Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 06:25, Duncan Murdoch wrote: | You could make a compatible version of `survivalmodels` available on a | non-CRAN website, and refer to that website in the | Additional_repositories field of DESCRIPTION. Every r-universe sub-site fits that requirement. For this package Google

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 11:56, Duncan Murdoch wrote: | I have mixed feelings about r-universe. On the one hand, it is really | nicely put together, and it offers the service described above. On the | other, it's probably a bad idea to follow its advice and use | install.packages() with `repos` as

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 13:28, Duncan Murdoch wrote: | What I'm seeing is that the tags are ignored, and it is distributing the | HEAD of the main branch. I don't think most users should be using that | version: in my packages it won't have had full reverse dependency | checks, I only do that bef

Re: [R-pkg-devel] Suggesting an archived package in the DESCRIPTION file

On 5 March 2024 at 15:12, Duncan Murdoch wrote: | On 05/03/2024 2:26 p.m., Dirk Eddelbuettel wrote: | > The default behaviour is to build after every commit to the main branch. But | > there are options. On the repo I mentioned we use | > | > "branch": "*rele

Re: [R-pkg-devel] new maintainer for CRAN package XML

Dear Uwe, Did CRAN ever reach a decision here with a suitable volunteer (or group of volunteers) ? The state of XML came up again recently on mastodon, and it might be helpful to share an update if there is one. Thanks, as always, for all you and the rest of the team do for CRAN. Cheers, Dirk

Re: [R-pkg-devel] Request for assistance: error in installing on Debian (undefined symbol: omp_get_num_procs) and note in checking the HTML versions (no command 'tidy' found, package 'V8' unavailable

Salut Annaig, On 21 March 2024 at 09:26, Annaig De-Walsche wrote: | Dear R-package-devel Community, | | I hope this email finds you well. I am reaching out to seek assistance regarding package development in R. | | Specifically, I am currently developing an R package for querying composite h

Re: [R-pkg-devel] How to store large data to be used in an R package?

On 25 March 2024 at 11:12, Jairo Hidalgo Migueles wrote: | I'm reaching out to seek some guidance regarding the storage of relatively | large data, ranging from 10-40 MB, intended for use within an R package. | Specifically, this data consists of regression and random forest models | crucial for

Re: [R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

Avi, That was a hickup and is now taken care of. When discussing this (off-line) with Jeroen we (rightly) suggested that keeping an eye on https://contributor.r-project.org/svn-dashboard/ is one possibility to keep track while we have no status alert system from CRAN. I too was quite confu

Re: [R-pkg-devel] using portable simd instructions

On 26 March 2024 at 10:53, jesse koops wrote: | How can I make this portable and CRAN-acceptable? But writing (or borrowing ?) some hardware detection via either configure / autoconf or cmake. This is no different than other tasks decided at install-time. Start with 'Writing R Extensions', as

Re: [R-pkg-devel] Check results on r-devel-windows claiming error but tests seem to pass?

On 26 March 2024 at 09:37, Dirk Eddelbuettel wrote: | | Avi, | | That was a hickup and is now taken care of. When discussing this (off-line) | with Jeroen we (rightly) suggested that keeping an eye on Typo, as usual, "he (rightly) suggested". My bad. D. | |https://con

Re: [R-pkg-devel] using portable simd instructions

ogle/crc32c [1] repo: https://github.com/google/highway docs: https://google.github.io/highway/en/master/ | | Op di 26 mrt 2024 om 15:41 schreef Dirk Eddelbuettel : | > | > | > On 26 March 2024 at 10:53, jesse koops wrote: | > | How can I make this portable and CRAN-acceptable? |

Re: [R-pkg-devel] Order of repo access from options("repos")

Greg, There are AFAICT two issues here: how R unrolls the named vector that is the 'repos' element in the list 'options', and how your computer resolves DNS for localhost vs 172.17.0.1. I would try something like options(repos = c(CRAN = "http://localhost:3001/proxy";,

Re: [R-pkg-devel] Order of repo access from options("repos")

On 31 March 2024 at 11:43, Martin Morgan wrote: | So all repositories are consulted and then the result filtered to contain just | the most recent version of each. Does it matter then what order the | repositories are visited? Right. I fall for that too often, as I did here. The order matters f

Re: [R-pkg-devel] Order of repo access from options("repos")

On 1 April 2024 at 17:44, Uwe Ligges wrote: | Untested: | | install.packages() calls available.packages() to find out which packages | are available - and passes a "filters" argument if supplied. | That can be a user defined filter. It should be possible to write a user | defined filter which

Re: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

Rolf, This question might have been more appropriate for r-sig-debian than here. But as Simon noted, the lack of detail makes is difficult to say anything to aid. It likely was an issue local to your setup and use. These days, I strongly recommend r2u [1]. As you already use R via CRAN through

Re: [R-pkg-devel] Problem with loading package "devtools" from CRAN.

On 30 April 2024 at 01:21, Rolf Turner wrote: | On Mon, 29 Apr 2024 06:30:20 -0500 | Dirk Eddelbuettel wrote: | | | | > These days, I strongly recommend r2u [1]. As you already use R via | > CRAN through apt, r2u adds one more repository after which _all_ R | > packages are handle

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

On 8 May 2024 at 11:02, Josiah Parry wrote: | CRAN has rejected this package with: | | * Size of tarball: 18099770 bytes* | | *Please reudce to less than 5 MB for a CRAN package.* Are you by chance confusing a NOTE (issued, but can be overruled) with a WARNING (more severe, likely a must-be-

Re: [R-pkg-devel] Fast Matrix Serialization in R?

On 9 May 2024 at 03:20, Sameh Abdulah wrote: | I need to serialize and save a 20K x 20K matrix as a binary file. Hm that is an incomplete specification: _what_ do you want to do with it? Read it back in R? Share it with other languages (like Python) ? I.e. what really is your use case? Also, y

Re: [R-pkg-devel] Overcoming CRAN's 5mb vendoring requirement

Software Heritage (see [1] for their website and [2] for a brief intro I gave at useR! 2019 in Toulouse) covers GitHub and CRAN [3]. It is by now 'in collaboration with UNESCO', supported by a long and posh list of sponsors [4] and about as good as it gets to 'ensure longevity of artifacts'. It

Re: [R-pkg-devel] CRAN packages dependency on bioconductor packages

On 16 May 2024 at 05:34, Duncan Murdoch wrote: | I forget now, but presumably the thinking at the time was that Suggested | packages would always be available for building and checking vignettes. Yes. I argued for years (cf https://dirk.eddelbuettel.com/blog/2017/03/22/ from seven (!!) years ag

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

Hi Michelle, On 21 May 2024 at 13:46, Nixon, Michelle Pistner wrote: | Hi all, | | I'm running into build issues for my package (fido: https://github.com/jsilve24/fido) on the r-devel-linux-x86_64-debian-clang system on CRAN (full check log here: https://win-builder.r-project.org/incoming_pre

Re: [R-pkg-devel] handling documentation build tools

As lyx is not listed in 'Writing R Extensions', the one (authorative) manual describing how to build packages for R, I would not assume it to be present on every CRAN machine building packages. Also note that several user recently had to ask here how to deal with less common fonts for style files

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

o condition on here? Michelle did AFAICT the Right Thing (TM) by 'borrowing' from the fairly mature check in RcppArmadillo. Dirk | | Thanks, | Michelle | ━━━ | From: Kurt Hornik | Sent: Wednesday, May 22, 2024

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

On 22 May 2024 at 14:03, Duncan Murdoch wrote: | On 2024-05-22 10:18 a.m., Dirk Eddelbuettel wrote: | > | > On 22 May 2024 at 13:54, Nixon, Michelle Pistner wrote: | > | Thank you both for your responses and help! Kurt-- your message makes a lot of | > | sense. I'll try to de

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

On 23 May 2024 at 20:02, Ivan Krylov wrote: | On Wed, 22 May 2024 09:18:13 -0500 | Dirk Eddelbuettel wrote: | | > Testing via 'nm' as you show is possible but not exactly 'portable'. | > So any suggestions as to what to condition on here? | | (My apologies if you

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

Kurt, Could you do me a favour and run on that clang18-using machine in question the following one-liner (provided your session has access to a .libPaths() including Rcpp) and, in the case of success, the resulting function? > Rcpp::cppFunction("int ompconfigtest() { return omp_get_num_thread

Re: [R-pkg-devel] gcc14 checks on fedora

On 24 May 2024 at 20:01, Brad Eck wrote: | I received a note that my package -- epanet2toolkit -- was showing a | warning in the fedora-gcc results on CRAN. | https://www.stats.ox.ac.uk/pub/bdr/gcc12/epanet2toolkit.out | | I'd like to reproduce the warning and fix it. Usually I'd do that with |

Re: [R-pkg-devel] Compile issues on r-devel-linux-x86_64-debian-clang with OpenMP

On 26 May 2024 at 13:31, Kurt Hornik wrote: | >>>>> Dirk Eddelbuettel writes: | | > Kurt, | | > Could you do me a favour and run on that clang18-using machine in question | > the following one-liner (provided your session has access to a .libPaths() | > includin

Re: [R-pkg-devel] No email with confirmation link on resubmission of package

On 6 June 2024 at 04:47, Paul Kabaila wrote: | When I resubmitted, I didn't realise that I needed to change the version number. As this comes up every now and then: This is still a _soft_ requirement. CRAN does not 'cache' what versions you used in uploads. I have often reiterated with the same

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

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 n

Re: [R-pkg-devel] R CMD BATCH plot output

On 28 July 2024 at 15:44, Duncan Murdoch wrote: | On 2024-07-28 1:48 p.m., Josiah Parry wrote: | > However, if plots are generated in the process, the plots are stored in | > Rplots.pdf. | > | > Is there a way via command line arguments to change the name of the pdf | > output. | > | > There mi

Re: [R-pkg-devel] R CMD BATCH plot output

On 29 July 2024 at 13:02, Ivan Krylov wrote: | On Sun, 28 Jul 2024 15:27:33 -0500 | Dirk Eddelbuettel wrote: | | > If we cannot (or do not want to) modify the given main.R, I would | > suggest something along the lines of | > | > Rscript -e 'pdf(myfilenamevar); source(&

Re: [R-pkg-devel] rhub (version 2) baulking at building a vignette.

On 2 August 2024 at 16:12, Ivan Krylov via R-package-devel wrote: | В Fri, 2 Aug 2024 11:10:59 + | Rolf Turner пишет: | | > The advice was to the effect that if the vignette was actually just a | > *.tex file, one could (after putting in some preparatory code, in the | > form of comments,

Re: [R-pkg-devel] Build process generated non-portable files

On 17 August 2024 at 17:22, Ivan Krylov via R-package-devel wrote: | В Fri, 16 Aug 2024 18:53:55 + | anj5x...@nilly.addy.io пишет: | | > In the past other packages have failed to build and not only on the | > intel container see | > "https://github.com/SpeakEasy-2/speakeasyR/actions/runs/10

[R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

Has anybody written a quick helper function that extracts the Authors@R field from tools::CRAN_package_db() and 'stems' it into 'Name, Firstname, ORCID' which one could use to look up ORCID IDs at CRAN? The lookup at orcid.org sometimes gives us 'private entries' that make it harder / impossible

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 19 August 2024 at 15:15, Thierry Onkelinx wrote: | Maybe checklist:::author2df() might be useful. It is an unexported function | from my checklist package. It converts a person() object to a dataframe. | https://github.com/inbo/checklist/blob/5649985b58693acb88337873ae14a7d5bc018d96 | /R/stor

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

Salut Thierry, On 20 August 2024 at 13:43, Thierry Onkelinx wrote: | Happy to help. I'm working on a new version of the checklist package. I could | export the function if that makes it easier for you. Would be happy to help / iterate. Can you take a stab at making the per-column split more rob

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

Hi Kurt, On 20 August 2024 at 14:29, Kurt Hornik wrote: | I think for now you could use something like what I attach below. | | Not ideal: I had not too long ago starting adding orcidtools.R to tools, | which e.g. has .persons_from_metadata(), but that works on the unpacked | sources and not th

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

many things at once... Dirk | I think that has become both recursive and demonstrating excellent | test-retest stability!  Oh boy do I know that issue! | | Chris | | On 20/08/2024 14:57, Dirk Eddelbuettel wrote: | > Hi Kurt, | > | > On 20 August 2024 at 14:29, Kurt Hornik wrote: | >

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 20 August 2024 at 07:57, Dirk Eddelbuettel wrote: | | Hi Kurt, | | On 20 August 2024 at 14:29, Kurt Hornik wrote: | | I think for now you could use something like what I attach below. | | | | Not ideal: I had not too long ago starting adding orcidtools.R to tools, | | which e.g. has

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 20 August 2024 at 15:47, Kurt Hornik wrote: | > Kurt Hornik writes: | | The variant attaches drops the URL and does unique. Nice. Alas, some of us default to r-release as the daily driver and then Error in unname(tools:::.ORCID_iD_canonicalize(o)) : object '.ORCID_iD_canonicalize

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 21 August 2024 at 07:43, Dirk Eddelbuettel wrote: | | On 20 August 2024 at 15:47, Kurt Hornik wrote: | | >>>>> Kurt Hornik writes: | | | | The variant attaches drops the URL and does unique. | | Nice. Alas, some of us default to r-release as the daily driver and then | |

Re: [R-pkg-devel] ORCID ID finder via tools::CRAN_package_db() ?

On 21 August 2024 at 15:47, Kurt Hornik wrote: | > Kurt Hornik writes: | | Committed now. That is just *lovely*: > aut <- tools::CRAN_authors_db() > dim(aut) [1] 47433 7 > head(aut) given family email orcid role comment

Re: [R-pkg-devel] Licensing of an R package

Chris, I am with Duncan here. You can license _your_ package any way you want and prefer. I like GPL. You seem to imply that the GPL license prohibits linking against commercial code. If that were the case we'd never have R, Emacs, gcc/g++, ... on Windows or macOS or any of the now-essentially

Re: [R-pkg-devel] Licensing of an R package

On 19 January 2018 at 10:00, Dirk Eddelbuettel wrote: | Also look eg at our Rblpapi package. The Bloomberg API is not open source, | but they allow distribution of the (pre-built) library and headers. Our | package, building on top, is GPL-2+. No issues. (This example is extra fun Correction

[R-pkg-devel] Working with R-devel

I am going in circles here and have lost my way. I used to have means to build R-devel (still do) and use it for local testing (no longer do). - Fresh build of R-devel - One entry in .libPaths() - I can install Rcpp, it ends up in that .libPaths() - I can load - With the _exact same settings

Re: [R-pkg-devel] Working with R-devel

On 24 January 2018 at 12:00, Martin Maechler wrote: | > Uwe Ligges | > I guess you actually pick up anotehr version of R. | > Carefully check what is on your PATH and perhaps some Renviron files | > that may be around? I did, a million times, hence the frustration. | Yes exact

Re: [R-pkg-devel] FIXED -- Working with R-devel

Thanks to Martin, my 'RD' script now points to ~/.R/check.Renviron-Rdevel in which I also set (or re-set) R_LIBS="/usr/local/lib/R-devel/site-library/" after having added this (for good measure) to my 'RD' script: unset R_PROFILE R_RENVIRON R_LIBS export R_CHECK_ENVIRON=~/.R/check.Ren

Re: [R-pkg-devel] Working with R-devel

On 24 January 2018 at 07:03, luke-tier...@uiowa.edu wrote: | If you are picking up an R 3.4.x that is trying to load a package | built by R-devel you should also see a warning that the package was | built under R version 3.5.0 Yes, I am of course very aware of the issue. But we had to separate o

Re: [R-pkg-devel] Working with R-devel

On 24 January 2018 at 07:55, William Dunlap wrote: | On Linux you can trace all the getenv calls with ltrace. It only | works on ELF files, not sh scripts: | | % R CMD ltrace -e getenv `R RHOME`/bin/*/R | libR.so->getenv("R_HOME") |= "/home/R/R-3.4.3/lib64/R" | libR.so->getenv("R

Re: [R-pkg-devel] fftw linking

On 4 February 2018 at 15:38, Denis Rastegaev wrote: | I try to upload my package on CRAN but the package | does not pass the incoming checks. How to link external | compiler with fftw? CRAN is a treasure trove with over 12k packages. Learn to search it. For example, package fftwtools has this li

Re: [R-pkg-devel] New CRAN package assistance

On 7 February 2018 at 21:54, Huw Campbell wrote: | I have just submitted a package for CRAN which works on my Mac and linux | boxes, but there are notes for Windows and my license file. There is little | indication as to what the actual problems are. | | The library is a simple binding for the sn

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission huxtable 2.0.2

On 7 February 2018 at 11:53, David Hugh-Jones wrote: | Hi guys, | | I've been having some problems with updating my 'huxtable' package on CRAN. | The latest issue is that I run a test which renders a rmarkdown document to | PDF, using rmarkdown::render. This passes R CMD check fine on my machine,

Re: [R-pkg-devel] R-devel warning: You used a knitr feature that depends on the digest package.

On 7 February 2018 at 15:03, luke-tier...@uiowa.edu wrote: | The problem is that this is an indirect dependency with knitr needing | digest and codetools to implement a feature (cacheing) that is being | asked for. And there is no obvious way (to me at least) of finding out | that these are needed

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

hich builds on my local mac but fails the online r-hub build | (interestingly, on a linux machine, which also puzzled me about cda's logs) | | https://builder.r-hub.io/status/isolve_1.0.tar.gz-757573eaf5b0cb30d8154d7b8f7e2bc7 | | Thanks for any advice, | | baptiste | | | | | | |

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

On 12 February 2018 at 22:16, Baptiste Auguie wrote: | As far as I can tell Armadillo added specialised methods for banded | matrices; the routines used to solve non-banded matrices probably haven't | changed. | | Coming back to the error itself, what puzzles me is that it seems to be | precisely

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

On 14 February 2018 at 17:12, Baptiste Auguie wrote: | Thanks Ralf, now it makes more sense to me. I had misunderstood the | situation on CRAN and r-hub and thought they used an external Lapack on | linux. This has been unchanged over the many years that you had these battles: - on Windows it is

Re: [R-pkg-devel] Windows binaries

On 14 February 2018 at 21:14, Kapur, Kush wrote: | Dear R development team, We're only regular list members here -- just like you. | I have also submitted the Windows binaries for the ssrm.logmer package using build_win function in devtools. Not sure I follow. You generally upload a _source_ t

Re: [R-pkg-devel] configuration failed on win-builder

Hi Carmen, On 15 February 2018 at 19:45, Carmen M. Livi wrote: | when submiting my R-package to CRAN I get the following error from the | windows machine: | | * installing *source* package 'spp' ... | ./configure.win: 2: Syntax error: word unexpected (expecting ")") | ERROR: configuration faile

Re: [R-pkg-devel] CRAN submission: Packages accepted if they run on two major R platforms

Carmen, On 16 February 2018 at 17:59, Carmen M. Livi wrote: | I am new here and have a question regarding package submissions: | | "CRAN Repository Policy" states that "packages will not be accepted that | do not run on at least two major R platforms". | | My package runs on MAC and Linux. So

Re: [R-pkg-devel] R package CRAN check error

Ilaria, On 16 February 2018 at 12:34, Ilaria Amerise wrote: | on submitting a new version of a package I got a rejection because of | the following Error in the CRAN-check. | | Any help would be highly appreciated. | | * using R version 3.4.3 (2017-11-30) | * using platform: x86_64-apple-darwin

Re: [R-pkg-devel] R package CRAN check error

On 16 February 2018 at 20:46, Georgi Boshnakov wrote: | You get a source package suitable for submission by running `R CMD check namepackage' or the equivalent devtools::build() Close: "R CMD build namepackage" creates the tar.gz file. And "R CMD check --as-cran namepackage_*.tar.gz" checks it

Re: [R-pkg-devel] MAX_ARGS limitation in foreign function calls

On 20 February 2018 at 09:33, Udaya B. Kogalur wrote: | We are hitting the MAX_ARGS ceiling in our R-C function calls in the | development of randomForestSRC. This limits to number of arguments to | 65 using .Call(). Is there a work around for this dilemma? Thank | you. The easiest is to avoid

Re: [R-pkg-devel] header file for "flockfile" function under windows

On 20 February 2018 at 20:56, Carmen M. Livi wrote: | I am using file-locking functions in C that can be found in the | in Unix | | extern void flockfile (FILE *__stream) __THROW; | extern int ftrylockfile (FILE *__stream) __THROW __wur; | extern void funlockfile (FILE *__stream) __THROW; | |

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 00:45, Marius Hofert wrote: | A package 'foo' uses a package 'bar' (in Imports). 'bar' has been | archived and the maintainer of 'foo' was asked to fix the dependency | on 'bar' according to WRE 1.1.3.1. | | Working with 'bar::' everywhere (and requireNamespace("bar", quiet

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 24 February 2018 at 19:41, Duncan Murdoch wrote: | Don't throw an error, work around it. If you have no alternative code, | then don't test the "bar" code unless "bar" is installed. | | The basic idea is that your package should pass tests without errors | even if "bar" is not available. 1

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 11:50, Marius Hofert wrote: | perfectly works (even if you don't have loon) *except* for the check | (--as-cran) to give me the warning: | * checking dependencies in R code ... WARNING | '::' or ':::' import not declared from: ‘loon’ | 'loadNamespace' or 'requireNamespace' c

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 11:51, meik michalke wrote: | 'Additional_repositories' is meant for R package repositories, it won't work | with source code git repos. if a package is in 'Suggests' and can't be found You missed the part where we create packages ("R CMD build") out of source repos, and

Re: [R-pkg-devel] How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 14:20, meik michalke wrote: | Am Sonntag, 25. Februar 2018, 06:35:52 CET schrieb Dirk Eddelbuettel: | > On 25 February 2018 at 11:51, meik michalke wrote: | > | 'Additional_repositories' is meant for R package repositories, it won't | > | work wi

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 15:00, Marius Hofert wrote: | okay, so (afaik) this is just a github repos which contains an exact | copy of the github version of the problematic package (here: loon). I Be very careful with terminology here: -- "github repo" is to most people a source code repo -- drat

Re: [R-pkg-devel] [FORGED] Re: How to (conditionally) use an archived package (without Suggests)?

On 25 February 2018 at 16:45, Hugh Parsonage wrote: | Not to mention a drat repository you can just fork with a single click! Yes, very easy -- but marginally expensive as you get the content (ie drat code history) mirrored. If you're at ease with git you can do it all by hand too. We still use

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

Tim, On 18 March 2018 at 18:58, Tim Keitt wrote: | I have an Rmd vignette that runs some benchmarks. It takes long enough (20+ | minutes) that eg TravisCI will choke. I've not tried submitting to CRAN. | What is the best practice for handling this situation? Do I generate | HTML/PDF output locall

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

On 18 March 2018 at 21:57, Tim Keitt wrote: | That's a great idea, however my problem is with building a vignette, not | running tests, unless they are linked in some way I'm not understanding. Similar idea applies: condition, just as Inaki and Thierry suggested. An example for a conditional vig

Re: [R-pkg-devel] Using shared libraries

On 28 March 2018 at 19:47, Ogan Mancarci wrote: | I have been looking for ways to use shared libraries in packages in CRAN | and be able to write tests for them. Well the basic problem here is that shared libraries are in fact provided by the _operating system_ and hence you just introduced an OS

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8

On 4 April 2018 at 14:15, Steven Scott wrote: | These appear to be caused by an ill formed std::set or std::function in the | STL implementation of the host machine. If I'm reading that wrong someone | please let me know. AFAICT it needs C++11 explicitly set which that machine (with a new clang-

Re: [R-pkg-devel] registering native routines

On 10 April 2018 at 23:30, Rampal Etienne wrote: | Yes, I followed all those suggestions but it did not fix the x64 notes. | Indeed I am using Windows. I am going to try this on a Linux system. You could consider the R Hub service at https://builder.r-hub.io/ and/or via the CRAN package rh

Re: [R-pkg-devel] CRAN pretest archived because of 2 NOTEs

On 18 April 2018 at 11:36, Gertjan van den Burg wrote: | While waiting to get this message posted to the list, I've solved the | problem by copying the stdlib rand() and srand() functions into my | package under a different name. This makes the check pass and ensures my | RNG does not interfere

Re: [R-pkg-devel] Explicitly Calling a Method of a specific Class in a Function

On 6 May 2018 at 11:42, Dr. rer. nat. Michael Thrun wrote: | Dear Developers, | I have currently one note in one of my packages I am unable to solve at my own: | “ | checking dependencies in R code ... NOTE | Unexported object imported by a ':::' call: ‘sp:::plot.SpatialPolygons’ | See the note

Re: [R-pkg-devel] questions about promptPackage(); -package.Rd; help(package="")

Ben, Been meaning to write a short blog post about it as it also affects two (old) packages of mine. My favourite is to just rely on the Rd macros to the fullest, and I generally just hand-edit it -- no promptPackage() use. See eg this side-by-side diff of the first of the two I need to update;

Re: [R-pkg-devel] CRAN pretest: Overall checktime 14 min > 10 min

I can't speak to the recent increase on Windows. It may be load; it may be related to R 3.5.0 --- but I'd even whittle things down from 5+ minutes. At one point in the past we were told to aim for 1 minute, give or take. So e.g. Rcpp has been using a scheme for _many_ years where I take a cue fr

Re: [R-pkg-devel] CRAN pretest: Overall checktime 14 min > 10 min

On 21 May 2018 at 17:46, Uwe Ligges wrote: | In addition to what Dirk said, I just added this experimental test for | CRAN incoming checks few days ago and it should not reject but lead to | manual inspection, this will be fixed on CRAN side shortly. | | Nevertheless: The idea is that we have t

Re: [R-pkg-devel] Compiled code checks raise a WARNING in Fedora 28

On 23 May 2018 at 17:22, Iñaki Úcar wrote: | Hi, | | For other Fedora users that may be struggling with this too... | | Fedora 28 introduced new hardening flags for compiled code (see [1]). | Particularly, -D_GLIBCXX_ASSERTIONS is added to the default CXXFLAGS | (verify the output of 'R CMD conf

Re: [R-pkg-devel] Compiled code checks raise a WARNING in Fedora 28

On 23 May 2018 at 18:09, Iñaki Úcar wrote: | 2018-05-23 17:40 GMT+02:00 Dirk Eddelbuettel : | > | > On 23 May 2018 at 17:22, Iñaki Úcar wrote: | > | Hi, | > | | > | For other Fedora users that may be struggling with this too... | > | | > | Fedora 28 introduced new hardeni

Re: [R-pkg-devel] RcppArmadillo-based package works in every tested OS except Debian

Hi Julia, On 28 May 2018 at 16:33, Julia A. Pilowsky wrote: | I am the maintainer of the colorednoise package, which employs RcppArmadillo. The package passes all checks on my local OS X install, on win_builder, and on Travis CI's Ubuntu distribution

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

On 29 June 2018 at 09:15, Mark van der Loo wrote: | 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-lik

Re: [R-pkg-devel] compilation flags WARNING

On 5 July 2018 at 22:19, Göran Broström wrote: | Thanks Heather and Iñaki: I understand. | | I have an old Makevars file in the src directory of the package. I | guess I can set the flags there? No, because those get scanned by R CMD check and friends. For the one you do not want, Heather's

Re: [R-pkg-devel] Reverse dependencies - again

On 11 July 2018 at 10:00, J C Nash wrote: | 2) Is it time to consider an effort to provide online revdep checking | that would avoid pressure on CRAN team directly and would provide | clearer indicators of the issues raised by a particular package? That is very close to my R Foundation Summit ta

[R-pkg-devel] C++11 and deprecated warnings "noise" for auto_ptr

As some of you may have noticed, or may have been told as well in kind "fix this or else ..." email, 'R CMD check' now also marks g++-7 / g++-8 warnings of 'deprecated declarations'. This can of course be addressed in the code itself, or suppressed with the '-Wno-deprecated-declarations' flag in

Re: [R-pkg-devel] Correct way to set title for vignette?

On 24 July 2018 at 16:46, Martin Møller Skarbiniks Pedersen wrote: | Hi, | | Some vignettes on Cran has the title: "Title of your vignette" | Eg. https://cran.r-project.org/package=ggpval | | The source for the vignette at | "https://raw.githubusercontent.com/s6juncheng/ggpval/master/vign

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

On 7 August 2018 at 16:27, Ossenbruggen, Paul wrote: | I am new to CRAN submissions and need assistance. | | I received this set of error messages previously. I removed all these hidden files before resubmitting my package. They are back. | Question #1 How do I prevent this this? 1. (Optional)

Re: [R-pkg-devel] CRAN note: src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS

On 20 August 2018 at 22:14, Georgi Boshnakov wrote: | Hi, | | Recently the results page of my package on CRAN at | https://cran.r-project.org/web/checks/check_results_sarima.html, | started to show the NOTE below for some systems. | I am using Rcpp/RcppArmadillo without any manual interventions

Re: [R-pkg-devel] Changing License

On 30 August 2018 at 08:34, Charles Determan wrote: | It has come to my attention that some of the code I am distributing in one | of my packages was previously licensed under the MIT license. I have | previously released my package under the GPL-3 license. Would it be more | appropriate for me

[R-pkg-devel] How do I prevent macOS from attempting to build my package?

Package status reports come in three different severities: NOTE, WARNING, and ERROR. Motivated by Brodie's nice (dependency-free) accessor function for per-maintainer status [1], I have looked into reducing the number of ERRORs. I hit a road block. Several of my packages depend on external libr

Re: [R-pkg-devel] How do I prevent macOS from attempting to build my package?

On 4 September 2018 at 17:07, Uwe Ligges wrote: | Disclaimer for this field in general (as others are listening, too): we | should always try not to use it alt all and produce cross platform code. It would be nice if the CRAN system was more open so that contributed builds could be used. With m

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 09:27, Gábor Csárdi wrote: | When are users running tests for packages at all? The tests are by default | no even installed with the package. The only time I usually do this is when Which some people consider to be the wrong decision by testthat. Base R has a set of funct

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 13:08, