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

On 20 September 2017 at 16:44, Martyn Plummer wrote: | On Wed, 2017-09-20 at 09:45 -0500, Dirk Eddelbuettel wrote: | > Thierry, | > | > This has always been a considerable puzzle, and the source of some amusement, | > to me. It is a clear design bug in Rscript because _cod

Re: [R-pkg-devel] Announcing Bazel for R packages

On 21 September 2017 at 22:40, Siddhartha Bagaria wrote: | We have released some Bazel rules for R packages. | https://github.com/grailbio/rules_r | | What is Bazel? | | Bazel is an industry tested build system that can be | used for continuous integration and testing in l

Re: [R-pkg-devel] Announcing Bazel for R packages

On 22 September 2017 at 00:28, Siddhartha Bagaria wrote: | I agree the open source version has not been around for that long. | | But... It is picking up adoption within many other companies this year: | https://github.com/bazelbuild/bazel/wiki/Bazel-Users | | And some adoption in academia as we

Re: [R-pkg-devel] How to fix R CRAN submission check warning: cannot load without being on the library search path

On 25 September 2017 at 20:23, Zhenke Wu wrote: | Hi all, | | I have submitted my package via CRAN submission page but had the following | error that I couldn't fix. It has something to do with package 'rrcov'. On | my machine (OSX), rrcov is installed. How can I make the CRAN package | checking

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

On 26 September 2017 at 22:52, Jens Oehlschlägel wrote: | also the Rcppverse Not really, in the context of this thread. Rcpp does not impose or suggest a particular way of doing things at the R level. Rcpp, really, is mostly about making it a little easier to interface with C/C++ level code fro

Re: [R-pkg-devel] Testthat environment using sourceCpp

Charles, I cannot help you with testthat or devtools, but the very issue of how to get C++ test files compiled (with the help of Rcpp) and used is deployed in a number of packages, both ours and other. To take but one example, RcppArmadillo does it with about half a dozen C++ files it keeps in a

Re: [R-pkg-devel] Add appveyor in package with RcppGSL dependency

On 22 October 2017 at 18:37, Julio Trecenti wrote: | We are trying to add CI to this package | https://github.com/brsantos/baquantreg. | | We are trying to do add appveyor to work with our package based on @stewid | solution here: https://github.com/stewid/SimInf. | | However, our shell knowledg

Re: [R-pkg-devel] Semantic versioning and maintenance releases

On 25 October 2017 at 11:23, Shivaram Venkataraman wrote: | Hello | | We have an R package that uses semantic versioning -- i.e. version numbers | are of the form major_version.minor_version.patch_version | | One of the ways we use the patch_versions is to make maintenance releases | or security

Re: [R-pkg-devel] Reducing installed package size with --strip-debug

On 31 October 2017 at 15:02, Ege Rubak wrote: | Based on Dirk's blog post [1] about stripping debug information from the | shared object of my package `s2` I reduced the shared object file size | from 7 to 0.7 MB and get rid of a NOTE about the installed package size | (on my local Linux machin

[R-pkg-devel] Why would src/Makevars be ignored?

Having a bit of a puzzle with a package at work (which I can't share). In src/Makevars I override CC, CXX, CXX11, CXX14 to point to a specific (version) of g++ on my system, say g++-x.y. I also set CXX_STD=CXX14 Only it doesn't work. I need an extra dot.RMakevars and an invocation via R_MAKE

Re: [R-pkg-devel] Why would src/Makevars be ignored?

On 21 November 2017 at 16:51, Duncan Murdoch wrote: | According to section 1.2.1 "Using Makevars" in Writing R Extensions, | R_HOME/etcR_ARCH/Makeconf is included after Makevars, so what you're | seeing is by design. I believe this is so that packages are built with | tools compatible with tho

Re: [R-pkg-devel] dependencies

On 21 November 2017 at 19:20, Cathy Lee Gierke wrote: | Thanks Bryan. All of my imports are in the namespace. Can you tell me why | this one should be in the description file? Because you need an entry in the DESCRIPTION file _and_ an entry in NAMESPACE. Dirk -- http://dirk.eddelbuettel.com

