Re: [R-pkg-devel] First CRAN submission - quick feedback

Generally you will want to use an application directory for storing these files (a la rappdirs) and, importantly, allow the user to consent to these files being downloaded and installed, which should not be done on load. On Sun, Mar 12, 2023 at 13:24 Ronald Bergmann wrote: > Hi r-package-devel,

Re: [R-pkg-devel] Current recommendations re. GitHub Action?

This warning says to update to v2 of the action from r-lib: Warning: r-lib/actions/setup-r@v1 is deprecated. Please update your > workflow to use the 'v2' version. Also look at the examples at > https://github.com/r-lib/actions/tree/v2/examples because '@v2' workflows > are much simpler than 'v1'

[R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

Hello, I noticed a strange error pop up for R-devel (2020-06-12 r78687) check on travis: https://travis-ci.org/github/grunwaldlab/poppr/jobs/697831376#L4653-L4654 * checking Rd cross-references ... WARNING Non-file package-anchored link(s) in documentation object 'aboot.Rd': ‘[ape:phylo]{ape:

Re: [R-pkg-devel] Proper way to ask a user to set permanent variables?

Options are not persistent between sessions unless the user wants them to be. You can have users set the options in their .Rprofile either in the working directory of the project or their home directory. This is the method that the {usethis} package has for storing default names. The only downside

Re: [R-pkg-devel] potential memory leak using openMP

I've had a problem like this before and I also thought that it was due to some weird magic in OpenMP, but it turned out to be a fence-post error on my part [1]. Unfortunately, the valgrind output is not as helpful as something like ASAN. My suggestion would be to go through that section of the code

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

/path/to/poppr > > Suggestion: > > Add a blank line before > >Examples of analyses are available in a primer written by Niklaus > J. Grünwald, Zhian N. Kamvar, and Sydney E. Everhart at > \url{http://grunwaldlab.github.io/Population_Genetics_in_R}.} > Zhian On Tue,

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

ou may have to make > more drastic omissions or additions in order for compilation to succeed. > > On Wed, 19 Jun 2019 at 12:37 am, Zhian Kamvar wrote: > >> Hello, >> >> I'm having a really strange problem that I cannot reproduce locally >> (Ubuntu >>

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

Hello, I'm having a really strange problem that I cannot reproduce locally (Ubuntu bionic) or on Rhub. I've run into an issue where the R package manual is failing only on this platform with ancient LaTeX runes that I struggle to decipher [0] > * checking PDF version of manual ... WARNING > LaTeX

Re: [R-pkg-devel] Proper way to document helper functions not accessible by user.

You can add #' @noRd to those functions and roxygen2 will not generate .Rd files for those entries. On Mon, Aug 13, 2018 at 2:08 PM Eggleston, Barry wrote: > Hello, > > I am working through my first submission and making good progress with the > CRAN review system, but now I need to understand

Re: [R-pkg-devel] Printing examples conditionally on another package in Suggests

l Message- > From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On > Behalf Of Zhian Kamvar > Sent: 10 August 2018 12:26 > To: Alexandre Courtiol > Cc: R-list Package Devel > Subject: Re: [R-pkg-devel] Printing examples conditionally on another > package in Suggests

Re: [R-pkg-devel] Printing examples conditionally on another package in Suggests

if (requireNamespace("some.package", quietly = TRUE)) > print(x) > Print("Hi") > Print("Hello") > Print("Goodbye") > > > > On Fri, 10 Aug 2018 at 12:33, Zhian Kamvar wrote: > >> Mainly, I would like to see the value printed after the p

Re: [R-pkg-devel] Printing examples conditionally on another package in Suggests

at 11:28 AM Alexandre Courtiol < alexandre.court...@gmail.com> wrote: > Hi Zhian, > Could you please explain what behaviour you would like to obtain? > I really don't understand what your problem is from your description... > Alex > > On Fri, 10 Aug 2018 at 12:18, Zhian

[R-pkg-devel] Printing examples conditionally on another package in Suggests

Hello, I know it's good practice to use if (require("some_package")) { # some code that needs some_package } In R examples that needs a package listed in Suggests. The problem with this approach is that if there are any print statements within this structure, then they only get printed after

Re: [R-pkg-devel] Can Submission Failure

Copy this output into a file called .Rbuildignore at the top of the directory: > .DS_Store > .RData > .Rhistory > ._* > .gitignore > .travis.yml > R/.DS_Store > R/._* > data/.DS_Store > data/.Rapp.history > man/.Rapp.history > vignettes/._* > vignettes/.gitignore > .Rproj.user > .gi

Re: [R-pkg-devel] Package builds, installs, and runs but does not pass devtools::check()

Using dplyr like that is for exploratory data analysis. You'll want to refer to dplyr's "Programming with dplyr" vignette for using dplyr in a package: https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html

Re: [R-pkg-devel] CRAN stable download url?

You might try using MRAN snapshots: https://mran.revolutionanalytics.com/documents/rro/reproducibility#standard For example: https://cran.microsoft.com/snapshot/2018-01-01/src/contrib/yaml_2.1.16.tar.gz

Re: [R-pkg-devel] Guidance on importind multiple text files for @example

I sent this earlier, but from a different email and it bounced on the list: You might try placing a directory (e.g. foo) of a few small dummy text files in inst/ and then in the example use: system.file("foo") as the input to your example. That being said, system.file() often confuses users, s

Re: [R-pkg-devel] Issue with including vignettes without building package

Perhaps you could add a Makefile with a rule that compiles the vignettes into the inst/doc directory? This might avoid the build process. - Zhian N. Kamvar, Ph. D. Postdoctoral Researcher (Everhart Lab) Department of Plant Pathology University of Nebraska-Lincoln > On Apr 20, 2017, at 15:3

Re: [R-pkg-devel] UseR! Session: Navigating the jungle of R packages.

Hello, Jumping in here because those of us in the population genetics community have semi-recently tried to tackle some of these issues of giving users a clear sense of how R packages can work together in an analysis [0]. We created a website [1] that hosts vignettes openly contributed and cura

[R-pkg-devel] Change in maintainer email address

Hello, Does anyone have experience in the process needed to change the maintainer's email address on a package? Should the the maintainer preemptively send an email to CRAN notifying the upcoming change, or should the package be submitted first? Thanks, Zhian __

Re: [R-pkg-devel] Build fails on Mavericks

Might it be an issue with your Makevars file? As far as I can tell, by default, OS X sets clang as the C compiler. If you installed gcc separately, then you have to tell R to use it in ~/.R/Makevars Here's an example of my Makevars file so that I can run C code with openmp: https://gist.github.

Re: [R-pkg-devel] [[openmx-dev]] Re: [[openmx-dev]] Re: openmp

The way several packages have implemented OpenMP is to wrap it in pre-compiler statements i.e.: // Include openMP if the compiler supports it #ifdef _OPENMP #include #endif This way, all compilers can build the code and those that have OpenMP (even modified versions of clang: https://clang-omp

[R-pkg-devel] How often does the r-devel docker file update?

Hello, I maintain a package that is going to be submitted for an update very soon. I utilize https://registry.hub.docker.com/u/rocker/r-devel/ to check my package with r-devel, but I cannot detect a pattern as to how often it updates. Is there a clear schedule of how often it updates? The reaso

Re: [R-pkg-devel] no visible global function definition

Does this also mean that we now need to include these packages (stats, graphics, etc) in the Imports field of the DESCRIPTION? Thanks, Zhian > On Jun 29, 2015, at 10:09 , Kevin Ushey wrote: > > Hi Uwe, > > It seems like this is quite a major change; I imagine it will affect many > packages (si

Re: [R-pkg-devel] how to skip tests on CRAN but NOT on travis-ci?

I don't know if this is the best way to do it, but I've been using the covr package (https://github.com/jimhester/covr) to run all of my tests on codecov.io even when I use testthat::skip_on_cran(). The only downside is that it increases the amount of time needed for the package to build. HTH,