Re: [R-pkg-devel] MSRV on Fedora

2024-07-23 Thread Hiroaki Yutani
> As such, I cannot manage the MSRV of the package's dependencies. It seems the reason for geographiclib-rs's MSRV is just that it uses std::sync::OnceLock. Maybe a possible workaround is to fork the repo and replace it with the once_cell crate? You should be able to override the dependency by

Re: [R-pkg-devel] MSRV on Fedora

2024-07-23 Thread Duncan Murdoch
I think saying that Fedora is not supported is the wrong solution, unless you know that Rust version 1.70 will never be supported on Fedora. Isn't the appropriate solution to document the MSRV in the SystemRequirements field of your DESCRIPTION file? When you submit, point out that you have

[R-pkg-devel] MSRV on Fedora

2024-07-23 Thread Josiah Parry
Hi all! I have 2 errors related to minimum supported rust version (MSRV) on fedora https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/rsgeo-00install.html that I do not know how to resolve. The package {rsgeo} has a dependency on the rust crate geo which itself has a

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-21 Thread Khue Tran
Thank you Duncan for providing detailed information on parsing in R. I will check it out and utilize the string inputs for my functions. Best regards, Khue Tran On Sat, Jul 20, 2024 at 4:40 AM Duncan Murdoch wrote: > Just for your info: > > > exp(mpfr("0.1", 152)) > 1 'mpfr' number of

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-21 Thread Khue Tran
Thank you Prof. Maechler! Indeed 0.1 is not the same as 1/10 and there are many ways to get more precise versions of it. I will look into how to take inputs as strings. Thank you! Best, Khue Tran On Sat, Jul 20, 2024 at 4:40 AM Duncan Murdoch wrote: > Just for your info: > > > exp(mpfr("0.1",

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-21 Thread Khue Tran
Dear Leonard, Thank you so much for the detailed response! Indeed, it would be nice to have it included in the BH header. Thank you for sharing your codes with me, I will definitely take a look at them to see if I can apply them to my case. I was steering away from mpfr type for a while since

Re: [R-pkg-devel] Is winbuilder "offline"?

2024-07-20 Thread Rolf Turner
On Sat, 20 Jul 2024 06:20:00 +0200 Uwe Ligges wrote: > > Strange. Your package has been processed. Have you tried again? > Are you sure the maintainer address is specified correctly and that > the auto generated message did not make it onto your spam box? > > If it still does not work, please

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-20 Thread Leo Mada via R-package-devel
Dear Khue, As mentioned before, you can use Rmpfr to read in strings or compute higher precision values, like x = mpfr(1, 192) /10; # 0.1 with 192 bits precision # or x = mpfr("0.1", 192); mpfr(1, 192) /10 - mpfr("0.1", 192) # 1 'mpfr' number of precision 192 bits # [1] 0 However, I do not

Re: [R-pkg-devel] Is winbuilder "offline"?

2024-07-19 Thread Uwe Ligges
On 20.07.2024 01:52, Rolf Turner wrote: On Fri, 19 Jul 2024 10:18:27 +0200 Uwe Ligges wrote: Not that I know, which queue do you mean? Apologies for my ignorance but I don't understand the question. I did not choose a "queue". I simply (as I have always done in the past) pointed my

Re: [R-pkg-devel] Is winbuilder "offline"?

2024-07-19 Thread Rolf Turner
On Fri, 19 Jul 2024 10:18:27 +0200 Uwe Ligges wrote: > Not that I know, which queue do you mean? Apologies for my ignorance but I don't understand the question. I did not choose a "queue". I simply (as I have always done in the past) pointed my browser at https://win-builder.r-project.org/

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-19 Thread Duncan Murdoch
Just for your info: > exp(mpfr("0.1", 152)) 1 'mpfr' number of precision 152 bits [1] 1.1051709180756476248117078264902466682245471948 So it looks like your approach of parsing the numbers yourself makes sense. You can find the R parser here:

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-19 Thread Duncan Murdoch
On 2024-07-19 12:37 p.m., Martin Maechler wrote: Khue Tran on Fri, 19 Jul 2024 09:32:14 +1000 writes: > Thank you for the suggestion, Denes, Vladimir, and Dirk. I have indeed > looked into Rmpfr and while the package can interface GNU MPFR with R > smoothly, as of right

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-19 Thread Martin Maechler
> Khue Tran > on Fri, 19 Jul 2024 09:32:14 +1000 writes: > Thank you for the suggestion, Denes, Vladimir, and Dirk. I have indeed > looked into Rmpfr and while the package can interface GNU MPFR with R > smoothly, as of right now, it doesn't have all the functions I need