Re: [R-pkg-devel] Installing Tests with R Build

On 23 November 2017 at 08:07, Joshua Ulrich wrote: | On Wed, Nov 22, 2017 at 4:21 PM, Bill Denney wrote: | > I have a package that I'm trying to make a validation vignette for. The validation vignette is intended to assist users with documentation that the tests work. | > | > When running R BU

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

On 27 November 2017 at 21:24, Tan, Senren wrote: | I have been developing an R package using Rcpp to call C++ functions that use the C subroutine library 'fftw3' that implements fast Fourier transform algorithm. Since I have the C library 'fftw3' installed on my laptop (running MacOS), when I c

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

On 28 November 2017 at 11:01, Ege Rubak wrote: | The obvious place to look for pointers of how to detect and link | correctly to fftw would be in the current CRAN package `fftwtools` that | does it without any Rcpp: | https://github.com/krahim/fftwtools And there is also fftw by Olaf and Uwe (!

Re: [R-pkg-devel] Errors in the pre-test after submitting the R package

Hi Senren, On 30 November 2017 at 16:49, Tan, Senren wrote: | Thank you very much for your reply. My pleasure. You did well here. | I have been trying to look at the R package fftw developed by Olaf and Uwe over the last few days. And I have tried to make use of the configure.ac. file in the

Re: [R-pkg-devel] Testing for a Specific R Error

On 2 December 2017 at 08:38, Bill Denney wrote: | Hi, | | I got a message last night that some of the tests in the PKNCA package do not follow best practices. ("Do not test the exact format of R messages (from R itself or from other packages): They change, and they can be translated.") Speci

Re: [R-pkg-devel] Error in re-building vignettes (SOLVED)

On 6 December 2017 at 11:40, Göran Broström wrote: | Hi again, | | today I INSTALLED R-devel (2017-12-05 r73849) and updated all packages | | > update.packages(checkBuilt = TRUE) | | and rebuilt eha_2.5.1 and now all checks passed! Maybe the update of | packages was necessary. Very much so,

Re: [R-pkg-devel] Rcpp Copyright Query

ht holders relating to the Rcpp package: | - Copyright (C) 2010 - 2012 Dirk Eddelbuettel and Romain Francois "Missing"? Sorry, but who is missing what? Presumably you are not _including_ Rcpp in your package and as such you are not _(re-)distributing_ the sources over which other people have a

Re: [R-pkg-devel] CRAN check FAIL due to pragmas in headers and code

On 14 December 2017 at 00:58, Iñaki Úcar wrote: | Hi all, | | Three days ago, Patrick Perry posted the following on R-devel: | | 2017-12-11 16:32 GMT+01:00 Patrick Perry : | > A recent change to r-devel causes an R CMD check warning when a C file | > includes a "#pragma GCC diagnostic ignored" p

Re: [R-pkg-devel] CRAN check FAIL due to pragmas in headers and code

On 14 December 2017 at 03:04, brodie gaslam via R-package-devel wrote: | This leads me to think that it is (maybe) possible that this is an issue with the latest version of the check tool? Which is what I tried to explain to Inaki when he first filed on as an Rcpp issue ticket: Sometimes you nee

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 17 December 2017 at 19:15, Baptiste Auguie wrote: | Hi, | | The CRAN maintainers recently informed me that my cda package now fails on | CRAN. The root cause seems to be this error: | | ** testing if installed package can be loaded | Error: package or namespace load failed for ‘cda’ in dyn.lo

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 17 December 2017 at 17:21, Dirk Eddelbuettel wrote: | | ** testing if installed package can be loaded | | Error: package or namespace load failed for ‘cda’ in dyn.load(file, DLLpath | | = DLLpath, ...): | | unable to load shared object ‘/home/hornik/tmp/R.check/r- | | release-gcc/Work/build

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 17 December 2017 at 17:50, Dirk Eddelbuettel wrote: | In short, but relying on (Rcpp)Armadillo, you are submit to it changing its That should have read: "... by relying on (Rcpp)Armadillo, you are subject to ..." My bad. | solver and it seems to have done so recently. A

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 18 December 2017 at 13:12, Ralf Stubner wrote: | On 18.12.2017 08:37, Baptiste Auguie wrote: | > What I don't really understand (because of the templating system etc.) is | > why this new routine in Armadillo would be needed at all, when cda does not | > solve banded linear systems. I wonder if

Re: [R-pkg-devel] Lapack: undefined symbol: zgbsv_

On 19 December 2017 at 13:41, Ralf Stubner wrote: | On 19.12.2017 09:38, Baptiste Auguie wrote: | > Thanks for the pointer to `arma::solve_opts::no_band`, it sounds like a | > good solution (assuming the compiler will then skip all the parts | > related to banded inversion routines). I've been una

Re: [R-pkg-devel] Debian: example file is no longer read correctly

On 20 December 2017 at 15:32, Göran Broström wrote: | > Or can someone tell me how to install the package using R devel on Linux? | | Good question (which I missed). I do it like this: | | (i) Download and unpack the tarball R-devel in ~/src/ | (ii) ./configure and make | (iii) Start R-devel

Re: [R-pkg-devel] File name error

Cristine, On 21 December 2017 at 08:21, Blume Christine wrote: | I also had troubles with debian (Fedora only gave warnings) May I ask you to be a little more careful in your attribution? Yes, it is too that the instance labeleb 'r-devel-debian' gave you an error. But that was not because of

Re: [R-pkg-devel] Portable method of stripping debug symbols

Christopher, On 3 January 2018 at 21:59, Christopher Lalansingh wrote: | I'm running into troubles with the total size of my package and I've found that when using Rcpp, one can reduce the size of shared objects by stripping out debug symbols by including `-Wl,-S' in PKG_LIBS. Unfortunately thi

Re: [R-pkg-devel] Portable method of stripping debug symbols

On 4 January 2018 at 00:27, Thibault Vatter wrote: | We faced a problem when we tried Dirk's solution for our package | rvinecopulib: there is a strip binary on OS X but it doesn't work as the | linux one. | | As such, to avoid calling OS X's strip which doesn't work, we use: | | strippedLib: $(

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

Hugh, You may be looking at this from the wrong angle. "Imports" is really an updated variant of "Depends". Both of them declaure _unconditional_ use of another package. (How they are used is the fine distinction between loading and attaching which we'll skip here). The key point is that a pack

Re: [R-pkg-devel] error messages

On 14 April 2021 at 01:03, csmatyi wrote: | Debian | | * using log directory ‘/srv/hornik/tmp/CRAN/hybridogram.Rcheck’ | * using R Under development (unstable) (2021-04-12 r80161) | * using platform: x86_64-pc-linux-gnu (64-bit) | * using session charset: UTF-8 | * checking for file ‘hybridogram

Re: [R-pkg-devel] Package gcc-ASAN issue

On 16 April 2021 at 10:27, Kevin Ushey wrote: | You can also try to verify locally using e.g. Docker; the rocker | images here are immensely helpful: | | https://github.com/rocker-org/r-devel-san Thanks but that container image may be stale at times. The daily rebuilds by Kevin's colleague Wins

[R-pkg-devel] Does a file in tests/ know which package it is being run from?

When a script in tests/ is being run by R CMD check and friends, can we know what package it is currently being part of? I want to access some package files via system.file(..., package=pkg) which works just fine, but it feels redundant to assign the package name to the pkg variable. Case in

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

You can default to have 'few tests'. That then happens at CRAN too when nothing else is set (as there simply is no variable to rely upon). You can then try to detect when you would want to run 'more tests'. Placing the tests somewhere else (as Duncan suggested) to explicitly opt in is one way (t

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

On 22 April 2021 at 16:28, Kevin R. Coombes wrote: | I'm trying to help clean up an R package for someone else to submit to | CRAN. He has used ggplot2 to implement a plotting function for the kinds | of things that his packages generates. His plotting routine basically | looks like (after cha

Re: [R-pkg-devel] winUCRT failures

On 25 April 2021 at 11:14, Duncan Murdoch wrote: | What I haven't tried to do is check any of them if *none* of the | suggested packages is available. Packages should still build and check | without ERRORs in this case, though I'd expect NOTEs and/or WARNINGs. | | This is an old issue: what

Re: [R-pkg-devel] winUCRT failures

On 25 April 2021 at 12:27, Duncan Murdoch wrote: | On 25/04/2021 11:35 a.m., Dirk Eddelbuettel wrote: | > I last wrote about that four years ago under the title "Suggests != Depends" | > http://dirk.eddelbuettel.com/blog/2017/03/22#suggests_is_not_depends | > | > Of c

Re: [R-pkg-devel] winUCRT failures

On 25 April 2021 at 11:46, Dirk Eddelbuettel wrote: | So yes, it is technically easy, and we could pool the resources. But nobody | is driving it so (as has been the case for years) nothing changes. Ever. Sorry, "nothing changes" is too harsh. We have in the last year or two gotten

Re: [R-pkg-devel] Large data package

have not seen it yet, the R Journal article Brooke and I wrote a few years ago covers exactly this use case, and walks through how to cover it in a fairly detailed way. https://journal.r-project.org/archive/2017/RJ-2017-026/index.html @article{RJ-2017-026, author = {G. Brooke Anderson and Dirk

Re: [R-pkg-devel] Large data package

On 2 May 2021 at 10:12, Ayala Hernandez, Rafael wrote: | Following Dirk's suggestion below, I have recently added a data package as a drat repository for my asteRisk package, placing it under Suggests in the main package. | In order to keep the code tidy and know exactly when I’m accessing the

Re: [R-pkg-devel] Large data package

On 2 May 2021 at 15:00, Ayala Hernandez, Rafael wrote: | Thanks a lot for your clarifications. Both of your explanations make sense. Indeed, I would rather not have any other packages depend on the data package, at least not for the time being, in case I find good reasons to make modifications

Re: [R-pkg-devel] Resubmitting archived package with new maintainer

On 4 May 2021 at 13:03, Michael Hellstern wrote: | I'm trying to resubmit a package to CRAN that was archived about 1 month | ago. The archived package has a different maintainer. We discussed and they | are OK with me taking over as the new maintainer. Do we need to email CRAN | confirming the c

Re: [R-pkg-devel] Unable to get past CRAN submission checks for package cubature

On 10 May 2021 at 13:01, Balasubramanian Narasimhan wrote: | It appears that I am unable to get beyond the auto-check service. Any | suggestions? I have tried for several weeks, and four emails, to get an answer concerning an auto-archived submission. Ironically, it aimed to address the very 'e

Re: [R-pkg-devel] Including header files with long filenames in an R pacakge

On 12 May 2021 at 11:03, Eric Dunipace wrote: | I did some searching and wasn’t able to find a good answer to my question, so I hope that someone here has knowledge of how to fix the problem. | | I’m currently trying to create an R package that bundles the CGAL header files (http://www.cgal.or

Re: [R-pkg-devel] What To Include In \donttest{}

Danielle, On 26 May 2021 at 21:23, Danielle Maeser wrote: | Please excuse the very simple question, but I received the following | message from a CRAN maintainer, and I am not sure what code to include | inside of the \donttest{}. This is meant to enclose code that typically | should be run, but

Re: [R-pkg-devel] Suggesting gurobi

On 4 June 2021 at 16:21, Balasubramanian Narasimhan wrote: | Suggests" would trigger an attempt to install gurobi, which is not on CRAN. To my understanding that is not the case. It would only do so if and when install.packages() is asked to also install packages in Suggests:. And point of Sugge

Re: [R-pkg-devel] Windows load error installing package

On 10 June 2021 at 09:22, J C Nash wrote: | Thanks to help from Duncan Murdoch, we have extracted the nls() functionality to a package nlspkg and are building | an nlsalt package. We can then run nlspkg::AFunction() and nlsalt::AFunction() in a single script to compare. | This works great in Li

Re: [R-pkg-devel] speeding up package code/build/test cycle

Hi Greg, On 24 June 2021 at 12:15, Greg Minshall wrote: | when developing packages, my current work flow is to change the code, | (re-)build the package, detach/load the package, test (to find the | N+1'st bug, sigh). | | the building step takes tens of seconds. You may benefit from looking in

Re: [R-pkg-devel] speeding up package code/build/test cycle

On 24 June 2021 at 16:31, Duncan Murdoch wrote: | This does the full compile again, so it's slow. ccache fixes that (as it has its own cache). It also works on macOS. Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-pack

