Re: [R-pkg-devel] Export everything whose name does not start with ".".

It would have been helpful for that person to specify their candidate regex, rather than just saying it could be simpler. That out of the way, I believe exportPattern("^[^.]") would be sufficient since the square brackets remove any special meaning the dot has. For an alternative, given the

[R-pkg-devel] Additional Issues: Intel

My package grattan fails the Intel[1] check with Error: segfault from C stack overflow I am unable to immediately see where in the test suite this error has occurred. I seek advice on how to fix this error. The only hunch I have is that the package uses C code and includes structs with

Re: [R-pkg-devel] checking CRAN incoming feasibility

> Surely the software just has to check that there is web connection to a CRAN mirror. Nope! The full code is in tools:::.check_package_CRAN_incoming (the body of which filled up my entire console), but to name a few checks it has to do: check that the name of the package is not the same as any

[R-pkg-devel] Canonical way to Rprintf R_xlen_t

ld", (long long) xlength(x)); Rprintf("%td, xlength(x)); or using the string macro found in Mr Kalibera's commit of r85641: R_PRIdXLEN_T Which would be most advisable for my update, required in the next fortnight? Hugh Parsonage __ R-package-devel@r

Re: [R-pkg-devel] How to identify what flags "Additional Issues" for UBSAN

In line https://github.com/alarm-redist/redist/blob/f1ed042841469456c1d8c149092bc818e2a5c1a5/src/wilson.cpp#L165 int max_try = 50 * remaining * ((int) std::log(remaining)); you need to ensure remaining > 0. At some point it became -1. On Thu, 23 Mar 2023 at 22:07, Ivan Krylov wrote: > > В

Re: [R-pkg-devel] [UNCLASSIFIED] Remotes in description when submitting a package until a dependency is fixed

I think you've misunderstood that excerpt. By "temporary development state", it means _between_ CRAN releases; packages in a development state are not suitable for CRAN, as the policy states: > CRAN hosts packages of publication quality and is not a development platform. You'll need to stop

Re: [R-pkg-devel] Best way to cache a dataframe available for all functions in a package

Agreed. One can also initialise such an environment as a package option in .onLoad which may be better or worse depending in part on how much restriction you want to place on the environment On Sat, 27 Nov 2021 at 12:41 am, Lionel Henry wrote: > Hello, > > The trick is to store cached objects

[R-pkg-devel] S3 is.unsorted registration

and source code I note that if I omit the na.rm = argument I will get the intended result (I was drawn to the solution by noting the .Internal call has omitted it) but I'm wondering whether this is correct. Best, Hugh Parsonage. __ R-package-devel@r-p

Re: [R-pkg-devel] Workaround for code/documentation mismatch

What is the behaviour of %while% if not preceded by an expression wrapped in do() ? On Wed, 11 Aug 2021 at 1:26 pm, Andrew Simmons wrote: > Hello, > > > I've written two functions to emulate do while/until loops seen in other > languages, but I'm having trouble documenting its usage. The

Re: [R-pkg-devel] Using parallel:::sendMaster despite warnings

Happily, package parallel is open-source. If you would like to make use of the unexported functions, you could copy the source code with acknowledgement into your package. Naturally this might be a lot of work and risks different behaviour between your package and parallel, but neither might be

Re: [R-pkg-devel] OpenMP on MacOS

Ensure you surround all your omp pragmas like so: #ifdef _OPENMP #pragma omp parallel ... #endif Essentially, detecting the operating system is not enough -- you need to condition your use of OpenMP if and only if _OPENMP is available. You should also do the same for #if _OPENMP #include

Re: [R-pkg-devel] Finding dependencies (Was: problem with submitting to CRAN (windows))

te: > > On 02/06/2021 6:57 a.m., Hugh Parsonage wrote: > > mvSLOUCH <--- TreeSim <-- phytools <-- gtools > > > > On Wed, 2 Jun 2021 at 20:35, Krzysztof Bartoszek > > wrote: > >> > >> Thank you. The only problem, as I wrote, is that neither m

Re: [R-pkg-devel] problem with submitting to CRAN (windows)

in mvSLOUCH do I use any call to anything from gtools > nor to any function called combinations. > > Best wishes > Krzysztof Bartoszek > > > Sent with ProtonMail Secure Email. > > ‐‐‐ Original Message ‐‐‐‐‐‐‐ > On Wednesday, June 2, 2021 10:25 AM, Hugh Parsonag

Re: [R-pkg-devel] problem with submitting to CRAN (windows)

Probably a consequence of gtools having build errors (https://cran.r-project.org/web/checks/check_results_gtools.html) I'd recommend reconsidering use of the package until the problems are resolved. In the meantime, put gtools is Suggests for the use of combinations(). Note the base R functions

Re: [R-pkg-devel] \donttest{} and writing outputs to tempdir()

Are you able to provide a link to your package? It's a bit hard to guess what's causing your examples etc to have these problems. On Wed, 2 Jun 2021 at 14:40, Danielle Maeser wrote: > > Hello, > > I received the following comments from a CRAN maintainer, and I don't > understand why they were

[R-pkg-devel] Valgrind warning: invalid size of 4, is it due to a simple overrun?

Hello, I received a valgrind warning about my package, hutilscpp, from CRAN (thank you). I believe I've tracked down and fixed the problem, but I wasn't able to reproduce the error on rhub (including with --leak-check=full etc) so I'd like to know if I'm missing something. The valgrind warning

Re: [R-pkg-devel] Problems with too much testing

My 2c is that if a package has actually tested something like that (say, the ordering of a list's elements), then it is 100% likely that a script out there depends on that behaviour too. In other words, the change is not inconsequential. R users are in debt to package developers but I think it

Re: [R-pkg-devel] Warning on r-oldrel-macos-x86_64

If you click on WARN in the table on your check results page (i.e. if you go to ) you will see in the first line: * using R version 3.6.2 (2019-12-12) Hope that helps. On Sun, 25 Oct 2020 at 21:10, Helmut

Re: [R-pkg-devel] details of CRAN's r-devel-linux-x86_64-debian-clang

_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_ not R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_ (i.e. you seem to have dropped the initial underscore)? On Sun, 25 Oct 2020 at 20:01, Jan Gorecki wrote: > > Dear community, > > I am getting an error on CRAN on r-devel-linux-x86_64-debian-clang

Re: [R-pkg-devel] Licenses

It’s necessary but not sufficient to use a licence from license.db On Fri, 23 Oct 2020 at 3:12 am, Duncan Murdoch wrote: > On 22/10/2020 11:55 a.m., Marc Schwartz wrote: > > > > > >> On Oct 22, 2020, at 11:19 AM, Marc Schwartz > wrote: > >> > >> On Oct 22, 2020, at 10:21 AM, Kevin R. Coombes <

[R-pkg-devel] Tracking down cause of UBSAN error

Hello, I am getting a UBSAN-clang failure on my package hutilscpp (). However I cannot reproduce the error on rhub, nor can I see an obvious problem with the code. (Though obviously there is something wrong.) The testthat.Rout log from CRAN reads

Re: [R-pkg-devel] installed package size problem on Mac but not Linux nor Windows

One of your vignettes is a 52-page pdf. It may be more suitable to provide a link to it rather than distributing it with the package, or distribute an excerpt. Some the images in the PDFs could be PDFs themselves, or be pngs with lower resolution. On Tue, 22 Sep 2020 at 5:04 pm, Spencer Graves <

Re: [R-pkg-devel] package CatDataAnalysis

If you’re not the author of the data, you can’t submit it as such. The website has a copyright message on it which, while not definitive, doesn’t suggest the use you’re proposing would be allowed. Bear in mind that you may expose CRAN not just yourself to liability if you try to conceal true

Re: [R-pkg-devel] Rbuildignore a file type from a top level directory only

Perhaps ^[^/]+\.R$ On Sun, 21 Jun 2020 at 22:31, Jan Gorecki wrote: > > Hi R developers, > > What is the proper way to define an entry in .Rbuildignore file to > exclude *.R files from a top level directory of R package? > Using ^.*\.R$ excludes every R script, including those in

Re: [R-pkg-devel] Including fst in inst/extdata

character columns to ASCII and changing the order of the columns changed the output of file to 'data'. Dropping a column also prevented the false identification. On Mon, 27 Apr 2020 at 22:12, Dirk Eddelbuettel wrote: > > > Hugh, > > On 27 April 2020 at 16:02, Hugh Parsonage wrote: &g

[R-pkg-devel] Including fst in inst/extdata

st/extdata/file.fst" I'm not sure whether this qualifies as a "rare false positive" as WRE mentions, but if it isn't is there a way to include fst files in a package without raising a warning? Hugh Parsonage. __ R-package-devel@r-proje

Re: [R-pkg-devel] note about dependency on archived package

The note is there to remind CRAN that the package previously had problems serious enough to warrant archival. Since you have solved the problem, you do not need to do anything else in your submission. On Wed, 18 Mar 2020 at 7:23 am, Gianmarco Alberti < gianmarcoalbe...@gmail.com> wrote: > Hello,

Re: [R-pkg-devel] GitHub problems

You published your token. You should revoke it. You probably don’t have the right permissions associated with git. On Sat, 14 Mar 2020 at 2:14 pm, Spencer Graves < spencer.gra...@effectivedefense.org> wrote: > Hello, All: > > >What do you suggest Jim Ramsay and I do to migrate the fda

Re: [R-pkg-devel] win-builder down?