Re: [R-pkg-devel] RTools 4.x Perl Incompatibility with WriteXLS CRAN Package

2024-07-19 Thread Marc Schwartz
Hi Ivan, Thanks kindly for your expedient reply and pointer to the LF/CRLF issue. Not sure that I would have found that issue so quickly, so was hoping for some intuition here, as you have provided. Thanks! Regards, Marc -Original Message- From: Ivan Krylov

Re: [R-pkg-devel] RTools 4.x Perl Incompatibility with WriteXLS CRAN Package

2024-07-19 Thread Ivan Krylov via R-package-devel
Dear Marc Schwartz, В Fri, 19 Jul 2024 10:49:31 -0400 Marc Schwartz пишет: > . No such file or > directory\Kleinbub\AppData\Local\Temp\RtmpuO4911/WriteXLS/1.csv This looks like an extra carriage return has messed up the output. By debugging WriteXLS and running the command line manually with

[R-pkg-devel] RTools 4.x Perl Incompatibility with WriteXLS CRAN Package

2024-07-19 Thread Marc Schwartz
Hi All, I recently became aware of what appears to be some kind of incompatibility between the Perl distribution that is included in the RTools 4.4 distribution and my WriteXLS package on CRAN, running R 4.4.1. As far as I can tell, since the vast majority of the users of my package, which

Re: [R-pkg-devel] Is winbuilder "offline"?

2024-07-19 Thread Uwe Ligges
Not that I know, which queue do you mean? Best, Uwe On 19.07.2024 00:45, Rolf Turner wrote: I submitted a package to winbuilder, yesterday. Twice. No response of any sort. Is the system down, for some reason? Anyone know? Ta. cheers, Rolf Turner

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Vladimir Dergachev
On Fri, 19 Jul 2024, Khue Tran wrote: I will need to run eigen() on a symmetric matrix, but I want to get arbitrary precise eigenvalues since we will need those eigenvalues for our further calculations. Does that make sense? For a symmetric matrix there is a nice algorithm that is simple

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Khue Tran
I will need to run eigen() on a symmetric matrix, but I want to get arbitrary precise eigenvalues since we will need those eigenvalues for our further calculations. Does that make sense? Best, Khue Tran On Fri, Jul 19, 2024 at 12:14 PM Vladimir Dergachev wrote: > > Do you need to run eigen()

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Vladimir Dergachev
Do you need to run eigen() on an arbitrary matrix or symmetric one ? best Vladimir Dergachev On Fri, 19 Jul 2024, Khue Tran wrote: Thank you Simon! This is very helpful! Regarding eigen, I found in the Boost library the following example for arbitrary precision matrix solver:

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Khue Tran
Thank you Simon! This is very helpful! Regarding eigen, I found in the Boost library the following example for arbitrary precision matrix solver: https://github.com/boostorg/multiprecision/blob/develop/example/eigen_example.cpp. I am not sure if the precision is fully preserved throughout the

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread J C Nash
On the other hand, Rmpfr did allow me to write an mpfr rootfinder for Martin M. in 2011 (he modified and streamlined it for use) since one can run R codes on mpfr objects as long as one is careful which operators are applied. So one probably could do something with a very pedestrian eigenvalue

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Simon Urbanek
Khue, > On 19/07/2024, at 11:32 AM, Khue Tran wrote: > > Thank you for the suggestion, Denes, Vladimir, and Dirk. I have indeed > looked into Rmpfr and while the package can interface GNU MPFR with R > smoothly, as of right now, it doesn't have all the functions I need (ie. > eigen for mpfr

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Khue Tran
Thank you for the suggestion, Denes, Vladimir, and Dirk. I have indeed looked into Rmpfr and while the package can interface GNU MPFR with R smoothly, as of right now, it doesn't have all the functions I need (ie. eigen for mpfr class) and when one input decimals, say 0.1 to mpfr(), the precision

[R-pkg-devel] Is winbuilder "offline"?

2024-07-18 Thread Rolf Turner
I submitted a package to winbuilder, yesterday. Twice. No response of any sort. Is the system down, for some reason? Anyone know? Ta. cheers, Rolf Turner -- Honorary Research Fellow Department of Statistics University of Auckland Stats. Dep't. (secretaries) phone:

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Dirk Eddelbuettel
Hi Khue, On 19 July 2024 at 06:29, Khue Tran wrote: | I am currently trying to get precise inputs by taking strings instead of | numbers then writing a function to decompose the string into a rational | with the denominator in the form of 10^(-n) where n is the number of | decimal places. I am

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Vladimir Dergachev
I see there are existing extended precision packages: Ryacas and Rmpfr, you might want to take a look at them and their representation of numbers with higher precision than a double. best Vladimir Dergachev On Fri, 19 Jul 2024, Khue Tran wrote: Hi, I am trying to create an Rcpp package

Re: [R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Dénes Tóth
Hi Khue, Have you already checked the Rmpfr package?: https://cran.r-project.org/package=Rmpfr Best, Denes On 7/18/24 22:29, Khue Tran wrote: Hi, I am trying to create an Rcpp package that involves arbitrary precise calculations. The function to calculate e^x below with 100 digits

[R-pkg-devel] How to get arbitrary precise inputs from R for an Rcpp package?

2024-07-18 Thread Khue Tran
Hi, I am trying to create an Rcpp package that involves arbitrary precise calculations. The function to calculate e^x below with 100 digits precision works well with integers, but for decimals, since the input is a double, the result differs a lot from the arbitrary precise result I got on

Re: [R-pkg-devel] Fwd: CRAN Submission rkriging 1.0.1

2024-07-18 Thread Ivan Krylov via R-package-devel
Hi Chaofan and welcome to R-package-devel! В Wed, 17 Jul 2024 11:52:53 -0700 Bill Huang <10billhuan...@gmail.com> пишет: > The package can be installed successfully locally and passed CRAN > auto-check. However, it cannot pass the gcc-UBSAN test with the > following error message: a problem with

Re: [R-pkg-devel] Disable parallelism on installation time

2024-07-18 Thread Matt Denwood
On the subject of extendr ... the recently published JOSS paper (which also mentions CRAN compliance under the "Creating Rust-powered R packages section") provides a good entry point for those interested in using extendr for their R/Rust packages:

[R-pkg-devel] Fwd: CRAN Submission rkriging 1.0.1

2024-07-18 Thread Bill Huang
Hi, Team. I am working on a package that uses RcppEigen. The package can be installed successfully locally and passed CRAN auto-check. However, it cannot pass the gcc-UBSAN test with the following error message: a problem with the LLT function in Eigen. I am not sure how to fix this. Any

Re: [R-pkg-devel] Disable parallelism on installation time

2024-07-17 Thread Chung-hong Chan
To add to this, I would like to point out that extendr actually has a guide on how to make an R package with Rust code CRAN compliance. https://github.com/extendr/rextendr/blob/main/vignettes/articles/cran-compliance.Rmd On Wed, Jul 17, 2024 at 10:21 AM Ivan Krylov via R-package-devel wrote: >

Re: [R-pkg-devel] Disable parallelism on installation time

2024-07-17 Thread Ivan Krylov via R-package-devel
В Tue, 16 Jul 2024 21:18:17 -0300 Alberson Miranda пишет: > besides examples, tests, vignettes and readme, what parts of code > runs during installation of a R package Neither. This is about `cargo build` compiling in parallel, not your package code computing in parallel. Giving the -j 2 flag

[R-pkg-devel] Disable parallelism on installation time

2024-07-17 Thread Alberson Miranda
Dear listeners, I'm having a hard time trying to figure out the following NOTE: |* checking whether package 'fio' can be installed... [202s/46s] NOTE Installation took CPU time 4.4 times elapsed time | Uwe asked if there's code running in parallel by default and, yes, there was: my code uses

Re: [R-pkg-devel] Properly referencing copied code

2024-07-15 Thread DRC via R-package-devel
Thank you everyone, I think this gives me everything I need to know and I have no problem spreading the copyright around. I'm not sure adding my dependencies to MXE is going to make sense here but open to being convinced otherwise. The package I am working on is wrapping functions from my own

Re: [R-pkg-devel] Properly referencing copied code

2024-07-15 Thread Ivan Krylov via R-package-devel
В Fri, 12 Jul 2024 20:17:22 + DRC via R-package-devel пишет: > > Has copyright holders of included software in a [ctb] role only > > I think I'm being asked to add the cph role to essentially every > author in addition to [ctb] That's how I'm reading it too. > but that doesn't seem to

Re: [R-pkg-devel] Properly referencing copied code

2024-07-13 Thread Tomas Kalibera
On 7/13/24 12:24, Simon Urbanek wrote: On 12 Jul 2024, at 10:07, Ivan Krylov via R-package-devel wrote: В Thu, 11 Jul 2024 20:58:53 + DRC via R-package-devel пишет: 1. How does linking to external libs differ from providing the source of a library and linking against that? I think

Re: [R-pkg-devel] Properly referencing copied code

2024-07-13 Thread Simon Urbanek
> On 12 Jul 2024, at 10:07, Ivan Krylov via R-package-devel > wrote: > > В Thu, 11 Jul 2024 20:58:53 + > DRC via R-package-devel пишет: > >> 1. How does linking to external libs differ from providing the source >> of a library and linking against that? > > I think that the author

Re: [R-pkg-devel] Properly referencing copied code

2024-07-12 Thread DRC via R-package-devel
Thanks that helps. Are there any thoughts on the feedback I was given? I'm still a bit confused on the note: > Has copyright holders of included software in a [ctb] role only I think I'm being asked to add the cph role to essentially every author in addition to ctp but that doesn't seem to be

[R-pkg-devel] relative vignette paths across CRAN check flavors

2024-07-12 Thread Slager, Dave
Hi, Do the r-oldrel-macos-* CRAN check servers use a different setting that affects how vignette paths work? These two flavors seem less robust to relative vignette paths than other flavors, and I haven't been able to figure out why by looking at the descriptions of the flavors or the R CMD

Re: [R-pkg-devel] Properly referencing copied code

2024-07-12 Thread Ivan Krylov via R-package-devel
В Thu, 11 Jul 2024 20:58:53 + DRC via R-package-devel пишет: > 1. How does linking to external libs differ from providing the source > of a library and linking against that? I think that the author information in the DESCRIPTION is about what your package provides by itself, not everything

[R-pkg-devel] Properly referencing copied code

2024-07-11 Thread DRC via R-package-devel
I'm trying to submit a package to CRAN that uses external C libs but properly crediting copyright holders and authors is the main issue holding up the submission and I've repeatedly failed to satisfy the requirements. I am having a lot of trouble understanding what/who I need to be listing in

Re: [R-pkg-devel] Options "reset" when options(opts)

2024-07-11 Thread Vladimir Dergachev
On Thu, 11 Jul 2024, David Hugh-Jones wrote: This surprised me, even though it shouldn’t have done. (My false internal model of the world was that oo <- options(); … options(oo) would overwrite the entire options list with the old values.) I wonder if it would be worth pointing out

Re: [R-pkg-devel] Help for understanding CRAN rejection

2024-07-11 Thread Matei Teleman
Dear Ivan, Thank you so much for your help. I followed your advices and I reduced the size of the example data, move one package from Import to Suggest. The type of the license is unfortunately not depending on me so I’ll try one last time with the CC license and the new improvements. Thank

Re: [R-pkg-devel] cpp11 and "non-API calls to R"

2024-07-11 Thread Chung-hong Chan
Not from CRAN, also not in a position to opine on cpp11 status, but I wrote about it recently. My solution for readODS back then was to vendor cpp11 and remove the SET_LENGTH call manually, like . But back then CRAN might not know about this. I think it should be easier now.

Re: [R-pkg-devel] Options "reset" when options(opts)

2024-07-11 Thread David Hugh-Jones
This surprised me, even though it shouldn’t have done. (My false internal model of the world was that oo <- options(); … options(oo) would overwrite the entire options list with the old values.) I wonder if it would be worth pointing out explicitly in ?options. Writing: wyclif.substack.com Book:

Re: [R-pkg-devel] Options "reset" when options(opts)

2024-07-11 Thread Greg Jefferis
Dear John, You need to collect the return value when setting options. This will include an explicit NULL value for an option that was previously NULL. Best, Greg Jefferis. options(digits.secs = NULL) noset2 = function() { opts <- options(digits.secs = 3) on.exit(options(opts))

Re: [R-pkg-devel] [External] Use of ‘R_InputHandlers’

2024-07-11 Thread luke-tierney
On Wed, 10 Jul 2024, Duncan Murdoch wrote: An update to the rgl package was rejected with this note: * checking compiled code ... NOTE File ‘rgl/libs/rgl.so’: Found non-API call to R: ‘R_InputHandlers’ Compiled code should not call non-API entry points in R. See ‘Writing portable

[R-pkg-devel] Options "reset" when options(opts)

2024-07-10 Thread John Muschelli
When setting options in a function, I have always used the following: opts <- options() on.exit(options(opts), add = TRUE) and assumed it "reset" options to what they were prior to running the function. But for some options that are set to NULL, it does not seem to reset them. Specifically,

[R-pkg-devel] Use of ‘R_InputHandlers’

2024-07-10 Thread Duncan Murdoch
An update to the rgl package was rejected with this note: * checking compiled code ... NOTE File ‘rgl/libs/rgl.so’: Found non-API call to R: ‘R_InputHandlers’ Compiled code should not call non-API entry points in R. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual, and

Re: [R-pkg-devel] Help for understanding CRAN rejection

2024-07-09 Thread Ivan Krylov via R-package-devel
(I am adding the mailing list back in Cc: because package licensing is a complicated topic.) В Tue, 9 Jul 2024 09:25:14 + Matei Teleman пишет: > I’ve added “ … SuperCell uses > [velocyto.R](https://github.com/velocyto-team/velocyto.R) for RNA > velocity. ” in the Description field. Is that

Re: [R-pkg-devel] NOTE about lack of prebuilt manual

2024-07-09 Thread Michael Dewey
Thank you to, in alphabetical order of given names, Iris, Ivan, Uwe and Wolfgang for your responses. I implemented Iris' suggestion and have successfully uploaded one of the packages to CRAN. Michael On 09/07/2024 10:06, Ivan Krylov wrote: В Tue, 9 Jul 2024 08:54:22 + "Viechtbauer,

Re: [R-pkg-devel] NOTE about lack of prebuilt manual

2024-07-09 Thread Ivan Krylov via R-package-devel
В Tue, 9 Jul 2024 08:54:22 + "Viechtbauer, Wolfgang (NP)" пишет: > This appears to be related to this change > (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html): > > - tools::checkRd() (used by R CMD check) detects more problems with > ⁠\Sexpr⁠-based dynamic content, including bad

Re: [R-pkg-devel] cpp11 and "non-API calls to R"

2024-07-09 Thread Hadley Wickham
Hi Mark, The cpp11 package is now maintained by Davis Vaughan and we will release a new version once the C API status is a little cleaner. This warnings generated from cpp11 will not interfere with your ability to submit your package; just let CRAN know that the warnings are coming from cpp11.

Re: [R-pkg-devel] NOTE about lack of prebuilt manual

2024-07-09 Thread Viechtbauer, Wolfgang (NP)
Hi Michael, I assume you are getting this note because you are using mathjaxr. I am also getting this and others have reported the same: https://github.com/wviechtb/mathjaxr/issues/15 (my response on the forum was a bit premature, since this note eventually did show up for me as well). This

Re: [R-pkg-devel] Help for understanding CRAN rejection

2024-07-09 Thread Ivan Krylov via R-package-devel
В Mon, 8 Jul 2024 15:12:24 + Matei Teleman пишет: > Non-FOSS package license (file LICENSE) > The license we’re using is the standard CC BY-NC-ND 4.0 and is listed > among the accepted licenses for CRAN Instead of putting the license text in a file inside the package (that would have to

Re: [R-pkg-devel] Notes while a new R package submission

2024-07-08 Thread Ben Bolker
The first NOTE is irrelevant. The second NOTE says that you must reduce the running time of your examples (so that the longest of them takes <10 seconds on the *slowest* CRAN testing platform). This thread might be useful: https://stat.ethz.ch/pipermail/r-package-devel/2021q4/007521.html

[R-pkg-devel] Help for understanding CRAN rejection

2024-07-08 Thread Matei Teleman
Hello everyone, I hope this email finds you well. I’m sorry to bother you, it’s the very first time I’m submitting a package to CRAN. Recently my submission got rejected with the following feedback: Non-FOSS package license (file LICENSE) Suggests or Enhances not in mainstream

[R-pkg-devel] Notes while a new R package submission

2024-07-08 Thread Mahadi Hassan
Hello everyone I need your attention. I have developed a new R package and submitted it to CRAN. In return main i got two notes they are: * using log directory 'd:/RCompile/CRANincoming/R-devel/drglm.Rcheck' * using R Under development (unstable) (2024-07-05 r86875 ucrt) * using platform:

Re: [R-pkg-devel] Segfaults on R-devel

2024-07-08 Thread Ben Bolker
I'm pretty sure this is from this R-devel commit: https://github.com/r-devel/r-svn/commit/92c1d5de23c93576f55062e26d446feface07250 This turns on stricter boundary checking, specifically see https://github.com/lme4/lme4/issues/794#issuecomment-2154948145 Arguably, accessing an element of

[R-pkg-devel] Segfaults on R-devel

2024-07-08 Thread Claborne, Daniel via R-package-devel
Seemingly starting with the most recent builds of R-devel, I�ve been getting segfaults related to a piece of cpp code that indexes a zero-size NumericVector. Essentially the same as this dummy example: ``` library(Rcpp) sourceCpp( code = ' #include using namespace Rcpp; //

Re: [R-pkg-devel] NOTE about lack of prebuilt manual

2024-07-08 Thread Uwe Ligges
On 08.07.2024 16:08, Iris Simmons wrote: This is something I'd run into recently as well. The R devs changed the default from building the manual to not building the manual. Now if you want (or need) to build the manual, you should add Well, not really, we still build manuals unless

Re: [R-pkg-devel] cpp11 and "non-API calls to R"

2024-07-08 Thread Josiah Parry
Hi Mark, As someone else affected by this issue, it is actually quite tough to resolve. This is because quite literally every other day, the list of what is and is not non-API is changing. It is particularly challenging since this is in R-devel and not any stable R release. If there were a

Re: [R-pkg-devel] cpp11 and "non-API calls to R"

2024-07-08 Thread Ben Bolker
Have you contacted the maintainer directly (i.e. by e-mail)? (Yes, they should be paying attention to Github, but trying another channel never hurts.) My personal experience is that I was succeeded in submitting a package update to CRAN even though there were NOTEs of this sort (in that

[R-pkg-devel] cpp11 and "non-API calls to R"

2024-07-08 Thread Mark Padgham
Dear R-pkg-dev folk, The cpp11 package, which was developed yet is no longer maintained by Jim Hester, now triggers warnings on some CRAN pre-submit checks for "non-API calls to R" via "SETLENGTH", "SET_TRUELENGTH", and others. The relevant issue is https://github.com/r-lib/cpp11/issues/355,

Re: [R-pkg-devel] NOTE about lack of prebuilt manual

2024-07-08 Thread Iris Simmons
This is something I'd run into recently as well. The R devs changed the default from building the manual to not building the manual. Now if you want (or need) to build the manual, you should add BuildManual: TRUE to your DESCRIPTION. On Mon, Jul 8, 2024, 10:05 Michael Dewey wrote: > Short

[R-pkg-devel] NOTE about lack of prebuilt manual

2024-07-08 Thread Michael Dewey
Short version I have recently tried to update two of my CRAN packages and I am getting the NOTE from R CMD check --as-cran Package has help file(s) containing install/render-stage \Sexpr{} expressions but no prebuilt PDF manual. (It comes on one line in the check.log) What am I doing

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-02 Thread Achim Zeileis
On Tue, 2 Jul 2024, Martin Maechler wrote: Achim Zeileis on Tue, 2 Jul 2024 01:05:07 +0200 (CEST) writes: > Kevin, R-Forge is still alive but there are problems with > the build queue as you noticed. The problems occurred > after R-Forge upgraded to R 4.4.0 - just as there was a

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-02 Thread Martin Maechler
> Achim Zeileis > on Tue, 2 Jul 2024 01:05:07 +0200 (CEST) writes: > Kevin, R-Forge is still alive but there are problems with > the build queue as you noticed. The problems occurred > after R-Forge upgraded to R 4.4.0 - just as there was a > switch in the maintenance

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-01 Thread Jeff Newmiller via R-package-devel
I cannot/will not to help you do this, but there are people out there who disagree with me who put considerable effort into doing this... the search term you would need in order to find them is "monorepo". But please reconsider... the whole point of putting code into separate packages is to

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-01 Thread Achim Zeileis
Kevin, R-Forge is still alive but there are problems with the build queue as you noticed. The problems occurred after R-Forge upgraded to R 4.4.0 - just as there was a switch in the maintenance team at WU Wien. The problem is with the Windows build/check tools which work fine when run

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-01 Thread Duncan Murdoch
While you can put multiple packages in one Git repository, I'd suggest that you don't do that. Most packages are in their own repository, and that means that users who want to contribute to your packages are familiar with that setup. If they have to fork 20 packages at once to make a

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-01 Thread Ben Bolker
I don't know about R-forge, but it's perfectly workable to put multiple packages within a single repo, with each package in its own subdirectory. You'll run into some headaches occasionally with (e.g.) CI machinery that assumes that the head of a git repo is also the primary package

Re: [R-pkg-devel] Is R-Forge dead?

2024-07-01 Thread Brian G. Peterson
Kevin, I can't speak to whether R-Forge is dead, we migrated our projects to github a long time ago. The most straightforward answer for R packages in git repositories is to use separate git projects. we were even able to import the entire SVN history and r-forge issue history to github for

[R-pkg-devel] Is R-Forge dead?

2024-07-01 Thread Kevin R. Coombes
Hi, I have been maintaining packages in R-Forge for many tears. Last week I sent an email to r-fo...@r-project.org to report problems with the build process. It appears that any changes I have pushed to R-Forge over approximately the last two months have resulted in the package remaining in

[R-pkg-devel] R-devel non-API & extendr v0.7.0

2024-06-30 Thread Josiah Parry
Hi folks, A new release of extendr v0.7.0 is now available. This release addresses the R-devel WARNings from non-API functions being used. This release also comes with breaking changes. We've written a brief migration guide which can be found at:

Re: [R-pkg-devel] Help needed with CRAN check error under MacOS and old-rel

2024-06-30 Thread Spencer Graves
Hello, Pedro et al.: Your package is on GitHub with GitHub Actions.[1] If whoever manages GitHub actions feels inclined to add macos-latest (oldrel-1), this would be one argument for doing that, though this kind of problem may be too rare to justify the expense. That's particularly true

Re: [R-pkg-devel] Help needed with CRAN check error under MacOS and old-rel

2024-06-30 Thread Duncan Murdoch
On 2024-06-30 5:17 a.m., Aphalo, Pedro J wrote: Hello, A few days ago I submitted to CRAN an updated version of package 'ggpp', it passed checks during submission and version 0.5.8 is now on CRAN. However I see errors for old-rel only for MacOS at

[R-pkg-devel] Help needed with CRAN check error under MacOS and old-rel

2024-06-30 Thread Aphalo, Pedro J
Hello, A few days ago I submitted to CRAN an updated version of package 'ggpp', it passed checks during submission and version 0.5.8 is now on CRAN. However I see errors for old-rel only for MacOS at https://cran.r-project.org/web/checks/check_results_ggpp.html and I am stuck as I do not have

Re: [R-pkg-devel] Vignette error: "there is no package called 'markdown'"

2024-06-29 Thread Spencer Graves
That was it. Thanks very much. Now I can go back to working on the "[.findFn" problem that you helped me identify. (I translated the Sweave vignette to RMarkdown to isolate that. Progress, with your help.) Spencer On 6/29/24 04:47, Ivan Krylov wrote: В Fri, 28 Jun

Re: [R-pkg-devel] Incomprehensible warning while checking

2024-06-29 Thread Ivan Krylov via R-package-devel
В Fri, 28 Jun 2024 17:57:13 -0400 Iris Simmons пишет: > * checking whether the namespace can be unloaded cleanly ... WARNING > unloading Here's what the check does (in a separate process): invisible(suppressMessages(loadNamespace("this.path"))); cat('\n unloading\n');

Re: [R-pkg-devel] Vignette error: "there is no package called 'markdown'"

2024-06-29 Thread Ivan Krylov via R-package-devel
В Fri, 28 Jun 2024 22:55:23 -0500 Spencer Graves пишет: > I'm getting, "Error: processing vignette 'sos.Rmd' failed > with diagnostics: there is no package called 'markdown'": > > > https://github.com/sbgraves237/sos/actions/runs/9721300082/job/26833793243 > > > This is in: >

[R-pkg-devel] Vignette error: "there is no package called 'markdown'"

2024-06-28 Thread Spencer Graves
Hello, All: I'm getting, "Error: processing vignette 'sos.Rmd' failed with diagnostics: there is no package called 'markdown'": https://github.com/sbgraves237/sos/actions/runs/9721300082/job/26833793243 This is in:

Re: [R-pkg-devel] Incomprehensible warning while checking

2024-06-28 Thread Jeff Newmiller via R-package-devel
Have you reviewed WRE 5.3? I don't have personal experience with R 4.4 much less the dev version, but it seems that often they add checks in new versions of R for rules that have been published but ignored. On June 28, 2024 4:00:06 PM PDT, Iris Simmons wrote: >Thank you Jeff! I'm not worried

Re: [R-pkg-devel] Incomprehensible warning while checking

2024-06-28 Thread Roy Mendelssohn - NOAA Federal via R-package-devel
>From https://r-pkgs.org/r-cmd-check.html: Checking whether the namespace can be unloaded cleanly. Runs loadNamespace("pkg"); unloadNamespace("pkg"). Check .onUnload() for problems. HTH, -Roy > On Jun 28, 2024, at 4:00 PM, Iris Simmons wrote: > > Thank you Jeff! I'm not worried about the

Re: [R-pkg-devel] Incomprehensible warning while checking

2024-06-28 Thread Iris Simmons
Thank you Jeff! I'm not worried about the NOTE about the URLs, I've submitted many previous versions of this package that all had that note and they've all been accepted. I'm worried about the WARNING when the namespace is unloaded. The message is just " unloading" with no further

Re: [R-pkg-devel] Incomprehensible warning while checking

2024-06-28 Thread Jeff Newmiller via R-package-devel
Google for "http 403 error"... likely win-builder has multiple packages with links to Posit, and the Posit web server is throttling automated hits. Theoretically this is just a warning and you can try submitting to CRAN, but CRAN may have even less luck accessing Posit than win-builder.

