Re: [R-pkg-devel] Skipping tests on CRAN

2021-04-20 Thread Mark van der Loo
Hi Ott, There is no documented way to detect whether you are running on CRAN. So there is nothing to rely on, on that side. You can only make your own machine detectable by the test code. For example by setting an environment variable that identifies your machine and make test execution depend on

Re: [R-pkg-devel] Interpret feedback: not write testthat-tests in examples

2020-07-16 Thread Mark van der Loo
Dear Richel, The comment itself is pretty clear I think: to be accepted on CRAN you should not use testthat tests in your examples. I can't speak for CRAN but I'm pretty convinced this is for testing in general. Tests are for testing, not for demonstration. Most users of your package will probab

Re: [R-pkg-devel] Fwd: CRAN submission radsafer 2.1.0

2019-12-17 Thread Mark van der Loo
I am not sure which 'check result page' you mean, but presumably you mean this one: https://cran.r-project.org/web/checks/check_results_radsafer.html The e-mail you got asks you to confirm that you are the author of the submitted package. After confirmation (and checking the boxes on the confirmat

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

2019-10-25 Thread Mark van der Loo
Adding a static PDF vignette is very easy. I have written about it here: http://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ Best, Mark Op vr 25 okt. 2019 13:22 schreef Berry Boessenkool < berryboessenk...@hotmail.com>: > > You could also consider a static vign

Re: [R-pkg-devel] CRAN policies with regards to runnable examples

2019-10-01 Thread Mark van der Loo
My experience is somewhat similar to that of Hong Ooi. An initial submission got refused. During resubmission I explained the necessity of \dontrun{} in certain cases and it was accepted. So the basic policy here is 'comply or explain'. >From now on, when I need to place a \dontrun{} anywhere, I

Re: [R-pkg-devel] General considerations about vignettes

2019-08-30 Thread Mark van der Loo
At the cost of some level of reproducibility, you could use a static vignette and be very clear about the package versions used in the comparisons: http://www.markvanderloo.eu/yaRb/2019/01/11/add-a-static-pdf-vignette-to-an-r-package/ As this does diminish the coherence of CRAN somewhat I'm not re

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

2019-05-15 Thread Mark van der Loo
For what it's worth, I recently submitted a new package that was initially refused (with comments) by CRAN. I updated number of them accordingly, but there were a few that with good reasons I could not change. I explained this in the comments when uploading a new version and it got accepted. So I

Re: [R-pkg-devel] Submitting CORELS (Certifiably Optimal Rule Lists) package with/without Windows support

2018-12-20 Thread Mark van der Loo
Dear Aditya, You ask: | Am I able to submit this without Windows support, or could somebody help us with supporting Windows? The CRAN policy[1] is pretty clear about this: "Package authors should make all reasonable efforts to provide cross-platform portable code. Packages will not normally be

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

2018-07-19 Thread Mark van der Loo
one shouldn't be using the convenience stuff > (pipes, dplyr, etc., etc.), even during the development stages. Can > you comment? Thanks. > > -- Mike > > > On Tue, Jul 17, 2018 at 2:53 AM, Mark van der Loo > wrote: > > Michael, > > > > Just a s

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

2018-07-17 Thread Mark van der Loo
Michael, Just a small side-track here. I would avoid using the not-a-pipe operator within functions or packages in general. It is great for interactive use, but it does make debugging and hence long-term maintenance of functions harder. There are two reasons for this. First, it hides intermediate

Re: [R-pkg-devel] Questions about making a database package (Rpolyhedra)

2018-06-29 Thread Mark van der Loo
Hi Alejandro, Brooke Anderson gave a nice talk at useR!2017 addressing this exact issue. See https://schd.ws/hosted_files/user2017/19/anderson-eddelbuettel-use_r_talk.pdf for the slides. The basic idea is to use an external CRAN-like repository for the data back-end. Brooke used 'drat' to set up s