Re: [R-pkg-devel] Change package maintainer

On 1 July 2021 at 20:00, Lluís Revilla wrote: | I have a question related to changing maintainers. | What happens when the old/current maintainer does not respond to | emails or other methods of contact? | Would the new maintainer need to wait until the package is removed | from CRAN to submit it

Re: [R-pkg-devel] package test returns error when R version 4.1.0

On 8 July 2021 at 10:41, Uwe Ligges wrote: | It was likely an interim version of Rcpp (which never made it to CRAN) | that was causing trouble. Yup, our bad. While we test against 2300+ reverse depends, we only test against them _under the most recent versions we have seen_ which affects the R

Re: [R-pkg-devel] Creating a package that links to a 3rd party library: Technical questions

Russell, On 24 July 2021 at 12:04, Russell Almond wrote: | I'm working on a package called RNetica which links to a 3rd party | library: Netica. Netica is available in both static (libnetica.a) and | shared (libnetica.so) version (also Netica.dll for windows, but that is | a separate topic)

Re: [R-pkg-devel] C++17

Section 2.7.3 'C++ Support' of the R Admin manual says, "C++ is not used by R itself, but support is provided ...". This is all stored from when R itself is configure (prior to compiling) and override-able in package configuration (Section 2.7.3 covers that) but as that in other places _it all d

Re: [R-pkg-devel] windows and configure scripts

If look closely enough at _Writing R Extensions_ you notice that it mentions 'configure.win' over half a dozen times. A powerful trick is to then use the fact that there are other packages on CRAN, in fact almost 18k of them. And e.g. this search https://github.com/search?q=org%3Acran+config

[R-pkg-devel] CRAN closed for a week

While we generally get an email about these things, CRAN appears to have closed shop for a week to take a well deserved break until September 1. Or so the message says---the hourly CRANberriesFeed cron job saw packages being processed, but that too is not uncommon when the queues get cleared. T

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

On 9 October 2021 at 12:08, Ben Bolker wrote: |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 https://cloud.r-project.org/package=RhpcBLASctl Dirk -- https://dirk.eddelbu

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

Agreed. I have used `.pkgenv` in a few packages (digest, rpushbullet, ...), and usually added a comment that it is package-global. And so have a few others: https://github.com/search?l=R&q=org%3Acran+pkgenv&type=Code Dirk -- https://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _

Re: [R-pkg-devel] CRAN no longer checking for solaris?

On 5 December 2021 at 17:23, Travers Ching wrote: | I see that there doesn't exist a Solaris flavor on any CRAN check page. | However, I'm certain that Solaris was being checked up until very recently. | | Is this just temporary? | | Is there any information for the future of Solaris on CRAN?

[R-pkg-devel] pandoc missing on r-{release,oldrel}-macos-x86_64

CRAN results flag NOTEs on the two platforms r-release-macos-x86_64 r-oldrel-macos-x86_64 because `pandoc` is apparently missing. These platforms being somewhat common, could pandoc be installed? Or are they running such a jurassic version that no premade pandoc is available _anywhere_ ?

Re: [R-pkg-devel] pandoc missing on r-{release,oldrel}-macos-x86_64

On 17 December 2021 at 09:51, Simon Urbanek wrote: | Sure, installed pandoc 2.16.2. Perfect, thank you! Dirk | Cheers, | Simon | | | > On Dec 17, 2021, at 9:21 AM, Dirk Eddelbuettel wrote: | > | > | > CRAN results flag NOTEs on the two platforms | > r-release-macos

Re: [R-pkg-devel] Error in inDL(x, as.logical(local), as.logical(now), ...) unable to load shared object

On 23 December 2021 at 11:07, Tomas Kalibera wrote: | You can have a look at CRAN package Rblpapi which is using an external DLL. Yes with one big caveat: You have to make sure the library follows what is the "hour-glass pattern": it needs to have an internal (the "narrow" part) C library coveri

Re: [R-pkg-devel] Error in inDL(x, as.logical(local), as.logical(now), ...) unable to load shared object

Ezra, [ A gentle plea: Can you please turn the encryption signing off when you reply? Thank you, it really confuses one of the email programs I use. ] What you state in passing is somewhere between misleading and just wrong, likely due to a misunderstanding. Quoting from your email: a stu

Re: [R-pkg-devel] Fix JFM package problem

On 11 January 2022 at 18:44, riccardo wrote: | Hallo, | | I wish to submit the following error rising running an example in a rcpp | function *only *in Debian check: | | > ### Name: least_square_plane_rcpp | > ### Title: returns the coefficients of the least square plane and the | > ### rela

Re: [R-pkg-devel] Is using global assignment in package tests allowed?