[R-pkg-devel] Incomprehensible warning while checking

2024-06-28 Thread Iris Simmons
Hi, I've got an update for my R package ready to go. It checks successfully on my own machine for r-oldrel and r-release, but when I submit it to R Win Builder for r-devel to be checked, it gives me a warning not seen before with an uninformative message: * checking whether the namespace can be

[R-pkg-devel] Survey from CRAN Cookbook project

2024-06-28 Thread Heather Turner
Dear All, If you would like to share your thoughts on the CRAN submission process, please fill this short survey from the CRAN Cookbook project   Survey: https://forms.gle/umdew9KHWeQSehq8A  Project announcement:

Re: [R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-26 Thread Agner Fog
Thank you, but I still think the Writing R Extensions manual needs to be updated. The manual lists a large number of remapped function names. These names cannot be used in any package in the current R version (4.4.1) because R_NO_REMAP is defined in the Debian build script (intentionally or

Re: [R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-25 Thread Tomas Kalibera
On 6/24/24 09:45, Agner Fog wrote: On 24/06/2024 08.56, Tomas Kalibera wrote: In principle it is the NEWS file that gives hints about important changes and then one can find the details in Writing R Extensions.  The NEWS file as of mid-April says that "R CMD check --as-cran" will compile

Re: [R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-24 Thread Agner Fog
On 24/06/2024 08.56, Tomas Kalibera wrote: In principle it is the NEWS file that gives hints about important changes and then one can find the details in Writing R Extensions.  The NEWS file as of mid-April says that "R CMD check --as-cran" will compile C++ code with -DR_NO_REMAP. And then

Re: [R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-24 Thread Tomas Kalibera
On 6/24/24 08:25, Agner Fog wrote: Jarrod Hadfield wrote: Using Rf_error() rather than error() fixed the problem. Not sure why the problem was only flagged on Debian, but it seems to have been triggered by R_NO_REMAP being defined (which will be default in R 4.5.0). I had the same

[R-pkg-devel] "Writing R Extensions" manual needs update [was: Error handling in C code]

2024-06-24 Thread Agner Fog
Jarrod Hadfield wrote: > Using Rf_error() rather than error() fixed the problem. Not sure why the > problem was only flagged on Debian, but it > seems to have been triggered by R_NO_REMAP being defined (which will be > default in R 4.5.0). I had the same problem. A lot of functions in my

Re: [R-pkg-devel] Windows binary package not at mirrors

2024-06-23 Thread Agner Fog
It is probably checking the version anyway. If a binary package is available for a later version, then it may say something like: "The latest version of the binary package does not match your currently installed version of R. You may update R, or you may compile the package for the installed

Re: [R-pkg-devel] Windows binary package not at mirrors

2024-06-23 Thread Duncan Murdoch
On 2024-06-23 8:01 a.m., Agner Fog wrote: Also, I think the system should recommend to the user to update RStudio when a package is not available for the installed version. The current message does not tell the cause of the problem. It just says: Do you want to install from sources the package

Re: [R-pkg-devel] Windows binary package not at mirrors

2024-06-23 Thread Agner Fog
Also, I think the system should recommend to the user to update RStudio when a package is not available for the installed version. The current message does not tell the cause of the problem. It just says: Do you want to install from sources the package which needs compilation? - Agner

Re: [R-pkg-devel] Windows binary package not at mirrors

2024-06-23 Thread Helmut Schütz
Duncan Murdoch wrote on 2024-06-23 13:04: […] One exception is the one run by Posit: because it is cloud based, I think they spend quite a lot of money on it. […] it means that it is very reliable, and it's the one I use almost all the time. I agree. It is also helpful for developers of

Re: [R-pkg-devel] Windows binary package not at mirrors

2024-06-23 Thread Duncan Murdoch
On 2024-06-23 5:44 a.m., Agner Fog wrote: On 23/06/2024 09.56, Duncan Murdoch wrote: CRAN only builds Windows binaries for the devel version, the current release, and the previous release, so nothing older than 4.3.0 will get it. Thank you. Updating R helped. BTW, I don't think we need so

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