Re: [R-pkg-devel] How to handle deprecated package dependency? 2 suggestions 1 question

2018-06-25 Thread Mark van der Loo
Dear Vincent, I think this is little known, but you can get the CRAN result status of any package from R, see tools::CRAN_check_results(). Best, Mark Op ma 25 jun. 2018 om 22:13 schreef Duncan Murdoch : > On 25/06/2018 3:21 PM, Vincent van Hees wrote: > > Dear all, > > > > One of my package de

Re: [R-pkg-devel] library dlstats -> cran_stats()

2018-03-16 Thread Mark van der Loo
unfortunately not. In any case, it would depend on the willingness of each CRAN mirror maintainer to record and publish such statistics. -M Op vr 16 mrt. 2018 om 16:57 schreef Knut Krueger : > Am 16.03.2018 um 13:44 schrieb Spencer Graves: > > > > > > On 2018-03-16 06

Re: [R-pkg-devel] library dlstats -> cran_stats()

2018-03-16 Thread Mark van der Loo
Knut AFAIR the download statistics are limited to downloads from RStudio's cloud service, so none of the other CRAN mirrors are included. I think there is no separation between updates, re-installs, or installs done automatically by CI-services, for example. -Mark Op vr 16 mrt. 2018 om 12:30

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

2018-01-08 Thread Mark van der Loo
Dear Hugh, this question was asked earlier on this list: http://r.789695.n4.nabble.com/executable-files-R-package-td4390488.html See especially the answer of Duncan Murdoch. Best, Mark Op di 9 jan. 2018 om 03:26 schreef Hugh Parsonage : > On https://cran.r-project.org/ , it says > > > Note that

Re: [R-pkg-devel] Questions about third-party package distribution, especially with respect to security

2017-09-17 Thread Mark van der Loo
Dear Robert, R supports package repositories out of the box. A repository is just a way of organizing files. The most popular repositories are CRAN and Bioconductor. There is even a package that allows you to set up your own repository on Github (the drat package). It depends on the repository ma

Re: [R-pkg-devel] New Package Proposal: Feather with Matrix Notation ( [ , ] $ ) Access

2017-09-17 Thread Mark van der Loo
You could first have a look at the LaF packge. It does a lot of what you want already. -M Op zo 17 sep. 2017 om 04:41 schreef Juan Telleria : > Dear R Developers, > > I am writing as I would like to propose a github project for the creation > of on-disk data.frames/tibbles. > > These new S3 class

Re: [R-pkg-devel] Submitting a package to C-RAN

2017-09-03 Thread Mark van der Loo
I suggest you follow the link and check the notes.. On Sun, Sep 3, 2017, 1:06 PM Travers Ching wrote: > I am trying to submit a package to CRAN. It did not pass the automated > checks. However, I don't understand what it is I am supposed to fix. > > I have run R CMD check ... -- as-cran and it

[R-pkg-devel] Error on rhub/fedora not appearing on CRAN

2017-08-10 Thread Mark van der Loo
Dear list, I'm getting some false 'R CMD check' positives on rhub / Fedora: errors appearing on rhub that are not reproduced by CRAN. I have reported the matter here: https://github.com/r-hub/rhub/issues/92 It happens reproducibly for at least two of my packages: validate and lumberjack (I have

Re: [R-pkg-devel] problem with package_native_routine_registration_skeleton

2017-06-22 Thread Mark van der Loo
I have had no problems recently (having updated a pkg or two with this over the last couple of weeks). Your question is not reproducible so its hard to help... best, Mark Op wo 21 jun. 2017 om 23:46 schreef Simon Barthelmé < simon.barthe...@gipsa-lab.fr>: > Dear list, > > Is anybody else having

Re: [R-pkg-devel] Spell checking

2017-06-20 Thread Mark van der Loo
I had the same experience. Also recently I uploaded a pkg without a vignette but with a vignette engine specified in the DESCRIPTION. This gave no error with R CMD check --as-cran (r-dev) but I did receive a request to fix it. -M On Tue, Jun 20, 2017, 17:50 Thomas J. Leeper wrote: > I've now h

Re: [R-pkg-devel] How do you discover and learn about R packages?

2017-03-20 Thread Mark van der Loo
Julia, Just took the poll. I think cranberries would deserve mention there as well. It is the only continuous feed that reports in new pkgs and updates (that I know of). Best, Mark On Mon, Mar 20, 2017, 14:57 Julia Silge wrote: > I am contributing to a session at userR 2017 this coming July t

Re: [R-pkg-devel] UseR! Session: Making R easier to use (was: Navigating the jungle of R packages)

2017-02-12 Thread Mark van der Loo
Fwiw, there's also something called the awesome lists ( https://github.com/sindresorhus/awesome, and see the R list here: https://github.com/qinwf/awesome-R), which is basically a kind of task views for any language, and controlled via git pull requests. Not sure if this would be a good alternativ

Re: [R-pkg-devel] Delaporte: Test Errors on Sun Sparc

2017-02-05 Thread Mark van der Loo
Avraham, I can't help you out directly but Jeroen Ooms has a VM image with Solaris & R available: https://github.com/jeroenooms/solarisvm best, Mark Op zo 5 feb. 2017 om 21:27 schreef Avraham Adler : > I recently changed the back-end compiled code for the Delaporte > package from C++ to Fortr

Re: [R-pkg-devel] Compiler choice on CRAN (R-windows-oldrel)

2016-08-25 Thread Mark van der Loo
__GNUC_MINOR__ <= 6 #else #define HAS_REDUCTION #endif #endif /* more code */ #ifdef HAS_REDUCTION #pragma omp parallel for reduction(min:imin), reduction(max:imax) #endif for (int i=0; i: > > > On 25.08.2016 13:14, Mark van der Loo wrote: > > Thank you Peter, good poin

Re: [R-pkg-devel] Compiler choice on CRAN (R-windows-oldrel)

2016-08-25 Thread Mark van der Loo
) > > You do have a 4th option: conditionalize the _code_ on the R version, then > remove old-style code when 3.2.x becomes history. > > -pd > > On 25 Aug 2016, at 11:20 , Mark van der Loo > wrote: > > > Dear listers, > > > > > > Compilation of my gowe

[R-pkg-devel] Compiler choice on CRAN (R-windows-oldrel)

2016-08-25 Thread Mark van der Loo
Dear listers, Compilation of my gower pkg fails on R-oldrel-windows. I am pretty sure that this is because it uses gcc 4.6.3 which has limited support for OpenMP (the errors are the same as I got on the old travis-ci build environment, see my related question[1]). Now, according to the Rtools pa

Re: [R-pkg-devel] openMP/reduction statement causes build crash on travis-ci

2016-08-03 Thread Mark van der Loo
On 3 August 2016 at 08:13, Mark van der Loo wrote: > | Dear pkg developers, > | > | > | I'm working on a package using C code and openMP. The package builds and > | tests fine on my own machine[1] and also on r-hub[2]. However on > travis-ci > | the build crashes[3] w

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

2016-08-03 Thread Mark van der Loo
than it is now. If you don't >have foo available, and you try to use foo::bar(), what would happen >other than an error? I think you're right there. . Best, Mark Op wo 3 aug. 2016 om 13:41 schreef Duncan Murdoch : > On 03/08/2016 5:32 AM, Mark van der Loo wrote: > > >

Re: [R-pkg-devel] Handling Not-Always-Needed Dependencies?

