[R-pkg-devel] Running tests on 32-bit and 64-bit

and 64-bit. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may

Re: [R-pkg-devel] Running tests on 32-bit and 64-bit

, Kasper On Mon, Aug 17, 2015 at 5:03 AM, Thierry Onkelinx thierry.onkel...@inbo.be wrote: Dear all, Is there an easy way to run the tests of a package on both a 32-bit and 64-bit version? Ideally it should work when using R CMD check --as-cran on all OS's. Although I expect that multi

[R-pkg-devel] Define S4 method for generic in other package

, signature = signature(A = myClass), definition = function( a, b ){ bar( a = myClass@A, b = myClass@B ) } ) When I build my package I get the error no existing definition for function 'bar'. Any suggestions? Best regards, ir. Thierry Onkelinx Instituut voor natuur- en

Re: [R-pkg-devel] Define S4 method for generic in other package

Dear Hadley, I've put a reproducible example at https://github.com/ThierryO/testS4 Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat

Re: [R-pkg-devel] Writing a portable package that imports functions only available on Windows

Have a look at the RODBC package. odbcConnectAcces() is only available on Windows. Op 19-sep.-2015 12:08 schreef "Richard Cotton" : > I have a package that uses win.version from the utils package. > > I've made my R code safe to use across platforms, I check that the OS is

Re: [R-pkg-devel] Absent variables and tibble

Dear Russell. The assertthat package (by Hadley) provides a has_name() function. > library(assertthat) > x <- data.frame(y = NA) > has_name(x, "y") [1] TRUE > has_name(x, "x") [1] FALSE Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderz

Re: [R-pkg-devel] Data-generating scripts in R packages

. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is

Re: [R-pkg-devel] Has GitHub been used as a CRAN-style repository?

Dear Bruce, Have a look at drat: http://dirk.eddelbuettel.com/code/drat.html I think that is what you are looking for. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics &

Re: [R-pkg-devel] Encoding problem

Dear David, Have you tried removing the exclamation mark in %!\VignetteEncoding{UTF-8}? I think it should be %\VignetteEncoding{UTF-8} Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg /

Re: [R-pkg-devel] package API change

between using the old version which still works but no longer maintained or the switched to the new version which is maintained but will break existing code. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie

[R-pkg-devel] Conflicting S3 imports?

quot;cA") has a slot of class "maybeInla", which is defined as setClassUnion("maybeInla", c("inla", "NULL")) - The "cA" class uses a slot of class "cB". "cB" is imported from package "B". Can someone explai

Re: [R-pkg-devel] Interplay between knitr() and View()

Dear Roy, In case you create a HTML vignette you can use datatable() from the DT package. That creates a dynamic table in the output. Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg /

Re: [R-pkg-devel] Doubt about adding files to a R package

Dear Dario, The attachments got stripped from the mail by the server. Can you provide a link to the results of R CMD check and the source code of the package? Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie

Re: [R-pkg-devel] package installation fails due to missing package not listed in NAMESPACE

Dear Jonathon, Is ggplot2 listed in the DESCRIPTION file? It needs to be at least in the Suggests: Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality A

Re: [R-pkg-devel] package installation fails due to missing package not listed in NAMESPACE

Try adding requireNamespace("ggplot2") in the function that rely on ggplot2. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070

Re: [R-pkg-devel] package installation fails due to missing package not listed in NAMESPACE

Yes. That is what I meant (but too lazy to write). ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the stat

Re: [R-pkg-devel] R force download of specific package versions in DESCRIPTION file

Dear Martin, We use Docker to create an image with R and specific versions of the required packages. You can find our docker image and the source code at https://hub.docker.com/r/inbobmk/rstable/ Best regards, ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute

[R-pkg-devel] loadMethod() not available with Rscript

, ...) : could not find function "loadMethod" loadMethod() is NOT used in mypackage and not imported. library(mypackage) my_function() Best regards, ir. Thierry Onkelinx Statisticus/ Statiscian Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH

Re: [R-pkg-devel] loadMethod() not available with Rscript

regards, ir. Thierry Onkelinx Statisticus/ Statiscian Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance thierry.onkel...@inbo.be Kliniekstraat 25

Re: [R-pkg-devel] tibbles are not data frames

to the _user_ to provide a data.frame (and a tibble is not a data.frame). Documenting this in the package documentation/FAQ or issuing a warning "don't use tibble" when the package is loaded should be sufficient. Best regards, ir. Thierry Onkelinx Statisticus/ Statistician Vlaamse Overheid /

Re: [R-pkg-devel] Fw: [CRAN-pretest-archived] CRAN submission nnfor 0.9

Dear Nikos, Your examples are taking too much time. Make them run faster. Or remove some of them. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team

[R-pkg-devel] creating indelible file during unit test

Sys.chmod(file, "000") which didn't work. Any suggestions? Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / T

Re: [R-pkg-devel] Help with Devtools Error

Dear Adrian, Answering this would be much easier when you have access to the code. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie

Re: [R-pkg-devel] Fixed for messages

using pdf as output format for the vignette? Consider using rmarkdown::html_vignette. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

s("LM2GLMM") or update.packages() Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Qua

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

Dear Alex, Another idea is to use pkgdown (http://pkgdown.r-lib.org) to convert all the documentation of your package (include the vignettes) into a website. Then you make that available to your students, e.g. through github pages. Best regards, ir. Thierry Onkelinx Statisticus / Statistician

Re: [R-pkg-devel] Warning: rBind is deprecated-- but I don't call it

Dear Bill, The best way to fix your problem is IMHO to have it fixed in lme4. I've cc'ed Ben Bolker (lme4 maintainer) to inform him of this problem. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

You can make things even a bit easier by setting "eval=myeval" and set "myeval <- FALSE" at the top of the vignette. In case you want to update the figures, you only have to set "myeval <- TRUE" and run the vignette. ir. Thierry Onkelinx Statisticus / Statist

[R-pkg-devel] txt data is undefined global variable

global variable" error. What is the proper way to use txt data in a package? Best regards, Thierry ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie &

Re: [R-pkg-devel] License of pre-built vignettes

describing and linking to the precompiled vignettes. Something like browseURL(system.file("precompiled.html", package = "yourpackage")) Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK

Re: [R-pkg-devel] MiKTex v. TeX Live?

Dear Spencer, I assume you are using R **3**.6.2. Consider TinyTeX (https://yihui.org/tinytex/). I found that working fairly easy on Windows machines, even by users without admin privileges. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government

Re: [R-pkg-devel] How to provide a finalized PDF file in a package?

Dear Neonira. Whatever file you place in the inst folder, will be available for the users when they install the package. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE

Re: [R-pkg-devel] Add SystemRequirements of imported package in description file?

Dear Dominik, IMHO you only need to list "first order" dependencies: things that your package directly uses. Listing higher order dependencies would be redundant as they are listed in the packages that have them as first order dependency. Best regards, ir. Thierry Onkelinx S

Re: [R-pkg-devel] DOI for archived package?

citations. So I won't waste time arguing over this and use that time to put it on Zenodo. Best regards, PS Zenodo is well funded (https://about.zenodo.org/infrastructure/) and IMHO equally likely to be permanent as CRAN is. ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid

Re: [R-pkg-devel] Formatting .Rbuildignore

Thanks for the feedback. It seems like I was under the impression that .Rbuildignore would follow similar rules as .gitignore. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE

[R-pkg-devel] Formatting .Rbuildignore

Dear all, Can we add blank lines in .Rbuildignore? Or lines with only comments (line starting with #)? Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team

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

/bad8a4cf42049faa72a04b202c5a4dfc233b4046/vignettes/efficiency.Rmd#L293 for an example. ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biomet

Re: [R-pkg-devel] Cache in vignette not working when checking a package

Dear Jose, I store the results of CPU intensive chunks in the package. Have a look at https://github.com/ropensci/git2rdata/blob/master/vignettes/efficiency.Rmd. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN

Re: [R-pkg-devel] Cache in vignette not working when checking a package

Probably because the cache is not installed into the package. I'd check the tar.gz file to see if the cache is present. ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team

Re: [R-pkg-devel] Cache in vignette not working when checking a package

That will be hard to do without your package. Note that I've suggested a work around in my first reply. ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie

[R-pkg-devel] rcmdcheck reports wrong version of lattice

21-03-08 ─ Packages package * version date lib source lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4) ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOS

Re: [R-pkg-devel] rcmdcheck reports wrong version of lattice

ibrary") solved the problem. So it looks like rcmdcheck ignored the first element of .libPaths(). I'm not sure if that is a bug of rcmdcheck. Shall I report an issue? Best regards, Thierry ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTI

[R-pkg-devel] which functions to deprecate

function. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance thierry.onkel...

[R-pkg-devel] circular suggested packages

in qrcode? And thus requiring qrcode to list opencv as a suggested package. I know this is not allowed when depending or importing packages. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH

Re: [R-pkg-devel] [External] circular suggested packages

The goal of opencv is to provide bindings to 'OpenCV' Computer Vision Library. Hence a much wider scope than just reading qrcodes. qrcode just focusses creating different qrcodes. The fact that they can use each other to test themselves is a happy coincidence. ir. Thierry Onkelinx Statisticus

Re: [R-pkg-devel] Question regarding listing base and recommended packages programmatically and efficiently

Dear Tony, Much will depend on what information you need from the output of installed.packages()? Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team

Re: [R-pkg-devel] Guidance on splitting up an R package?

Dear Vincent, Have a look at the spatstat package which was split into several smaller packages (https://github.com/spatstat/spatstat). Maybe the maintainers of that package can share some insights. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government

Re: [R-pkg-devel] Questions regarding a new (seperated package) and how to submit them to cran

loop. Best regards, ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance thierry.onkel...@inbo.be Have

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

The cascade is even longer. prediction got archived because ffbase was no longer available. https://cran.r-project.org/web/packages/ffbase/ ir. Thierry Onkelinx Statisticus / Statistician Vlaamse Overheid / Government of Flanders INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE