Re: [R-pkg-devel] No email with confirmation link on resubmission of package

Check your spam folder(s) ? Try the web form just in case something is wonky with devtools::submit_cran() ? On 2024-06-05 4:19 a.m., Paul Kabaila wrote: (1) Today, I submitted my R package to CRAN using devtools::submit_cran() which resulted in

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Zenodo and OSF (see e.g. ) are both non-profit organizations that support archiving -- that is, they both make stronger guarantees of permanent availability than GitHub does. Possibly Software Heritage https://www.softwareheritage.org/features/ ?

Re: [R-pkg-devel] Urgent Review of R Packages in Light of Recent RDS Exploit

This is true, and useful. Many old-school R users are nervous about coming to rely on tools that are controlled by a company that may rescind that availability in the future, or may possibly use your code in ways you don't want (I have not gone all the way through

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

On 2024-04-18 9:41 a.m., 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 ffbase is *very

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

*in the opposite direction* -- i.e. if A Enhances B, it's not entirely clear why the disappearance of B should matter at all ...) On 2024-04-18 9:35 a.m., 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

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

a given body of data. ~ John Tukey /// <https://www.inbo.be> Op do 18 apr 2024 om 15:25 schreef Ben Bolker <mailto:bbol...@gmail.com>>:    Thank you! (I know about package_dependencies() but ran into precisely the same problem and didn't want to re-imp

Re: [R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

is not available on CRAN, however. On Thu, Apr 18, 2024 at 9:05 AM Ben Bolker <mailto:bbol...@gmail.com>> wrote:    The 'dotwhisker' package was archived on CRAN: from https://cran.r-project.org/web/packages/dotwhisker/index.html <https://cran.r-project.org/web/pa

[R-pkg-devel] puzzling removal of 'dotwhisker' from CRAN

The 'dotwhisker' package was archived on CRAN: from https://cran.r-project.org/web/packages/dotwhisker/index.html Package ‘dotwhisker’ was removed from the CRAN repository ... Archived on 2024-04-12 as requires archived package 'prediction'. However, I can't for the life of

Re: [R-pkg-devel] Avoid Possibly misspelled words in DESCRIPTION

AFAICT isn't actually mentioned anywhere in the docs ...) What do you mean by "already inserted these words in the WORDLIST"? cheers Ben Bolker On 2024-04-12 9:18 a.m., Gabriel Constantino Blain wrote: Hello, When I apply the devtools::check_win_devel() to my package it shows the

Re: [R-pkg-devel] Package vulnerabilities

FWIW there is a repo for R advisories. https://github.com/RConsortium/r-advisory-database with a front-end here https://osv.dev/list?ecosystem=CRAN= At present all of the *reported* vulnerabilities seem to be caused by problems with underlying/bundled libraries ... On 2024-04-03 4:37

Re: [R-pkg-devel] help diagnosing win-builder failures

++), but there is not enough information to give a conclusive diagnosis. On Sun, 17 Mar 2024 14:01:33 -0400 Ben Bolker wrote: 2. an ERROR running tests, where the output ends with a cryptic Anova: .. (please try to refrain from snarky comments about not using testthat ...) Pardon my ignorance

[R-pkg-devel] help diagnosing win-builder failures

...) Full log is here, at least for a little while: https://win-builder.r-project.org/9I5WG5R8WJg3/00check.log We could admit defeat and throw ourselves on the CRAN-maintainers' mercy, but we would like to resolve these if we can. cheers Ben Bolker __

[R-pkg-devel] confusion over spellchecking

I am working on a package and can't seem to get rid of a NOTE about Possibly misspelled words in DESCRIPTION: glmmTMB (10:88) lme (10:82) on win-builder. I have set export _R_CHECK_CRAN_INCOMING_USE_ASPELL_=TRUE locally, and have tried to set up the .aspell defaults as specified by

Re: [R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

https://github.com/r-lib/revdepcheck does the 'step 3 twice' part. I have had a few issues with it but overall it's been very helpful. https://github.com/HenrikBengtsson/revdepcheck.extras may also be useful. On 2024-01-30 10:56 a.m.,

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

Are you sure the issue that CRAN has is the library sizes, and not the issues flagged by the "LTO" platform ? https://www.stats.ox.ac.uk/pub/bdr/LTO/rar.out I would check with CRAN for clarification before you spend a lot of time trying

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

now what the warning looks like, but the ?tar help page discusses the issues. Duncan Murdoch On 12/12/2023 3:10 p.m., Ben Bolker wrote:    FWIW the R-windows FAQ says: Yet another complication is a 260 character limit on the length of the entire path name imposed by Windows. The limit applies

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

e R source tree. It would be helpful to have the exact wording of the NOTE/WARNING (?) that is thrown ... (I know I could make my own mini-package with a long path length in it somewhere but ...) cheers Ben Bolker On 2023-12-12 2:57 p.m., Simon Urbanek wrote: Justin, now that you clarif

Re: [R-pkg-devel] NOTE: Examples with CPU time > 2.5 times elapsed time

Wow. On Mon, Dec 4, 2023, 5:43 PM Ivan Krylov wrote: > Dear Artur, > > You've got a well-written package. There are some parts I wasn't able > to understand (e.g. changing the class of a variable by reference using > SET_CLASS and later changing it back), but there are no obvious places > where

Re: [R-pkg-devel] Question regarding finding the source file location without R-packages outside of R-Studio

Not sure, but I think the 'here' package might do what you want. It's tidyverse-affiliated but pretty stable On Thu, Nov 23, 2023, 2:39 PM Tony Wilkes wrote: > Hi everyone, > > I have a question. I hope it's not a stupid question. > > Suppose you'd want to perform version control and project

Re: [R-pkg-devel] Check warning around sprintf: Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system

You may also be able to use Rprintf ? https://teuder.github.io/rcpp4everyone_en/060_printing_massages.html On 2023-11-18 8:07 p.m., Iris Simmons wrote: Yes, the reason for the error is the use of sprintf. You can instead use snprintf where n is the maximum number of bytes to write, including

Re: [R-pkg-devel] What happened to mlr3proba on CRAN?

ect.org/src/contrib/Archive/mlr3proba/mlr3proba_0.4.9.tar.gz if you want to follow up with them ... cheers Ben Bolker On 2023-10-08 5:28 p.m., Dr. Franz Király wrote: Dear all, can someone explain to me what exactly happened to mlr3proba on CRAN? https://cran.r-project.org/web/packages/m

Re: [R-pkg-devel] Suppressing compiler warnings?

This also doesn't answer your question, but: A trick that the TMB package uses to help users is to suggest that they add "CXXFLAGS += -Wno-ignored-attributes" to their `.R/Makevars` file. This means that *they* don't have to see useless warnings when compiling code. In your case I don't

[R-pkg-devel] status of "possibly invalid URL/403 error" NOTEs?

I have a package whose documentation includes the reference \doi{10.1137/18M1186411} which redirects here: https://epubs.siam.org/doi/10.1137/18M1186411 Running R CMD check --as-cran on the package gives Found the following (possibly) invalid URLs: URL:

Re: [R-pkg-devel] LICENSE file in an R package for CRAN submission

11:15 a.m., Ben Bolker wrote:    You have two choices: * put LICENSE in your .Rbuildignore file so that it shows up on Github but is excluded from the package * follow the instructions in https://cran.r-project.org/doc/manuals/R-exts.html#Licensing to refer to LICENSE in your DESCRIPTION f

Re: [R-pkg-devel] LICENSE file in an R package for CRAN submission

You have two choices: * put LICENSE in your .Rbuildignore file so that it shows up on Github but is excluded from the package * follow the instructions in https://cran.r-project.org/doc/manuals/R-exts.html#Licensing to refer to LICENSE in your DESCRIPTION file. However, CRAN generally

[R-pkg-devel] "Version contains leading zeroes" note: clarity

<https://github.com/r-devel/r-svn/blob/0252cdbf14c73acd26ae2090df3c04aa6118b523/src/library/tools/R/check.R#L6009>: wouldn't that be more appropriate here?) cheers Ben Bolker __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Package PowerSDI NOTES

See also https://ropensci.org/blog/2022/01/21/ropensci-news-digest-january-2022/#to-quote-or-not-to-quote-non-existing-words-in-description https://stat.ethz.ch/R-manual/R-patched/library/utils/html/aspell-utils.html On 2023-07-18 3:11 p.m., Duncan Murdoch wrote: On 18/07/2023 12:37 p.m.,

Re: [R-pkg-devel] Public URLs for help for versions of base packages

Nice! (I like "A longer description will go here eventually.") It would be cute/handy to have navigation links available for "go to this help page in the next (previous) version of R" (if it's not a huge pain) On 2023-06-30 11:10 a.m., David Hugh-Jones wrote: OK, so I took Jeff's hint

Re: [R-pkg-devel] masked from 'package:utils':,, ?

   This is harmless and should be accepted by CRAN (if masking existing functions were illegal half of the tidyverse would be banned ...).  It's there because it needs to be defined in order to enable the ??? alias for findFn().  sos:::"?" (and experimentation) show that use of a single ? is

Re: [R-pkg-devel] Acknowledging small functions from another package

In fact Martin Maechler added this in 2021: https://github.com/wch/r-source/blob/trunk/src/library/utils/R/str.R#L19-L21 ## A pearl from ggplot2 et al. NB: often needs '(.)' :%||% ( ) ## *not exported* [should rather be in 'base' than exported here] `%||%` <- function(L,R)

[R-pkg-devel] new/slightly mysterious CRAN warnings

Submission of most recent version of lme4 threw a NOTE on CRAN's Debian platform that we had not seen when running "R CMD check --as-cran" with the most recent SVN checkout, nor when submitted to win-builder/R-devel. These are legitimate issues (all now fixed), but we were taken by surprise

Re: [R-pkg-devel] Replacing dplyr by stats functions

    If you use Depends: in your package I think this is unavoidable (but, I don't think these should be counted against you as warnings by CRAN - they're "Warnings" not "WARNINGs" :-) )    The only way I know of to avoid this would be to Import: rather than Depend:, and import only the

Re: [R-pkg-devel] Checking timings of packages

I would try running them on https://win-builder.r-project.org/ . If the Windows timings are OK on that platform I think you can make a good case to CRAN that you've done your best ... On 2023-03-14 9:52 a.m., Chris Brien wrote: Dear list members. I have run into a problem with examples

[R-pkg-devel] URL timeout in win-builder check: suggestions?

of fluff (click through if you want to see), but I don't want it causing hiccups in my CRAN submission (i.e., I could take it out if necessary but would prefer not to ...) Suggestions? === * checking CRAN incoming feasibility ... NOTE Maintainer: 'Ben Bolker ' Found the following (possibly

[R-pkg-devel] FAIL output in CRAN checks?

forms() Error in curl::curl_fetch_memory(url, handle = handle) :   Peer certificate cannot be authenticated with given CA certificates: [builder.r-hub.io] SSL certificate problem: certificate has expired   I guess I could report that ...   cheers    Ben Bolker ___

Re: [R-pkg-devel] Package submission rejected as it fails checks on Debian

Not important (of course) but where does the 5000 kWh per tree number come from? Is that (dry weight) x (50% carbon per dry weight) / (carbon content of CO2 emissions per kWh) ? https://www.epa.gov/energy/greenhouse-gas-equivalencies-calculator#results If we say 200 watts x 15 minutes

Re: [R-pkg-devel] CRAN Packages over 5 MB & Time Length for Manual Inspection

Out of curiosity, what was the recently added package? It looks like the previous version of your package from about a year ago is only a 1.2MB tarball. Also out of curiosity, what caused the increase? cheers Ben Bolker On 2023-01-29 1:53 p.m., EcoC2S - Irucka Embry wrote

Re: [R-pkg-devel] Pretest failed and I fail to find out what's the problem

Seems pretty mysterious to me! (No cryptic NOTEs anywhere in the logs, other than the inevitable "Note_to_CRAN_maintainers") I will be curious to see if anyone else finds something, but my guess is a hiccup on the CRAN end (i.e., you'll end up sending e-mail to the CRAN maintainers to

Re: [R-pkg-devel] Mysterious "invalid z limit"

On 2023-01-08 1:38 p.m., Spencer Graves wrote: On 1/8/23 11:36 AM, Kevin Coombes wrote: I have been using R-Forge for many years for package development. And I have been using GitLab for other projects almost as long. However, over the past few months, the R-Forge support seems to be

Re: [R-pkg-devel] How to reduce examples in a package that takes more than 5 seconds to run?

On 2022-12-15 9:57 a.m., Brian G. Peterson wrote: On 12/15/22 08:34, Ismail Otoakhia wrote: The R package 'ardl.nardl' has some examples that take more than 5 seconds to run. I was advised by the CRAN team to reduce the run time to less than 5 seconds. How can this be achieved? - you

Re: [R-pkg-devel] Issue handling datetimes: possible differences between computers

Right now as.POSIXlt.Date() is just function (x, ...) .Internal(Date2POSIXlt(x)) How expensive would it be to throw a warning when '...' is provided by the user/discarded ?? Alternately, perhaps the documentation could be amended, although I'm not quite sure what to suggest. (The sentence

Re: [R-pkg-devel] Found the following (possibly) invalid URLs:

I get a 404. On 2022-09-29 4:50 p.m., Roy Mendelssohn - NOAA Federal via R-package-devel wrote: In testing a new version of one of my package on win builder, I get the following: Found the following (possibly) invalid URLs: . . . URL:

Re: [R-pkg-devel] Package ‘wflo’ was removed from the CRAN repository.

the NOTE definitely seems like something CRAN would object to, so you should fix it before resubmitting ...) good luck, Ben Bolker On 9/22/22 4:15 PM, Carsten Croonenbroeck wrote: Hi Lluís, thanks for the clarification. And kudos to your detective flair. I’m serious about that, as I would

Re: [R-pkg-devel] Warning... unable to translate 'Ekstrm' to a wide string; Error... input string 1 is invalid

 The help pages are at https://github.com/wch/r-source/blob/trunk/src/library/base/man/iconv.Rd or the equivalent at https://github.com/r-devel/r-svn or https://svn.r-project.org/R/trunk/src/library/base/man/iconv.Rd   they still have \x examples in them, but maybe the use of \x is not

Re: [R-pkg-devel] DOI / URL issues in package vignettes

On 2022-05-18 6:56 a.m., Ivan Krylov wrote: В Wed, 18 May 2022 12:06:03 +1000 Joshua Wiley пишет: curl -I -L https://doi.org/10.1037/met434 gives the below on my system, which (I think?) means you get the expected redirect for a DOI and then a 403 forbidden error. On the

[R-pkg-devel] nit-picking about CRAN repository policy

ey refine their 'noSuggests' test so that it conforms to the wording in the CRP, or that they change the CRP wording to something stricter like > Any package listed in ‘Suggests’ or ‘Enhances’ should be used conditionally in examples, tests, and vignettes. ? cheers

Re: [R-pkg-devel] Using \donttest with R >= 4.0.0

(This crossed with Martin Ondrus's reply). In the past few years CRAN screeners have gotten more strict about \dontrun{}; a first-round screening often comes back requesting that \dontrun{}, and commented-out examples, not be used.

Re: [R-pkg-devel] [Tagged] Re: multithreading in packages

FWIW there is some machinery in the glmmTMB package for querying, setting, etc. the number of OpenMP threads. https://github.com/glmmTMB/glmmTMB/search?q=omp On 10/9/21 11:45 AM, Vladimir Dergachev wrote: On Sat, 9 Oct 2021, Jeff Newmiller wrote: Keep in mind that by embedding this

Re: [R-pkg-devel] [External] Formula modeling

There's a Formula package on CRAN that's designed for this use case. lme4 and nlme don't use it, but implement their own formula manipulation machinery. (The cleanest version of this machinery is actually in glmmTMB at

Re: [R-pkg-devel] Internet resources and Errors

I think you're not supposed to stop(). You should just proceed with the other tests (skipping any tests/examples that depend on access to the inaccessible internet resources, or values derived from the failing call, to work) Does that help? On 9/24/21 10:49 AM, Roy Mendelssohn - NOAA

