> It has to have the "datetime" entry. If you can't fix your network you can
> skip that test with
>
> _R_CHECK_FUTURE_FILE_TIMESTAMPS_=FALSE
I'm quite sure that is overridden 'R CMD check' when using the
--as-cran flag. The workaround that I have found is to set environment
variable:
_R_CHECK_S
As a first step, this sounds like something for the 'tools' package,
e.g. tools::cleanup_R_user_dir() that wipes package subfolders of
packages no longer installed, or the specified package, iff given.
With that in place, one could argue for adding a 'cleanup' argument to
remove.packages() that use
Two parallel processes are okay, so you can use two callr background
processes ("children"), as long as you don't do heavy computations on
the main R process ("parent"). This is commonly done in many R
packages, e.g.
library(parallel)
cl <- makeCluster(2)
y <- parLapply(cl = cl, X = 1:10, fun = sl
On Thu, May 9, 2024 at 3:46 PM Simon Urbanek
wrote:
>
>
>
> > On 9/05/2024, at 11:58 PM, Vladimir Dergachev
> > wrote:
> >
> >
> >
> > On Thu, 9 May 2024, Sameh Abdulah wrote:
> >
> >> Hi,
> >>
> >> I need to serialize and save a 20K x 20K matrix as a binary file. This
> >> process is significa
On Thu, Apr 18, 2024 at 6:41 AM Uwe Ligges
wrote:
>
> On 18.04.2024 15:35, Ben Bolker wrote:
> > Yes, but ffbase was archived a long time ago (2022-04-04) and CRAN
> > has apparently just caught up to checking. What's a little frustrating
> > (to me) is that the dependence of prediction on ff
35 RtmpURWeVC"
[9] "15.02.2024 04:00 RtmpUrwhHU"
[ reached getOption("max.print") -- omitted 17165 entries ]
Time difference of 18.67841 secs
So, yeah, wow! I'll look into fixing this, probably by removing this
fallback approach, which is ver
Author of R.utils here. I happen to investigate this too right now,
because of extremely slow win-builder performance of R.rsp checks,
which in turn depends on R.utils.
It's not obvious to me why this happens on win-builder. I've noticed
slower and slower win-builder/cran-incoming checks over the
Some thoughts for what the next steps could be:
I could be wrong, but I doubt that there's someone out there that
wants to pick up 'XML' and start developing it beyond keeping the
lights on. I also think the community agrees that 'xml2' is the
recommended package to use for XML-related needs. If
On Thu, Jan 25, 2024 at 9:23 AM Berwin A Turlach
wrote:
>
> G'day Duncon,
>
> On Thu, 25 Jan 2024 11:27:50 -0500
> Duncan Murdoch wrote:
>
> > On 25/01/2024 11:18 a.m., Henrik Bengtsson wrote:
> [...]
> > I think you're right that syntax errors in help
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,
>
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.com";) |> req_dry_run()
> >
> >
> > Since r-oldrel (acc
On Wed, Dec 13, 2023 at 8:06 AM McGrath, Justin M wrote:
>
> On Windows, packages will be in "C:\Users\[User
> Name]\Documents\R\win-library\[R version]\[Package Name]".
In R (>= 4.2.0), the default R_LIBS_USER path has moved to under
LOCALAPPDATA, e.g. "C:\Users\[User
Name]\AppData\Local\R\win-
On Tue, Nov 28, 2023 at 1:21 PM Tomas Kalibera wrote:
>
>
> On 11/28/23 21:50, Henrik Bengtsson wrote:
> > Daniel, I get those compiler warnings for '%td" MS Windows. It works
> > fine on Linux.
>
> Please let me clarify. %td works in R on Windows i
, now there is a way to debug these things.
>
> PS. I also tried using rhub, but it takes a long time and often results in a
> PREPERROR.
>
> On Nov 28, 2023, at 3:58 PM, Henrik Bengtsson
> wrote:
>
> CAUTION: The Sender of this email is not from within Dalhousie.
>
&g
"%td" is not supported on all platforms/compilers. This is what I got
when I added it to 'matrixStats';
* using log directory 'D:/a/matrixStats/matrixStats/check/matrixStats.Rcheck'
* using R Under development (unstable) (2023-11-26 r85638 ucrt)
* using platform: x86_64-w64-mingw32
* R was compil
I'm asking here to spare the CRAN Team a direct message, but also
because the answer is of interest to others:
Consider a package PkgA that was archived on CRAN, because it fails
checks and errors that were not corrected in time. At the moment when
package PkgA is archived, it will trigger automa
On Tue, Oct 17, 2023 at 12:45 PM John Fox wrote:
>
> Hello Dirk,
>
> Thank you for the additional information.
>
> As you suggest, what you did to distribute pre-built PDF vignettes is
> quite similar to what R.rsp does, except that the latter also supports
> pre-built HTML vignettes, which is wha
On Sat, Oct 14, 2023 at 5:25 AM Martin Maechler
wrote:
>
> > Ivan Krylov
> > on Thu, 12 Oct 2023 18:50:30 +0300 writes:
>
> > On Thu, 12 Oct 2023 11:32:24 -0400
> > Mikael Jagan wrote:
>
> >> > mk <- file.path(R.home("share"), "make", "vars.mk")
> >> > pp <- sub("^.*=
On Tue, Oct 3, 2023 at 7:46 AM Jan Gorecki wrote:
>
> Hello,
>
> I noticed some packages define Imports in DESCRIPTION file listing base R
> packages like methods, utils, etc.
>
> My question is that if it is necessary to list those* dependencies in
> DESCRIPTION file, or is it enough to have them
Hello,
this is *not* a new behavior on CRAN, at least on (re-)submissions to
CRAN. The package has to pass R CMD check --as-cran with all OK. If
one of the Suggests:ed package is not installed, but one of your
examples or package tests needed it, that would be detected by the
check system.
The w
To reproduce this, you can use tools:::.news_reader_default(), e.g.
> utils::download.file("https://raw.githubusercontent.com/gertvv/rsmaa/master/smaa/NEWS";,
> "NEWS", quiet = TRUE)
> news <- tools:::.news_reader_default("NEWS")
Warning messages:
1: Cannot process chunk/lines:
smaa 0.3-0
2: Ca
I've got a check_news() function to test that a NEWS.md can be parsed
as expected. See attached file (if that gets dropped in the
interwebs, it's also at
https://gist.github.com/HenrikBengtsson/2361371be4ae8681b3ee2eb361730990).
Call it in the folder where the NEWS.md file is.
My $.02
/Henrik
O
Not sure if it's already been said, but note that we can only use
'Additional_repositories' for *optional* dependencies, which are
listed under 'Suggests' (and less used 'Enhances'). We cannot use
them for *hard* dependencies, which are listed under 'Depends' or
'Imports'. From the CRAN Policies
(
Hello.
As already pointed out, the current R implementation treats any
non-empty value on _R_CHECK_LIMIT_CORES_ different from "false" as a
true value, e.g. "TRUE", "true", "T", "1", but also "donald duck".
Using '--as-cran' sets _R_CHECK_LIMIT_CORES_="TRUE", if unset. If
already set, it'll not t
I think it's because it suggests that the package uses more than 250%
of CPU load on average, which suggests it runs in parallel with more
than two parallel workers, which is the upper limit in the CRAN
Policies (https://cran.r-project.org/web/packages/policies.html);
"If running a package uses mu
Hi.
> * checking for detritus in the temp directory ... NOTE
> Found the following files/directories:
> 'Rscript306c1f1adf1' 'Rscript3fb41f1adf1'
Whenever seeing detritus files with name Rscript like these,
it's a strong suggestion that parallel workers on MS Windows are
involved. More precisely
Hi,
it's not just you; the win-builder server is down for all of us (e.g.
https://downforeveryoneorjustme.com/win-builder.r-project.org?proto=https).
Uwe Ligges, who maintains this, mentioned (in another thread
somewhere) that there were networking issues at his university that
are being worked on
Hello,
are you aware of https://win-builder.r-project.org/? It'll allow you
to validate that your package passes all the requirements before
submitting it to CRAN.
My $.02
/Henrik
On Mon, Sep 26, 2022 at 11:23 AM Jahajeeah, Havisha
wrote:
>
> Dear team,
>
> My second attempt at submitting the
Hello. It looks like things to have changed since;
$ R CMD check --as-cran wflo_1.6.tar.gz
* using log directory ‘/tmp/wflo.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘wfl
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.
>
> The
$ 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 functio
86_64 builder mentioned 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>
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
4
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, Bioconducto
ngle':d code output. If we want the latter,
we're 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
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 y
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 pac
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 containe
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 skippe
k
On Wed, Dec 16, 2020 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)
> #
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 \dontrun
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)) {
...
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 before
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 R-3.6.0-win.ex
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 p
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 there'
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 b
20 at 1:17 AM 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 Bengt
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();
# Acco
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
'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 Thu
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 prop
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 -E
about those packages.