Are CRAN staff located in Europe only? Is there a case to have a limited staff across multiple timezones with a rolling roster? Obviously if something is reported it’s best if it can be actioned immediately. On Sun, 1 Mar 2020 at 12:29 pm, Henrik Bengtsson wrote: > FYI, in past when queues got

Re: [R-pkg-devel] function name conflict problem

Package karon is the problem. Is that package in your depends or imports? Does that package use Depends? On Wed, 5 Feb 2020 at 8:24 am, wrote: > In trying to develop a package to be submitted to CRAN, when I do Install > and Reload or devtools::check(), I get the warning: > > > > Warning:

Re: [R-pkg-devel] Error while checking if Pandoc is available

Change | to || On Fri, 6 Dec 2019 at 11:08 pm, Pere Millan Martinez wrote: > Yesterday the publication of the new brinton package war archived > (https://cran.r-project.org/web/packages/brinton/index.html) because the > following line produces the following error: > >

Re: [R-pkg-devel] Issue with Biostrings-- can't find the base rgb function on r-devel

rgb is from package grDevices not package base. On Thu, 5 Dec 2019 at 2:48 pm, Dalgleish, James (NIH/NCI) [V] via R-package-devel wrote: > Question: > > NIPTeR is experiencing new warnings when loading Biostrings. I have the > exact same warnings with my package, CNVScope. > > It seems a little

Re: [R-pkg-devel] roxygen2 7.0.1 backslash escape error

You could (a) install the updated roxygen from github and rebuild the man/ files ; (b) manually edit the Rd files without using roxygen ; or (c) remove the examples until you can apply the fix. On Sun, 1 Dec 2019 at 1:26 am, Yoni wrote: > I received a message from CRAN yesterday stating my

Re: [R-pkg-devel] Problem loading package on Windoze --- update.

I wonder if Dropbox “smartsync” is the culprit here. I’ve noticed this feature can create confusion between programs when Dropbox provides (a link to) the file when it is opened but only when it recognizes the file is being opened. On Tue, 5 Nov 2019 at 7:46 pm, Gábor Csárdi wrote: > I am not

Re: [R-pkg-devel] What counts as an API change?

> The approach I take is a major version increment is required if it > requires an existing unit test to be changed or if it requires a reverse > dependency to change a unit test. > > (With the exception of tests marked explicitly as unstable.) > > In my view the test suite is a good way to

Re: [R-pkg-devel] R package manual failing only on R-devel-linux-x86_64-debian-gcc

Unfortunately this error is caused by a hyperlink straddling a page, so it’s difficult to solve uniformly. The LaTeX error message provides a clue as to where the hyperlink might be (near an \item near a \code) but no exact location. My advice would be to look where you have hyperlinks

Re: [R-pkg-devel] .Rd, LaTeX and Unicode

utf8x is deprecated https://tex.stackexchange.com/questions/13067/utf8x-vs-utf8-inputenc#13070 On Tue, 18 Jun 2019 at 7:52 pm, Serguei Sokol wrote: > Hi, > > I am preparing a package where I would like to use UTF characters in .Rd > files. When the LaTeX comes to play, I got well known

Re: [R-pkg-devel] CRAN student assistants

I can't speak for Hadley, but my read of his email was that CRAN has appointed new staff and while extra staff are clearly justified, it was unclear how they were appointed and whether they had equal seniority and authority as existing members. Indeed, the fact they use titles which are clearly

[R-pkg-devel] Use of assignInNamespace in package

Hello, I'm considering a package submission. I have used assignInNamespace, which is hideous but seems better than the alternatives. I see that it returns a NOTE on R CMD check, suggesting that it is not absolutely prohibited, but would require justification. The justification I would make is

Re: [R-pkg-devel] Building my R package: issue when importing two functions with the same name

Does your package import or depend on 'GmAMisc'? This package appears to Depend on both spatstat and pROC. Alternatively you have imported both packages in your NAMESPACE. If neither of these clues help, could you post your DESCRIPTION and NAMESPACE files? Probably all we'd need. On 6 August