On 27 January 2022 at 11:18, Ben Bolker wrote: |I have spent hours trying to understand the scoping behaviour of | testthat, mostly without success. It may bear repeating that use of a test runner package is NOT required by CRAN Repo Policy, Writing R Extensions, or any other official text

Re: [R-pkg-devel] Failing Valgrind Passing R CMD check

On 8 March 2022 at 18:01, Sebastian Meyer wrote: | Not an expert here, but that does seem to be possible, according to WRE | (Section 4.3.2): | | > It is possible to run all the examples, tests and vignettes covered by R CMD check under valgrind by using the option --use-valgrind. If you do th

Re: [R-pkg-devel] Ensuring permanence and SHA consistency of released CRAN packages for validated software

On 16 March 2022 at 14:01, Henrik Bengtsson wrote: | Related to this, there's also been discussion (here or on R-devel), of | having `R CMD build` produce identical tarballs when the input doesn't | change, but the injection of `Packaged: ; ` to the | `DESCRIPTION` file prevents this. If I recall

[R-pkg-devel] pandoc missing on r-release-macos-x86_64, r-oldrel-macos-x86_64

Two (related) questions: 1. Could pandoc be installed on the macoOS machines CRAN uses? If not, could R Core devise a way to have a registered vignette builder fail gracefully? 2. Could CRAN define and publish a minimal set of external applications available on each build + test machine?

Re: [R-pkg-devel] Should the LaTeX package pdfpages be available for use in vignettes?

On 23 April 2022 at 18:05, Greg Hunt wrote: | I want to incorporate a static PDF (created from LaTeX source separately | from the R package) into an R package as a vignette. I do that in several vignettes via a zero-depends approach described by Mark in this blog post: https://www.markvanderloo

Re: [R-pkg-devel] advice on a rejected package (I think, because time was 13min, in excess of 10min limit)

On 11 May 2022 at 19:07, Daniel Kelley wrote: | Today I tried to update the CRAN oce package to version 1.7-3, to address a problem with 1.7-2 on one of the CRAN build platforms. I used devtools::release() to submit it. I just received the text I've pasted at the bottom of this email. I've

Re: [R-pkg-devel] No news entries found

On 8 July 2022 at 14:23, Plamen Mirazchiyski wrote: | to what actual the problem is. Unfortunately, the r-svn repository on | GitHub does not have the possibility to report this as an issue. Please see https://bugs.r-project.org/but also see old mailing list (and elsewhere) posts on how to

Re: [R-pkg-devel] CRAN valgrind reports with zero leaks - actionable?

Dear CRAN Team, On 18 August 2022 at 06:55, Dirk Eddelbuettel wrote: | | [ Five days ago, I sent (most) of the message below to a CRAN team member. I | have not had a reply, and it now appears that we are asked to email here so I | am resending. ] An answer would be much appreciated after the

Re: [R-pkg-devel] [Solved, sort-of] CRAN valgrind reports with zero leaks - actionable?

Based on further (off-list) follow-ups with Simon and Uwe, the situation can now be summarized as follows: - there appears to be no word about non-leak errors reported by valgrind in the official documentation; I will have to plead that those with the power to amend these documents maybe

Re: [R-pkg-devel] Error checking in an independent C code and printing (perror, printf, etc.)