Re: [R-pkg-devel] Solaris segfaults

hurdle I encountered last time I tried, it was probably some weird idiosyncratic thing. For the record I haven't tried valgrind recently, but the CRAN versions of the valgrind tests weren't throwing any errors ... https://cran.r-project.org/web/checks/check_issue_kinds.html thanks Ben Bolk

[R-pkg-devel] Solaris segfaults

ithub.com/glmmTMB/glmmTMB/issues/732 (with some red herrings) if anyone is interested. cheers Ben Bolker __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] (no subject)

cieve more mails. *Best regards,* *Krishan Gupta* *PhD scholar, the Sengupta Laboratory* [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel chee

Re: [R-pkg-devel] Solaris Support

.] So, at least as far as publicly viewable policies go, the CRAN maintainers would be able to ask you to make "all reasonable efforts". (In my opinion, figuring out how to make your package work properly with ODS 12.6 would take more than a "reasonable" effort, but .. ??

Re: [R-pkg-devel] Expired Incoming Package

That would be my best guess. On 8/23/21 3:19 PM, Reed A. Cartwright wrote: If my submission is no longer visible using foghorn::cran_incoming(), that means it has expired and I should resubmit, right? -- Reed A. Cartwright, PhD Associate Professor of Genomics, Evolution, and Bioinformatics

[R-pkg-devel] advice on reminders/nags to CRAN maintainers

but I'm loath to do that unnecessarily ... thoughts? Ben Bolker --- (Some previous history omitted here for brevity; there had been a bit of back-and-forth about this package previously.) 07/30: Submitted version 1.1.2.2 of the glmmTMB package. Got a "pretest-waiting-recheck"

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

participates in the discussion on r-devel and is convinced of the utility and harmlessness of your modifications the last step might be unnecessary). cheers Ben Bolker On 7/23/21 1:17 PM, David Norris wrote: My understanding about this issue with progressr is that it is nontrivial

Re: [R-pkg-devel] best LICENSE practices: AGPL-3 + LaTeX Project Public License

there (as the required files seem to be present on every _other_ Linux platform I've tried). (For future readers/references, the huxtable package is driving these requirements.) cheers Ben Bolker On Thu, Jul 15, 2021 at 9:49 PM Hadley Wickham wrote: > > On Wed, Jul 14, 2021 at 9:11 AM Ben Bolker

Re: [R-pkg-devel] best LICENSE practices: AGPL-3 + LaTeX Project Public License

quot;AGPL-3 + file LICENCE" ? * Do I just include the files without comment, since I have complied (as far as I can tell) with the terms of the LPPL? * Is there a way to signal to R CMD check that I *have* complied with the terms?    cheers     Ben Bolker ___

[R-pkg-devel] best LICENSE practices: AGPL-3 + LaTeX Project Public License

(as far as I can tell) with the terms of the LPPL? * Is there a way to signal to R CMD check that I *have* complied with the terms? cheers Ben Bolker __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] clarification about missing suggested packages.

standing on CRAN but is not available on a particular CRAN testing platform, as long as package A only uses package B conditionally. Thoughts/opinions/evidence? cheers Ben Bolker --- From the current CRAN policy: Packages on which a CRAN package depends should be available from a mains

Re: [R-pkg-devel] weird C stack traces from win-builder, due to brms/rstan load?

On 7/5/21 2:01 PM, Duncan Murdoch wrote: On 05/07/2021 10:32 a.m., Ben Bolker wrote:    I'm running into trouble checking a new release of the 'broom.mixed' package <https://cran.r-project.org/web/packages/broom.mixed/index.html> on win-builder.  I think it is some kind of rstan p

[R-pkg-devel] weird C stack traces from win-builder, due to brms/rstan load?

with one of the brms references avoided instead runs into trouble when loading rstan ...), I don't see what I can do ... <https://win-builder.r-project.org/YArr24tuYZ8G/00check.log> cheers Ben Bolker __ R-package-devel@r-project.org mai

Re: [R-pkg-devel] How to sent possible bug report to maintainer

I did some web searching. "Xiang Lyu Purdue" doesn't turn up anything current/useful, but there appears to be someone with the same name in the Biostats PhD program at Berkeley , who *might* be the same person.

Re: [R-pkg-devel] pairwiseAlignment

of bioinformatics people) You may be asked to provide a reproducible example (e.g. by simulation or random generation ...) cheers Ben Bolker On 6/16/21 9:14 PM, csmatyi wrote: Hello, I am trying to align two sequences, in DNAString format using the R command pairwiseAlignment. I keep

Re: [R-pkg-devel] Question about preventing CRAN package archival

the compatibility requirements? I will attempt to reach out to the package author - thanks for your help! On Wed, Jun 2, 2021 at 10:31 AM Ben Bolker wrote: That all sounds exactly right. GPL >= 2 allows you to use the material without asking permission as long as your package is com

Re: [R-pkg-devel] Question about preventing CRAN package archival

ity confusion, but I rate that as unlikely based on other facebook snooping) I don't think a short, polite e-mail request would be out of bounds, they can always ignore it or tell you to go away. cheers Ben Bolker On 6/2/21 1:15 PM, Ben Staton wrote: Hello, Thank you for your detailed l

Re: [R-pkg-devel] Puzzling error from win-builder

Without thinking about it very much, my first guess would be that this is a transient problem on win-builder, i.e. the caret package is temporarily unavailable for some reason (e.g. because some update step hung); a new version of the package was published *fairly* recently (2021-05-15),

Re: [R-pkg-devel] autotesting on GitHub with Travis or ...?

GitHub Actions ?usethis::use_github_action Probably start here if you are moving from Travis: https://deanattali.com/blog/migrating-travis-to-github/ On 5/13/21 8:00 PM, Spencer Graves wrote: Hello, All:   What are the current recommendations for automatic testing of an R

Re: [R-pkg-devel] Using ggplot2 within another package

red in the environment that contains FUN. -Bill On Sat, Apr 24, 2021 at 6:18 AM Martin Maechler mailto:maech...@stat.math.ethz.ch>> wrote: >>>>> Ben Bolker >>>>>     on Thu, 22 Apr 2021 17:27:49 -0400 writes:     > For some reason tha

Re: [R-pkg-devel] Using ggplot2 within another package

For some reason that I don't remember, an R core member once told me that they prefer x <- y <- NULL to utils::globalVariables(c("x","y")) - although I have also encountered problems with that strategy in edge cases. Here's an example from StackOverflow from today where for some reason I

Re: [R-pkg-devel] R CMD build --resave-data not working

Hmm, I may have written too quickly. I find these lines from R CMD build --help confusing: --resave-data=re-save data files as compactly as possible: "no", "best", "gzip" (default) --resave-data same as --resave-data=best The first line suggests

Re: [R-pkg-devel] R CMD build --resave-data not working

maybe R CMD build --resave-data=best ... ? On 3/11/21 3:57 PM, Jonathan Callahan wrote: I am building a package using R 4.0.4 on OS X 10.15.7. In a terminal I type: R CMD build --resave-data AirSensor Then, I check with: R CMD check --as-cran AirSensor_1.0.8.tar.gz Everything is fine

Re: [R-pkg-devel] Note_to_CRAN_mainteners

As far as I know, this is a harmless note and can be disregarded. (And, can't be eliminated.) (It would be nice if that were clearer in the documentation ... maybe it is and I just haven't checked lately ...) On 3/11/21 2:16 PM, William Andrés Herrera Cáceres wrote: Hi everyone, I am a

Re: [R-pkg-devel] testing for NaN in C++ code

On Fri, Mar 5, 2021, 20:55 Ben Bolker <mailto:bbol...@gmail.com>> wrote: I would like to test for NaN inside C++ code that lives inside a CRAN package. Following the StackOverflow question linked below, I was using #define isNAN(a)  (a!=a) which I *think* use

[R-pkg-devel] testing for NaN in C++ code

the problem upstream and detect it where it happens (see the answer titled "nan prevention" on SO), but in the meantime it would be nice to be able to do this robustly across all the platforms it's likely to see. cheers Ben Bolker https://stackoverflow.com/questions/57066

Re: [R-pkg-devel] Advice on R-forge to Github migration

I think it should be fine to have your package in a subdirectory: this works as expected. remotes::install_github("dmurdoch/rgl/pkg/rgl") The only disadvantages to this structure are (1) it's a little bit surprising to users (who might try install_github("r-forge/rgl" and wonder why it

Re: [R-pkg-devel] Advice on R-forge to Github migration

I think it should be fine to have your package in a subdirectory: this works as expected. remotes::install_github("dmurdoch/rgl/pkg/rgl") The only disadvantages to this structure are (1) it's a little bit surprising to users (who might try install_github("r-forge/rgl" and wonder why it

[R-pkg-devel] GitHub actions incantation for package living in a subdirectory?

on with a working GH actions setup)? Recent attempts: https://github.com/glmmTMB/glmmTMB/commits/github_actions Most recent attempt: https://github.com/glmmTMB/glmmTMB/commit/d1a08058636df0a4835f897d1e43909510f9c652 happy holidays to all ... Ben Bolker

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

On 12/12/20 5:53 PM, Duncan Murdoch wrote: On 12/12/2020 4:41 p.m., Ben Bolker wrote: On 12/12/20 4:08 PM, Spencer Graves wrote: Hi, Ben et al.: On 2020-12-12 13:43, Ben Bolker wrote:     Apologies if I'm telling you something you already know:     By default, fda::CRAN() uses

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

On 12/12/20 5:50 PM, Duncan Murdoch wrote: On 12/12/2020 4:08 p.m., Spencer Graves wrote: Hi, Ben et al.: On 2020-12-12 13:43, Ben Bolker wrote:     Apologies if I'm telling you something you already know:     By default, fda::CRAN() uses the presence of environment variables matched

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

On 12/12/20 4:08 PM, Spencer Graves wrote: Hi, Ben et al.: On 2020-12-12 13:43, Ben Bolker wrote:    Apologies if I'm telling you something you already know:    By default, fda::CRAN() uses the presence of environment variables matched by the regexp "^_R_" as a heuristic

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

Apologies if I'm telling you something you already know: By default, fda::CRAN() uses the presence of environment variables matched by the regexp "^_R_" as a heuristic to decide whether it's being running on CRAN. testthat::skip_on_cran() calls testthat::on_cran() to look for an

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

I think you're supposed to skip the example (throwing a warning, if you like ...) if rgl isn't available, rather than throwing an error ... ? On 12/12/20 11:24 AM, Michael L Friendly wrote: I got the email below concerning 3 of my packages but wonder if they are false alarms or if not, how

Re: [R-pkg-devel] Assigning a variable to global environment

e best to find a way to solve your problem without assigning to the global workspace. Can you assign to an environment that is contained within your package, which all of the functions in your package will also have access to? cheers Ben Bolker On 12/11/20 1:52 PM, Tiago Olivoto wrote:

Re: [R-pkg-devel] Conditional timeout for httr request when running R CMD check

  as pointed out to me the last time I was struggling with similar issues, if (interactive()) { ... } is another potential solution On 11/30/20 2:48 PM, Henrik Bengtsson wrote: The problem here was regarding user facing example():s, not package tests. In order to keep a neat example for the

Re: [R-pkg-devel] devtools::release() does not release

Maybe off-topic, but I see that the tarball is 100+Mb ... won't that raise flags upon CRAN submission? (The current CRAN tarball is <1 Mb ...) From the CRAN policies, there's no explicit limit given but ... = Packages should be of the minimum necessary size. Reasonable compression

Re: [R-pkg-devel] help interpreting a response from CRAN

ons are typically sufficient for tests. It is also possible to run less important tests only conditionally if some environment variable is set that you only define on your machine. Best, Uwe Ligges On 22.11.2020 20:36, Dirk Eddelbuettel wrote: On 22 November 2020 at 13:44, Ben Bolker wrote: |   

Re: [R-pkg-devel] help interpreting a response from CRAN

problems, but it's hard and time-consuming (at least for me) ... cheers Ben Bolker On 11/22/20 4:06 PM, Uwe Ligges wrote: Thanks Dirk. Yes, for lme4 the tests for each archiecture take longer than 5 min, so the overall check time exceeds 10 min. So one can follow Dirk's advise

[R-pkg-devel] help interpreting a response from CRAN

o be run on 386 and x64 ...) An alternative is that this is a confusingly worded message indicating that there are strong rev dependencies so the package needs to be further checked? (That seems unlikely as it explicitly asks me to resubmit) Can anyone confirm/support those guesses? cheers Ben

Re: [R-pkg-devel] Best practise in including third party code

or other improvements in the upstream code. cheers Ben Bolker On Wed, Nov 18, 2020 at 5:45 AM Wolfgang Lenhard wrote: > > Dear R developer list, > in general, if functionality from other packages are used in one's own > package, it is of course the best way to declare the o

Re: [R-pkg-devel] Run-times of examples in vignettes

My general solution is to run time-consuming computations in advance and store the results in (e.g.) inst/vignette_data, whence they can be retrieved via system.file("vignette_data", "output.rda", package="my_pkg"). (I might also include the R script required to generate the file so that

Re: [R-pkg-devel] Pre-test failure

Can you share the links to the CRAN pre-test logs? Someone here might be able to guess what went wrong ... (FWIW I always *think* I'm testing very carefully, and I almost always get something wrong ...) On 10/23/20 11:18 AM, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: I

Re: [R-pkg-devel] Usage of internet resources in examples

On 10/20/20 5:10 PM, Gábor Csárdi wrote: On Tue, Oct 20, 2020 at 10:07 PM Ben Bolker wrote: On 10/20/20 4:51 PM, Gábor Csárdi wrote: On Tue, Oct 20, 2020 at 9:45 PM Ben Bolker wrote: [...] if (testthat::skip_on_cran()) all seem like reasonable solutions. I don't think you can

Re: [R-pkg-devel] CRAN pending status , left up in the air

My 'revdepcheck' is obsolete, superseded by r-lib/revdepcheck (which it does predate by about a year ...) Dirk Eddelbuettel maintains an automated system for diffs of the CRAN repository policy https://github.com/eddelbuettel/crp , or follow @CRANPolicyWatch -- similar to your idea about

[R-pkg-devel] checking windows timing?

ecked on both i386 and x86_64 architectures). Testing is currently taking 6 minutes on my local machine (newish Ubuntu 18.04 laptop), so I guess have more work to do, but I wonder if anyone has suggestions ... cheers Ben Bolker __ R-pa

Re: [R-pkg-devel] puzzling CRAN rejection

On 10/12/20 7:37 PM, Duncan Murdoch wrote: On 12/10/2020 6:51 p.m., Ben Bolker wrote: On 10/12/20 6:36 PM, Duncan Murdoch wrote: On 12/10/2020 6:14 p.m., Ben Bolker wrote: I'd say a mismatch in saved output isn't a small problem, it's either a too-sensitive test or something

Re: [R-pkg-devel] puzzling CRAN rejection

On 10/12/20 6:36 PM, Duncan Murdoch wrote: On 12/10/2020 6:14 p.m., Ben Bolker wrote: I'd say a mismatch in saved output isn't a small problem, it's either a too-sensitive test or something serious. Duncan Murdoch     That's fair enough, but it would be nice if (1) this were a NOTE

Re: [R-pkg-devel] puzzling CRAN rejection

I'd say a mismatch in saved output isn't a small problem, it's either a too-sensitive test or something serious. Duncan Murdoch That's fair enough, but it would be nice if (1) this were a NOTE and (2) it were made explicit in the CRAN policy that, *except by special exception*, an

Re: [R-pkg-devel] puzzling CRAN rejection

o I interpret correctly that the advice is to address this problem, bump the version number, and re-submit? cheers Ben Bolker On 10/12/20 5:18 PM, Uwe Ligges wrote: Actually more than 23 minutes check time for a single package is really excessive, can you pls cut that down? This comes f

  1   2   >