Re: [R-pkg-devel] Get an empty note for "checking DESCRIPTION meta-information" when I run devtools::build_win()

Thank you. Could you provide the contents of DESCRIPTION too? That might provide the richest clue. If you have a link to an online copy of the package that could be helpful too. On Wed, 25 Jul 2018 at 12:01 Eggleston, Barry wrote: > I am working through my first package submission. When I

Re: [R-pkg-devel] Versioning conventions

3.5.1.0 with the 4th number (0) for within-release changes. Lovely package by the way -- I was looking for it earlier this year but thought it had been lost! The link in the GitHub description appears broken, however. On 10 July 2018 at 23:59, David Hugh-Jones wrote: > Hi all, > > Just updated

Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN submission bwt 1.1.0

Hi, There are a few problems with the submission. Probably more than can be resolved by people on the mailing list. Speaking generally, a WARNING in a CRAN check is something that *must* be fixed, rather than something which you can just acknowledge. The two warnings that you mentioned are that

[R-pkg-devel] Very large packages in Additional_repositories

Dear list, I'm considering submitting a package to CRAN. The package would be a 'foyer' or API to a much larger package (>1GB tarball) containing geographical data that the 'foyer' package would use to perform tasks like geocoding. The foyer package would be usable, though quite limited, as a

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

Not to mention a drat repository you can just fork with a single click! On Mon, 26 Feb 2018 at 3:25 am, Dirk Eddelbuettel wrote: > > On 25 February 2018 at 15:00, Marius Hofert wrote: > | okay, so (afaik) this is just a github repos which contains an exact > | copy of the github

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

The relevant part of the repository policy: > Packages on which a CRAN package depends should be available from a > mainstream repository: if any mentioned in ‘Suggests’ or ‘Enhances’ fields > are not from such a repository, where to obtain them at a repository should > be specified in an

Re: [R-pkg-devel] Strange Additional_repositories NOTE followed by package install error

NOTE Maintainer: 'Hugh Parsonage <hugh.parson...@gmail.com>' Possibly mis-spelled words in DESCRIPTION: Grattan (18:24) indices (17:77) repos (19:34) taxstats (19:23) Suggests or Enhances not in mainstream repositories: taxstats Availability using Additional_repositories specification:

[R-pkg-devel] Strange Additional_repositories NOTE followed by package install error

with _R_CHECK_CRAN_INCOMING_ = true I get the expected NOTE: * checking CRAN incoming feasibility ... NOTE Maintainer: ‘Hugh Parsonage <hugh.parson...@gmail.com>’ Suggests or Enhances not in mainstream repositories: taxstats Availability using Additional_repositories specification: taxstats

[R-pkg-devel] Is it ever appropriate (or mandatory) to Suggests: R (>= version) ?

I believe it is a requirement that if package A imports package B, and package B lists package C in Depends: then package A must also list package C in Depends: A popular stackoverflow answer states this.[1] I can't find any other source but it makes sense. What if package B is suggested by

Re: [R-pkg-devel] R-package did not pass the incoming checks automatically

Use the url at the bottom of the linked page, i.e. https://cran.r-project.org/package=ewoc On Sun, 21 Jan 2018 at 5:06 am, Roy Mendelssohn - NOAA Federal < roy.mendelss...@noaa.gov> wrote: > Hi Márcio: > > I do not have solutions to your specific problems, but the errors do > appear to be coming

[R-pkg-devel] rcnst issue

;). Do I need to stop using %fin% inside packages to avoid this error, or is the cause of the error elsewhere? I have some doubt that %fin% is totally to blame as the package through which %fin% is eventually called does not encounter the same error. Many t

[R-pkg-devel] CRAN policy on binary submission

On https://cran.r-project.org/ , it says > Note that we generally do not accept submissions of precompiled binaries due > to security reasons I note it says 'generally', not 'always'. Are there any packages on CRAN which were submitted as precompiled binaries? Under what circumstances would

Re: [R-pkg-devel] Assignments to the Global environment

I'm not CRAN, but something like this might be permissible while satisfying your requirements. z <- function(..., assign.env = parent.frame(1)) assign(as.character(s), temp3, envir = assign.env) The problem with assigning to the global environment is that z might be called where it is

[R-pkg-devel] Imports: vs Suggests:

package (like stats) or a recommended package (like KernSmooth)? Hugh Parsonage Grattan Institute __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel