'
>
ISSUE:
The TMPDIR validation done in src/gnuwin32/system.c:
/* in case getpid() is not unique -- has been seen under Windows */
snprintf(ifile, 1024, "%s/Rscript%x%x", tm, getpid(),
(unsigned int) GetTickCount());
ifp = fopen(ifile, "w+b");
if(!ifp) R_Suicide(_("creation
in the post has the
> wrong version of rtracklayer for R-devel.
>
> Martin Morgan
>
> On 5/18/21, 11:49 AM, "R-package-devel on behalf of Henrik Bengtsson" <
> r-package-devel-boun...@r-project.org on behalf of
> henrik.bengts...@gmail.com> wrote:
>
>
It's a problem with Bioconductor and a broken release history of
'rtracklayer' on MS Windows (e.g.
https://bioconductor.org/packages/3.12/bioc/html/rtracklayer.html)
plus how each Bioconductor version is tied to a specific R version.
In other words, even if they fix it in Bioconductor 3.13 (for R
On Wed, May 5, 2021 at 2:13 AM Martin Maechler
wrote:
>
> > Gabriel Becker
> > on Tue, 4 May 2021 14:40:22 -0700 writes:
>
> > Hmm, that's fair enough Ben, I stand corrected. I will say that this
> seems
> > to be a pretty "soft" recommendation, as these things go, given
;Failed with error: 'there is no package called 'nlme'".
(*) BTW, '../bin/R CMD make test-BasePackages' gives "make: *** No
rule to make target 'test-BasePackages'. Stop."
Thanks,
/Henrik
On Tue, May 4, 2021 at 12:22 PM Dirk Eddelbuettel wrote:
>
>
> On 4 May 2021
FWIW,
$ ./configure --help
...
--with-recommended-packages
use/install recommended R packages [yes]
/Henrik
On Tue, May 4, 2021 at 11:17 AM Dirk Eddelbuettel wrote:
>
>
> On 4 May 2021 at 11:07, Henrik Bengtsson wrote:
> | Thanks, but I don't understand.
for a way to validate such an installation.
If your comment is on the 'stats' examples' hard dependency on 'MASS'
despite it's being a suggested packages, I still don't follow.
/Henrik
On Tue, May 4, 2021 at 10:16 AM Dirk Eddelbuettel wrote:
>
>
> On 4 May 2021 at 09:31, Henrik Bengts
I'm on Linux (Ubuntu 18.04). How do I check an R build when using
--without-recommended-packages? 'make check' assumes 'recommended'
packages are installed, so that fails without them available.
DETAILS:
When I build R from source without 'recommended' packages:
curl -O
Ben, it's most like what Peter says. I can confirm it works; I just
installed https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz
on an up-to-date CentOS 7.9.2009 system using the vanilla gcc (GCC)
4.8.5 that comes with that version and R compiles just fine and it
passes 'make check'
Not that it solves your problem per se, but here's what I think CRAN
only has rtracklayer 1.48.0 installed on WIndows, i.e. why you get
error "namespace 'rtracklayer' 1.48.0 is being loaded, but >= 1.51.5
is required.":
* The current Bioconductor "release" is version 3.12
* As you say,
In ?base::.libPaths, there's a paragraph saying:
The library search path is initialized at startup from the environment
variable R_LIBS (which should be a colon-separated list of directories
at which R library trees are rooted) followed by those in environment
variable R_LIBS_USER. Only
that is different from the check asking for a specific version for no
> particular reason (as far as I can ascertain).
>
> Best,
> Kasper
>
> On Thu, Apr 8, 2021 at 8:13 PM Henrik Bengtsson
> wrote:
>>
>> > I believe in the past we tried suggesting removing a R d
> I believe in the past we tried suggesting removing a R dependency altogether
> but that R CMD check complained not having an R dependency? Maybe someone
> remembers more about this.
There are no such requirements in 'R CMD check'. The only requirement
around 'Depends: R (>= x.y.z)', if
Correcting: the env var is R_LIBS_USER and nothing else.