/Henrik
>
> G.
>
> On Tue, Jan 21, 2020 at 5:30 PM Henrik Bengtsson
> wrote:
> >
> > The R.rsp::asis and R.rsp::tex could easily be pulled out from R.rsp
> > in a standalone package with zero dependencies. However, it would be
> > b
The R.rsp::asis and R.rsp::tex could easily be pulled out from R.rsp
in a standalone package with zero dependencies. However, it would be
better if they could be brought into the 'tools' package. This is why
I never went down the path or making a standalone package (adding yet
another package to
It sounds like you want the PDF to have it appear as a package
vignette. You can use the R.rsp::asis vignette engine
(https://cran.r-project.org/package=R.rsp) to add static PDFs as
vignettes to your package. The PDF is included as-is during the
package *build* process (R CMD build) like other pa
The R.cache package on CRAN provides can be used for this purpose. It
works on all platforms. Per CRAN Policies, it will prompt the user
(in an interactive session) whether they wish to use a persistent
cache folder, or to fall back to temporary one. For example,
> path <- R.cache::getCachePath(
Hugh is correct. To clarify, update
if (!rmarkdown::pandoc_available() || rmarkdown::pandoc_version() < "1.12.3") {
stop("'brinton' requires Pandoc v < 1.12.3 (https://pandoc.org/)")
}
The reason is that when using 'a || b', expression 'b' will NOT be
evaluated if 'a' is not TRUE. In contrast,
Disclaimer, I'm the author: You can include a static PDF using the
R.rsp::asis vignette engine:
https://cran.r-project.org/web/packages/R.rsp/vignettes/R_packages-Static_PDF_and_HTML_vignettes.pdf
Better is if you've got the LaTeX source (with figures etc.), then use
the R.rsp::tex vignette en
There's also R Hub by Gábor Csárdi:
https://builder.r-hub.io/advanced
It provides a win-builder-like service where you can test your package
with different R setups, including 'Debian Linux, R-devel, GCC
ASAN/UBSAN'. There's also an 'rhub' package that allows you to run
all this from the R pro
;
> Gabor
>
> On Tue, Sep 24, 2019 at 7:08 PM Henrik Bengtsson
> wrote:
> >
> > 'R CMD check' will give a warning that 'speed' is an unknown variable in:
> >
> > low_speeds <- function(limit) {
> > subset(datasets::cars,
'R CMD check' will give a warning that 'speed' is an unknown variable in:
low_speeds <- function(limit) {
subset(datasets::cars, speed <= limit)
}
We can tell 'R CMD check' that 'speed' is a false positive by
declaring it a "global" variable. This can be done, by:
low_speeds <- functi
As first step of being able to reproduce the error, have a look at
R-Hub (https://blog.r-hub.io/2019/03/26/why-care/). It'll allow you
to use their servers to test your package on many different
configurations. It helped me several times. You can launch it all
from you local R prompt, e.g.
> rhu
FWIW, when running
R CMD check mypkg_1.0.tar.gz
the example output is captured to the file
'mypkg.Rcheck/mypkg-Ex.Rout', so you could monitor that one for what's
going on.
/Henrik
On Mon, Jul 1, 2019 at 7:00 PM Rolf Turner wrote:
>
>
> I am currently working on a package such that when "R CMD
Duncan and others, see one of Serguei comments above. Specifically,
`R CMD check --as-cran` will set
_R_CHECK_LENGTH_1_LOGIC2_="package:_R_CHECK_PACKAGE_NAME_,abort,verbose"
which will (i) check those coding mistakes only in the package that is
checked but not any of its dependencies, (ii) it
I agree that setwd(), tempdir(), etc. clutter up examples. At the
same time, I respect the CRAN policy - it's conservative approach has
helped us avoid a wild-west working environment. One approach that
might help bring some standardization, instead of each package
developer rolls their own, and a
FWIW, you should be able to reproduce at least the following NOTEs
with your current R 3.5.2 and R CMD check --as-cran:
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘cartogRaflow ’
New submission
Version contains large components (0.0.0.9000)
Possibly mis-spelled words in DESCRIPTI
os
> >
> > On Wed, 13 Mar 2019 at 10:05, Maëlle SALMON via R-package-devel <
> > r-package-devel@r-project.org> wrote:
> >
> > >
> > >
> > >
> > > -- Forwarded message --
> > > From: "Maëlle SALMON"
> > > To: Dunc
You can also "follow" your package submission on the CRAN FTP server:
ftp://cran.r-project.org/incoming/
/Henrik
On Tue, Mar 12, 2019 at 1:26 PM Duncan Murdoch wrote:
>
> On 12/03/2019 2:57 p.m., Τόλης Χαλκής wrote:
> > Dear all,
> >
> > We have submitted a package to CRAN in 25th of Februar
I take a complementary approach; I condition on, my home-made,
R_TEST_ALL variable. Effectively, I do:
if (as.logical(Sys.getenv("R_TEST_ALL", "FALSE"))) {
...