On 7 September 2022 at 11:58, Ivan Krylov wrote: | there at all. On the other hand, my package that uses the | R_InitOutPStream and R_Serialize entry points seems to have passed the | CRAN review. A table of all public entry points including short | descriptions and whether they allocate could be

Re: [R-pkg-devel] Invalid UTF-8

On 17 October 2022 at 13:20, Göran Broström wrote: | Thanks Ivan, | | I found two simple ways to convert this old file to UTF-8: | | (i) In emacs, C-x f (default is utf-8) That's a good ti[. I had actually hand-edited two lines down to 'seven bits' instead of this. Umlaute, accents and spec

Re: [R-pkg-devel] How ton print in the console from Rcpp

On 20 October 2022 at 14:46, Ivan Krylov wrote: | В Thu, 20 Oct 2022 12:43:30 +0200 | Elysée Aristide пишет: | | > What I understood is that it is better to use Rcpp functions. So I | > used: | > | > Rcpp::Rcout << "beta: \n"; | > Rcpp::print(betacpp); | > Rcpp::Rcout << "log-likelihood: " <<

Re: [R-pkg-devel] How ton print in the console from Rcpp

On 20 October 2022 at 13:16, Elysée Aristide wrote: | Thank you very much for your answers. | | I finally noticed that the issue comes from the numerical optimization, in which I use the class MFuncGrad of the package RcppNumerical. Is there any problem in using this class? This is the only wa

Re: [R-pkg-devel] Compiled code should not call non-API entry points in R

On 3 November 2022 at 21:09, Andrew Simmons wrote: | I had some R code for dealing with connections, and I was using | summary.connection(). I rewrote it in C, so I was doing something more | like: | | #include | | Rconnection Rcon = R_GetConnection(file); | Rcon->description or Rcon->class |

Re: [R-pkg-devel] Writing to users config directory for CRAN package

On 5 November 2022 at 19:32, David Hugh-Jones wrote: | I'm considering submitting the package onetime ( | https://github.com/hughjonesd/onetime/) to CRAN. | | Onetime has functions for showing a message or warning only once (ever per | user). It does this by writing to a file in the user's confi

Re: [R-pkg-devel] vignettes - size of pdf

On 11 November 2022 at 16:06, Ivan Krylov wrote: | В Fri, 11 Nov 2022 12:54:52 + | "Grose, Daniel" пишет: | | > * checking sizes of PDF files under 'inst/doc' ... WARNING | > 'gs+qpdf' made some significant size reductions: | > compacted 'cpop.pdf' from 805Kb to 547Kb | > consider

Re: [R-pkg-devel] R, Rust and CRAN

On 12 November 2022 at 19:27, Jeroen Ooms wrote: | On Sat, Nov 12, 2022 at 12:49 AM Simon Urbanek | wrote: | > | > this does not directly address your question, but I think it would make a lot of sense to standardize the process, given how many issues there were with packages using Rust (mainl

Re: [R-pkg-devel] R, Rust and CRAN

On 13 November 2022 at 08:15, Simon Urbanek wrote: | sorry, I think you misunderstood: CRAN machines have the compilers, but the packages were not detecting it properly and/or were violating the CRAN policies as noted, so that's why I was saying that it would make sense to have a unified appro

Re: [R-pkg-devel] How ton print in the console from Rcpp

Ivan, Thanks for following-up but I think this issue is local to the OP as R is already setup exactly that way to skip `assert()` in builds (in perfect congruence with the CRAN Repository Policy) edd@rob:~$ grep NDEBUG /etc/R/Makeconf R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG ALL_

Re: [R-pkg-devel] How ton print in the console from Rcpp

On 14 November 2022 at 16:34, Elysée Aristide wrote: | I was convinced that the issue is local. The warning message only appears | on MAC. | I did not try with another computer. I used CRAN macbuilder service and got | the warning message. I guess this is also the computer CRAN uses. Some furthe

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

On 16 November 2022 at 06:36, Duncan Murdoch wrote: | On 15/11/2022 11:59 p.m., Hugh Parsonage wrote: | > 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 polic

Re: [R-pkg-devel] Two packages with the same name

On 28 November 2022 at 12:15, Peter Carbonetto wrote: | I maintain the mashr R package (https://cran.r-project.org/package=mashr), | which has been on CRAN a little over 2 years. The mashr package depends on | another package, flashr, which is available from an external repository | (via *Additio

[R-pkg-devel] Minimum macOS version ?

One package I stand behind as maintainer does ## Take care of 10.14 requirement for Intel macOS if test x"${uname}" = x"Darwin" -a x"${machine}" = x"x86_64"; then AC_MSG_CHECKING([for Darwin x86_64 use minimum version override]) CXX17_MACOS="-mmacosx-version-min=10.14" AC_M

Re: [R-pkg-devel] Minimum macOS version ?

Simon, On 9 December 2022 at 10:00, Simon Urbanek wrote: | the minimum required version for the high-sierra build is 10.13 and for big-sur build is 11.0 (as the names imply). Although it is not unrealistic to move Intel to macOS 10.14, it would be more problematic to move to 10.15 since it is

Re: [R-pkg-devel] Do you run R on Fedora or Debian?

On 10 December 2022 at 14:00, Roy Mendelssohn - NOAA Federal via R-package-devel wrote: | CRAN has sent me a notice about the following: | | https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out | | I can not reproduce it. I test on my Mac, the cache space is properly handled (by

Re: [R-pkg-devel] Do you run R on Fedora or Debian?

raction. If CRAN reports this to you, they see it. You should have access to `tempdir()` and friends to make things per-session, or else you need to ask the user (once) and then store in user-supplied location. I think that was discussed here recently. Good luck, Dirk [1] Also commonly ca

Re: [R-pkg-devel] checking sizes of PDF files under‘inst/doc’ ... WARNING

On 16 December 2022 at 20:30, EcoC2S - Irucka Embry wrote: | While running R CMD check on my iemisc package, I receive the following | warning: | | * checking sizes of PDF files under ‘inst/doc’ ... WARNING |‘gs+qpdf’ made some significant size reductions: | compacted ‘Comparing_Manni

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

On 27 December 2022 at 13:27, Duncan Murdoch wrote: | On 15/12/2022 10:25 a.m., Spencer Graves wrote: | > I know that some on this list do not like this construct, but it has | > helped me manage this problem for several years. NOTE: This CRAN | > function is NOT maintained by anyone on C

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

As the error is common against your _all three_ of your Ubuntu runs, you could consider the possibility that the events are correlated. Most often it simply means a (temporary, usually) network or server outage. I would wait, and then relaunch (which these days you can do just for the failed jo

Re: [R-pkg-devel] replacements of sprintf in compiled code

On 21 January 2023 at 05:27, Duncan Murdoch wrote: | On 21/01/2023 5:15 a.m., Holger Hoefling wrote: | > Is there a simple replacement that I can use? | | You should use snprintf() which has an extra argument to state the size | of the buffer receiving the string. For example, | | char text

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

Can you share the repo URL? It may be a a fairly simple and standard issue some of us can spot easily. Hth, Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/

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

On 20 February 2023 at 21:41, Vasileios Nikolaidis wrote: | Oh yes thank you. I just realized I did not mention the repo on my | previous reply. It is | https://github.com/VNNikolaidis/nnlib2Rcpp Thanks for that -- I can confirm the error. The packages compiles all source files without issue o

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

On 20 February 2023 at 22:37, Vasileios Nikolaidis wrote: | Thanks for taking the time to check it. The hint about the virtual | 'layer' class is valuable. | I will look into it. Sounds good, glad to have been of assistance. On a lark, I also tried your most recent CRAN release, and it install

Re: [R-pkg-devel] Ignoring a compiler warning?

On 27 February 2023 at 14:32, Duncan Murdoch wrote: | I am in the process of updating rgl to use the glad loader | (https://github.com/Dav1dde/glad). This replaces system standard gl.h | and glext.h files with new ones that include function pointers to be | filled in at run-time, so that rgl

Re: [R-pkg-devel] DLL requires the use of native symbols

On 20 March 2023 at 12:43, Duncan Murdoch wrote: | It appears that you have some uses of .Call() where you are passing a | character variable as the first argument, instead of registering the | entry point and passing the variable containing the registration | information. Correct. And to mak

Re: [R-pkg-devel] DLL requires the use of native symbols

checks and balances. (One micro nit for something else I noticed: you have a nice pkgdown site, but not linked to it anywhere.) Cheers, Dirk | | On 3/20/23 17:56, Dirk Eddelbuettel wrote: | > On 20 March 2023 at 12:43, Duncan Murdoch wrote: | > | It appears that you have some uses of .Call

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