/Henrik
On Wed, Apr 7, 2021 at 1:20 PM Henrik Bengtsson
wrote:
>
> Can you go via a temporary file instead, i.e. output what you want to
> grab to a temporary file and pull the info from that instead?
>
> Side tracking ...
Can you go via a temporary file instead, i.e. output what you want to
grab to a temporary file and pull the info from that instead?
Side tracking ...
> I thought about using --vanilla but I use .Rprofile to set my library path,
> so ignoring that file completely defeats the point in my setup.
FWIW, I ran into a similar problem when I moved R.cache
(https://cran.r-project.org/package=R.cache) from using ~/.Rcache to
~/.cache/R/R.cache (etc). I decided on making it 100%-backward
compatible, i.e. if there's already a legacy ~/.Rcache cache folder,
it'll keep using that, otherwise the new
getting into literate programming, and we already have several
vignette engines for that.
Just a thought,
Henrik
On Thu, Mar 4, 2021 at 7:20 PM Rolf Turner wrote:
>
>
>
> I have now tried out building vignettes from plain LaTeX source,
> following the admirably lucid instructions pro
FYI, and in case others wonder or search for this later, the warnings:
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
are harmless and has nothing to do with your problem reported here.
It happens because on the system
The R.rsp has a vignette engine for plain LaTeX sources. See
https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-LaTeX_vignettes.pdf
for how. It's straightforward. Maybe that helps.
Henrik
On Wed, Mar 3, 2021, 18:51 Rolf Turner wrote:
>
> I am trying to create a vignette in a
Related: Does Bioconductor support 'Additional_repositories'? From RWE:
The ‘Additional_repositories’ field is a comma-separated list of
repository URLs where the packages named in the other fields may be
found. It is currently used by R CMD check to check that the packages
can be found, at least
FYI, I just sent an email to 'maintai...@bioconductor.org' regarding
this but it bounced with the below errors (I've truncated your
address):
From: Mail Delivery System
Date: Thu, Feb 25, 2021 at 12:39 PM
Subject: Undelivered Mail Returned to Sender
To: ...
This is the mail system at host
Hi,
you're probably already aware of it, but 'rgl' depends on 'magrittr'
which depends on 'rlang', and the latter requires R (>= 3.3.0).
BTW, I find Singularity (https://github.com/hpcng/singularity/) more
convenient to work with than Docker, e.g. you run as host $USER also
"inside" the
R CMD check --as-cran will give an ERROR if not all Suggest:ed
packages are installed and available when it runs.
/Henrik
On Fri, Jan 8, 2021 at 11:25 AM Greg Freedman Ellis wrote:
>
> > It should almost certainly be included in Suggests, and nowhere else.
> > If that means your tests are
020 at 12:27 PM Henrik Bengtsson
wrote:
>
> Colin, you can do:
>
> Imports: tools
>
> NAMESPACE:
> if (getRversion() >= 4) importFrom(tools,R_user_dir)
>
>
> R/000.namespace.R:
> ## Create a dummy R_user_dir() for R (< 4.0.0)
> ## to please R CMD ch
Colin, you can do:
Imports: tools
NAMESPACE:
if (getRversion() >= 4) importFrom(tools,R_user_dir)
R/000.namespace.R:
## Create a dummy R_user_dir() for R (< 4.0.0)
## to please R CMD check
if (getRversion() < 4) {
R_user_dir <- function(...) NULL
}
and then use:
if (getRversion() < 4) {
The problem here was regarding user facing example():s, not package tests.
In order to keep a neat example for the user to play with, I'd
probably wrap the example code in a \donttest{} statement. Though, I
don't remember if CRAN tests with R CMD check --run-dontest, or not.
There's also
Without having dug into the details, it could be that one could update
the parser by making a 'return' a keyword and require it to be
followed by a parenthesis that optionally contains an expression
followed by end of statement (newline or semicolon). Such a
"promotion" of the 'return' statement
FWIW, 'R CMD check --as-cran' in R-devel checks for "bogus return"
statements but I think that's only for the case when one forgets the
parentheses, e.g. 'return' instead of 'return()'.
I don't think it catches this case but I'm also not sure. Though, I can
imagine it might be possible to enhance
I'm quite sure you want to use the following:
Suggests: knitr, rmarkdown, formatR
VignetteBuilder: knitr
Here are the details. For the 'VignetteBuilder' field, you want to
put all packages that provide the **vignette engines** you are using.
For example, if your package vignettes use either of
You can change your package from using:
Imports: countreg
to use:
Suggests: countreg
For this to work, you'll have to update your code, package tests,
examples, and vignettes, to run conditionally on 'countreg' being
installed, e.g.
if (requireNamespace("countreg", quietly = TRUE)) {
us. Reverse SSH
tunneling is super simply; all you need to to is something like:
rshopts <- c(sprintf("-R %d:%s:%d", rscript_port, master, port), rshopts)
/Henrik
On Fri, Nov 6, 2020 at 4:37 PM Duncan Murdoch wrote:
>
> On 06/11/2020 4:47 p.m., Balamuta, James Joseph wrote:
>
Related to this:
It would be neat to have a dashboard that reports on the current
latency is on the different CRAN "queues" are, e.g. how long is the
average waiting time when submitting a new package ("newbies") until
you get a manual reply or it's on CRAN, submitting an update with all
OK
onductor git
> repository.
>
> Nitesh
>
> On Oct 1, 2020, at 11:57 AM, Henrik Bengtsson
> wrote:
>
> Doesn't a git rewrite break all existing clones, forks out there? I'm
> happy to be corrected, if this is not the case.
>
> /Henrik
>
> On Thu, Oct 1, 2020, 08:16
Doesn't a git rewrite break all existing clones, forks out there? I'm happy
to be corrected, if this is not the case.
/Henrik
On Thu, Oct 1, 2020, 08:16 Nitesh Turaga wrote:
> Hi,
>
> The BiocCheck will complain on the build system about the > 5MB package
> size.
>
> The rewrite of the history
Getting R to run well on Wine would be really neat. Here are some
additional comments that might encourage someone to move this forward.
On Ubuntu 18.04, you can install and run R 3.6.0 on Wine as:
curl -O https://cloud.r-project.org/bin/windows/base/old/3.6.0/R-3.6.0-win.exe
wine
Without having read all of the comments already made here, but my
understanding why ::: is not allowed is because you are reaching into
the internal API that the package owner does not guarantee will exist
in the next release. If you rely on the internal code of another CRAN
package in your CRAN
I've "moved" this to
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17919 to make sure
it's tracked. /Henrik
On Thu, Sep 3, 2020 at 7:25 AM Dirk Eddelbuettel wrote:
>
>
> On 2 September 2020 at 23:38, Henrik Bengtsson wrote:
> | WORKAROUND:
> | Setting R_USER or H
ISSUE:
It looks like Rgui.exe never processes ~/.Renviron - only ./.Renviron.
REPRODUCIBLE EXAMPLE:
On Windows, create the following ~/.Renviron and ~/.Rprofile files:
C:\Users\alice> Rscript -e "cat('FOO=123\n', file='~/.Renviron')"
C:\Users\alice> Rscript -e "cat('print(Sys.getenv(\'FOO\'))',
Hi, it looks like:
> stats:::`[.formula`
function (x, i)
{
ans <- NextMethod("[")
if (length(ans) == 0L || as.character(ans[[1L]])[1L] == "~") {
class(ans) <- "formula"
environment(ans) <- environment(x)
}
ans
}
doesn't like to extract NULL components on either
FWIW,
> sapply(X, length) - always numeric(1) (integer(1) or double(1) for vectors of
> more than 2^31 - 1 elements)
Actually, the length of length(x) may not be 1L, e.g.
> x <- Formula::Formula(~ x)
> length(x)
[1] 0 1
>From help("length", package = "base"):
"Warning: Package authors have
These recently introduced 'R CMD check' WARNINGs were disabled again
in R-devel on July 8, 2020:
r78793:
https://github.com/wch/r-source/commit/ccd903e47ab42e1c181396256aea56454a2e70c9
r78794:
https://github.com/wch/r-source/commit/b70f90ae11dd516c1c954ed15eb5a7c2a304b37f
This is because
action reports? We would like to submit the package for moderation soon
> but we're unsure if we can due to this problem. Thank you.
>
> Il 29/07/2020 19:25, Henrik Bengtsson ha scritto:
> > From a very quick look at this, I think you also need to explicitly
> > install the p
>From a very quick look at this, I think you also need to explicitly
install the package itself for it to be available in external R
session (contrary to when using forked processing as on Linux and
macOS). Something like this:
- name: Install dependencies
run: |
gt; Hi Henrik,
>
> A bit late, but you can take a look at smbache's {import} package [1]
> in case you didn't know it. I believe it does what you are describing.
>
> [1] https://github.com/smbache/import
>
> Iñaki
>
> On Tue, 23 Jun 2020 at 22:21, Henrik Bengtsson
> wrote
If the point of having, say,
stopifnot(add(1, 2) == sum(c(1, 2))
is to make it explicit to the reader that your add() function gives
the same results as sum(), then I argue that is valid to use in an
example. I'm pretty sure I've used that in some of my examples. For
the purpose, there should
Kurt Hornik wrote:
...
> But perhaps simply wait for a few more days ...
Oh, this is good news.
I see that these new warnings have already been disabled in R-devel.
Thxs,
Henrik
On Wed, Jul 8, 2020 at 1:17 AM Kurt Hornik wrote:
>
> >>>>> Henrik Bengtsson writes:
>
> &g
Here's another "Non-file package-anchored link(s) ..." issue. I'd
like to reference parallel::mclapply() in my help pages. With the new
R-devel requirements, you have to link to the file and not the topic.
However, there is no cross-platform stable file reference for
parallel::mclapply();
#
Hi,
I'm developing a package whose API is only meant to be used in other
packages via imports or pkg::foo(). There should be no need to attach
this package so that its API appears on the search() path. As a
maintainer, I want to avoid having it appear in search() conflicts by
mistake.
This
Was this resolved upstream or is this something that R should/could
fix? If the latter, could this also go into the "emergency release" R
4.0.2 that is scheduled for 2020-06-22?
My $.02
/Henrik
On Sun, May 31, 2020 at 8:13 AM Gábor Csárdi wrote:
>
> Btw. it would be also possible to create a
On Wed, Jun 3, 2020 at 10:40 PM Vincent Carey
wrote:
>
> On Wed, Jun 3, 2020 at 11:48 PM stefano wrote:
>
> > Hello Community,
> >
> > I am used to document function although hey are not exported
> >
> >
> I suppose you are talking about tidybulk? I am somewhat mystified by the
> behavior
> of
RStudio provides pre-built R package for Linux and since a some weeks
now, they can be used on GitHub Actions
(https://github.com/r-lib/actions). In addition, the run-time limit
on GitHub Actions is several hours compared to the 50 minutes you've'
got on Travis, so even if you install from
Interesting problem. I'm very rusty on S4 but would one solution be
to, already now, add 'simplify = TRUE' to the S4 method and document
it;
setMethod("apply", signature(X = "Speclib"),
function(X,
FUN,
bySI = NULL,
...,
On Wed, May 20, 2020 at 11:10 AM brodie gaslam via R-devel
wrote:
>
> > On Wednesday, May 20, 2020, 7:00:09 AM EDT, peter dalgaard
> wrote:
> >
> > Expected, see FAQ 7.31.
> >
> > You just can't trust == on FP operations. Notice also
>
> Additionally, since you're implementing a "mean"
What's the gist of the problem of making/having this part of the public
API? Is it security, is it stability, is it that the current API is under
construction, is it a worry about maintenance load for R Core, ...? Do we
know why?
It sounds like it's a feature that is useful. I think we missed
>> include it my initial email. It sounds like an RStudio issue, and it seems
> >> like that it’s quite intrinsic to how forks interact with RStudio. Given
> >> this code is eventually going to be a part of a package, should I expect
> >> it to
Hi, a few comments below.
First, from my experience and troubleshooting similar reports from
others, a returned NULL from parallel::mclapply() is often because the
corresponding child process crashed/died. However, when this happens
you should see a warning, e.g.
> y <- parallel::mclapply(1:2,
I'm sure this exists elsewhere, but, as a trade-off, could you achieve
what you want with a separate helper function F(expr) that constructs
the function you want to pass to [lsv]apply()? Something that would
allow you to write:
sapply(split(mtcars, mtcars$cyl), F(summary(lm(mpg ~
I'd second Jim's feature request - it would be useful to be able to
disable this in CI and elsewhere.The concept of using an "unusual"
version component such as a very large number does a nice job of
indicating "unusual" and serves as a blocker for submitting
work-in-progress to CRAN by
While at it, would it be worth mentioning in the NEWS for R 4.0.0 that
options 'stringsAsFactors' is being deprecated, e.g.
$ options(stringsAsFactors = TRUE)
Warning message:
In options(stringsAsFactors = TRUE) :
'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
?
sion.
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15128#c1
/Henrik
On Tue, Mar 20, 2018 at 2:11 PM Henrik Bengtsson
wrote:
>
> Contrary to, say, Sys.setenv(), Sys.setlocale() returns it's value
> visibly. This means that if you for instance add:
>
> Sys.setlocale(&qu
n Windows (see, there's some advantages to be on
that OS).
/Henrik
On Wed, Mar 18, 2020 at 9:38 PM Henrik Bengtsson
wrote:
>
> On Wed, Mar 18, 2020 at 8:04 PM Dirk Eddelbuettel wrote:
> >
> >
> > On 18 March 2020 at 19:19, Henrik Bengtsson wrote:
> > | AFAIU, 'R
On Wed, Mar 18, 2020 at 8:04 PM Dirk Eddelbuettel wrote:
>
>
> On 18 March 2020 at 19:19, Henrik Bengtsson wrote:
> | AFAIU, 'R CMD check --as-cran' tries to hide any site and user package
> | libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary
>
>
AFAIU, 'R CMD check --as-cran' tries to hide any site and user package
libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary
to R_LIBS_SITE, it fails for R_LIBS_USER and the user's personal
library is still available for test scripts. Should I revise my
assumptions, or is that
You can single quote them to avoid them being spell checked, e.g. ...
using methods of 'Kruskall' and 'Brainerd'. This is a common and
accepted practice.
This is hinted at in "Writing R Extensions" (e.g. help.start());
The mandatory ‘Description’ field should give a comprehensive
description of
Maybe it's related to:
* The plot() S3 generic function is now in package base rather than
package graphics, as it is reasonable to have methods that do not use
the graphics package. The generic is currently re-exported from the
graphics namespace to allow packages importing it from there to
'fpalomares', it's not clear if you can reproduce this locally or not,
but make sure you can reproduce it locally. I could using:
R CMD check --as-cran SSLR_0.9.0.tar.gz
with R 3.6.3 on Ubuntu 18.04. In other words, this is neither a
problem with the CRAN incoming checks nor win-builder.
Yes,
1. I'd guess it helps Uwe a bit you clarify exactly which queue you think
is stuck - otherwise he has to check them all. They're independent.
2. You can look at the different win-builder queues yourself via ftp, see
https://stat.ethz.ch/pipermail/r-package-devel/2020q1/005098.html
/Henrik
On
FYI, in past when queues got stuck, Uwe told me it's often a package that
launches an external process (e.g. java.exe) that doesn't terminate and
prevents R CMD check from terminating/timing out. He got watchdogs to kill
such stray events but there are false negatives.
A couple of weeks ago I
Here's a simpler example that should reproduce that error for you:
ans <- utils::select.list(c("hello", "world", "again"), graphics=TRUE)
Does it?
FYI, I installed R 3.6.3 from source on CentOS 7 a few hours ago, and
for me the above works just fine.
For your immediate needs of selecting a
Could be. FYI, I think the different win-builder queues are
independent, i.e. when one get stuck it does not affect the others.
For example, I just verified that R-devel_gcc8 works.
$ date --iso-8601=seconds
2020-02-29T07:41:53-08:00
$ curl -s ftp://win-builder.r-project.org/R-oldrel/ | sed
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