}
and set R_TEST_ALL=TRUE when I want to run that part of the test. You
can also imagine refined versions of this, e.g. R_TEST_SETS=
Does R CMD check --as-cran test for newly opened connections or any
open connections? Could the check for stray connection in
examples/vignettes be:
1. Record what connections are open
2. Attach the package
3. Record what connections are open
4. Run the example
5. Assert that no *new* connections
As a workaround, until resolved, you could precompile your vignette
into a PDF and then use the 'R.rsp::asis' vignette engine
(%\VignetteEngine{R.rsp::asis} etc) to include it as a static PDF.
This is described in the vignettes
(https://cran.r-project.org/package=R.rsp).
-Henrik
On Thu, Aug 2, 201
On Tue, Jul 10, 2018 at 7:00 AM David Hugh-Jones
wrote:
>
> Hi all,
>
> Just updated my rcheology package with data on functions for R 3.5.1 (no
> change from R 3.5.0 afaik). See https://github.com/hughjonesd/rcheology.
>
> I'm wondering how to version this package. It's not on CRAN yet so it woul
Below are more details on/examples of changes due to ORCID URLs being
added to the DESCRIPTION file (from
https://github.com/easybuilders/easybuild-easyconfigs/pull/6446#issuecomment-396574744):
$ diff -ru RWeka.orig RWeka
diff -ru RWeka.orig/DESCRIPTION RWeka/DESCRIPTION
--- RWeka.orig/DESCRIPTIO
n Thu, Apr 26, 2018 at 10:04 AM, Henrik Bengtsson
> wrote:
>>
>> On Thu, Apr 26, 2018 at 6:28 AM, Spencer Graves
>> wrote:
>> >
>> >
>> > On 2018-04-26 07:11, Jose A Guijarro wrote:
>> >>
>> >> El 25/04/18 a las 20:21, Duncan
On Thu, Apr 26, 2018 at 6:28 AM, Spencer Graves
wrote:
>
>
> On 2018-04-26 07:11, Jose A Guijarro wrote:
>>
>> El 25/04/18 a las 20:21, Duncan Murdoch escribió:
>>>
>>> On 25/04/2018 1:32 PM, Sarah Goslee wrote:
Don't change the working directory! That has all kinds of unpleasant
si
R CMD check, which is used internally runs checks in standalone
background R processes. Output from these is not capturable/sinkable
by the master R process. The gist of what's happening is:
> sink("output.log")
> system("echo hello") ## not sinked/captured
hello
> sink()
> readLines("output.lo
On Thu, Mar 8, 2018 at 12:39 PM, Jonathon Love wrote:
> hi,
>
> i'm bundling some R packages to go into a flatpak/flathub application. for
> that it is necessary to provide the download URLs for all the required
> dependencies in advance - including R packages. this works, *except* when an
> R pac
On Mon, Jan 8, 2018 at 7:31 AM, Roy Mendelssohn - NOAA Federal
wrote:
> Hi All:
>
> In tesitng a package on winbuild-devel (but not on release) I get the
> following errors or warnings:
>
>> Warning in engine$weave(file, quiet = quiet, encoding = enc) :
>> The vignette engine knitr::rmarkdown
Uwe/Kurt, is this controlled by R itself or by the host system? I
suspect one of my R.filesets tests(*) fails (since a few days) because
of this, but it might actually be a false positive. I fail to
reproduce it on Ubuntu 16.04 with:
* using R Under development (unstable) (2017-12-20 r73933)
* u
For the translation part, you can test the received error message against
the translated message. You can get the translated version from the
original one using gettext("").
This should be agile to user's language settings but, of course, not to
changes that the developer does to the the error mes
>> On 30.11.2017 12:52, Andrew Holding wrote:
>> [...] I know the new Bioconductor on devel is unstable [...]
Does CRAN support packages in the Bioconductor *devel* repository?
/Henrik
On Thu, Nov 30, 2017 at 2:54 PM, Andrew Holding wrote:
> Dear Uwe,
>
> Just submitted the package again and go
Looks like a hiccup to me - this never happened to me. I suggest
sending cran@... an email about this. /Henrik
On Sun, Sep 10, 2017 at 4:02 AM, Jacob Long wrote:
> I noticed my package, jtools (
> https://cran.r-project.org/web/packages/jtools/index.html), didn’t
> increment its version number o
Your package uses parallel processing (foreach w/ doParallel).
Peeking at the code, it looks like the vignette is using single-core
processing via doParallel::registerDoParallel(np) where np = 1. On
Unix-like system, this *forks* off a single R process, and on Windows
it *launches* a single backgr
On Tue, Feb 28, 2017 at 2:47 PM, Duncan Murdoch
wrote:
> On 28/02/2017 5:17 PM, Patrick Schratz wrote:
>>
>> Thanks Duncan, that was the problem! Although the Rbuildignore entry
>> pointed to the main dir
>
>
> No, it contains patterns, not paths, and is matched "case-insensitively
> against the f
On Tue, Feb 7, 2017 at 2:10 PM, Gábor Csárdi wrote:
> On Tue, Feb 7, 2017 at 8:16 PM, Henrik Bengtsson
> wrote:
> [...]
>>
>>
>> So, to me it's not clear how this could make a difference in Patrick
>> case. By disabling this, i.e. Sys.setenv(R_TESTS=&quo
ure I do similar tests, which
is on top of the foreach package. I don't use testthat and I also
don't use doParallel in my testing.
/Henrik
>
> Gabor
>
> On Mon, Feb 6, 2017 at 2:17 AM, Henrik Bengtsson
> wrote:
>>
>> In case someone else bumps into t
cross but tests are
>> still running infinite..
>>
>> cl <- makeCluster(par.args$par.units, outfile = out.progress)
>> registerDoParallel(cl)
>>
>> foreach()
>>
>> parallel::stopCluster(cl)
>> doParallel::registerDoSEQ()
>> doParallel::stopImpli
Use
registerDoParallel(cl)
The number of parallel workers is already contained in the 'cl'
object, so don't
specify 'cores'! (If you do that, I suspect you create yet another cluster
(a multicore one) which is used but never closed)
registerDoParallel() should ideally give an error in your ca
What's already been said is good advice. At first, it may be a bit
tricky to under copyright and licenses. When I started out, I for the
longest held back on releasing software / packages because I somehow
thought I basically had to make a final decision on the license at
that moment and that the
It sounds like memoization could help here. Package examples for this:
memoise and R.cache
Henrik
On Oct 27, 2016 11:19, "Glenn Schultz" wrote:
> All,
>
> Thank you, I have built the package such that it passes an object
> TermStrutrure to those functions which require it as an input. The pack
I think R CMD check calls
res <- system2("du", "-k", TRUE, TRUE)
also on Windows, cf.
https://github.com/wch/r-source/blob/trunk/src/library/tools/R/check.R#L3859
It could be that you have a corrupt / different `du` tool on your
PATH. As a first thing, try calling the above from within you pack
I second Dirk. Also, from my experience:
A good rule of thumb is that you should fix all NOTEs (i.e. not have
them) when you submit to CRAN. It's only when you have a really good
reason you could try to convince CRAN that they are there and that
they cannot be fixed easily. I've got 20+ package
If it's not feasible to create a fast vignette or to avoid downloading
files, an alternative is to pre-generate the vignette and include it
as a static PDF/HTML vignette, cf.
https://cran.r-project.org/package=R.rsp. If it's a LaTeX-based
vignette (e.g. Sweave/knitr), you could pre-generate the La
On Sat, May 21, 2016 at 8:22 AM, Marius Hofert
wrote:
> Hi,
>
> I have (co-)developed two packages: 'qrmtools' and 'qrmdata'. The
> latter contains data sets and is currently only available on R-Forge
> (as it is larger than 5MB and thus not accepted for CRAN [although
> there are much larger pack
On Wed, Apr 27, 2016 at 12:40 PM, Ramon Diaz-Uriarte wrote:
> Dear Bruce,
>
>
> On Wed, 27-04-2016, at 19:00, Bruce Hoff wrote:
>> Following up to my earlier post: It looks like Dirk Eddelbuettel has in
>> fact built what I was asking for with 'drat',
>> https://github.com/eddelbuettel/drat. Th
The CRAN Policies [https://cran.r-project.org/web/packages/policies.html] say:
"- Packages should not write in the users’ home filespace, nor
anywhere else on the file system apart from the R session’s temporary
directory (or during installation in the location pointed to by
TMPDIR: and such usage
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