2016-08-03 Thread Mark van der Loo
After reading the link in Dirk's initial reply, how about adding fields 'Recommends' and 'Build-Depends' to DESCRIPTION as in Debian? Recommends: only gets installed, can be used via if(requireNamespace()) from the package and in pkg tests[1]. [Debian: The Recommends field should list packages tha

[R-pkg-devel] openMP/reduction statement causes build crash on travis-ci

2016-08-03 Thread Mark van der Loo
Dear pkg developers, I'm working on a package using C code and openMP. The package builds and tests fine on my own machine[1] and also on r-hub[2]. However on travis-ci the build crashes[3] with the following message (plus a few similar): gower.c:297:29: error: expected ‘+’, ‘*’, ‘-’, ‘&’, ‘^’,

Re: [R-pkg-devel] relation between vignettes and help files

2016-07-13 Thread Mark van der Loo
Afaik the only way to link to a vignette from the help file is to instruct the reader to do something like vignette('intro','mypkg') On the R command-line. In general, the Rd files describe the public API of your pkg. Each exported function should have a help file that ideally can be read and un

Re: [R-pkg-devel] Package was removed from CRAN "despite reminders" -- but I did not receive any such messages

2016-06-01 Thread Mark van der Loo
Mail the CRAN team. On Wed, Jun 1, 2016, 10:24 Dean Attali wrote: > My package 'ddpcr' was accepted into CRAN in 2016-02-19 and then updated on > 2016-03-17. There were no errors or warnings or notes in my submission and > it was accepted right away. > > I just tried going to its CRAN page and

Re: [R-pkg-devel] install from github

2015-12-03 Thread Mark van der Loo
>> is someone aware of a way to easily install a package hosted on github without using devtools::install_github? Personally, I love Dirk's[1] drat package. It allows authors to set up a personal CRAN-like system on their github pages. This means that the author of the package can decide when a (b

Re: [R-pkg-devel] Diagnosing error on CRAN's old R, old Windows

2015-10-08 Thread Mark van der Loo
I had the same problem recently. It was apparently a windows-only oldrel-only problem (and a specific oldrel, I can't remember which one). I opted to adjust the DESCRIPTION to depend on a higher R version. Main reason was that I don't have access to the right type of Windows version to test it loca

Re: [R-pkg-devel] extending a few functions from another package

2015-08-28 Thread Mark van der Loo
Implanting is indeed a dirty trick. You could contact the maintainers of geoR and ask if your code can be added to the package. Or perhaps they can export some of the functionality you need. /M Op vr 28 aug. 2015 om 16:58 schreef Facundo Muñoz : > Dear list, > > I have built a package geoR

Re: [R-pkg-devel] why doesn't CRAN add -fopenmp to SHLIB_OPENMP_CXXFLAGS for Mac OS?

2015-08-28 Thread Mark van der Loo
It is not a question of whether the CRAN maintainers _could_ do it. Technically anything's possible[1]. But, as is nicely pointed out[2] "The time of the volunteers is CRAN’s most precious resource[...]" If you ask me, the voluntary CRAN team is already supporting an amazing range of architec

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

2015-08-24 Thread Mark van der Loo
this fashion. > Supplying binaries seems the only option unless clang developers decide to > support OpenMP, which seems unlikely since Apple wants to promote its own > parallel computing tools. > > Michael Neale > mcne...@mac.com > > > > On Aug 24, 2015, at 3:38 PM,

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

2015-08-24 Thread Mark van der Loo
At least on linux, CRAN builds using openMP. I got a valgrind report once [shame on me btw] showing that 9 (out of 10) threads were running examples. So my best guess is that it will do the same for Windows since it also has openMP support according to WRE[1]. I wouldn't know why not, except for

Re: [R-pkg-devel] browseURL in examples

2015-08-18 Thread Mark van der Loo
Berry, why not use \href{[your link]}{[link text]} in the documentation details[1]? Best, Mark [1] https://cran.r-project.org/doc/manuals/R-exts.html#Marking-text Op di 18 aug. 2015 om 13:21 schreef Duncan Murdoch : > On 18/08/2015 6:12 AM, Berry Boessenkool wrote: > > Hi all, > > > > In th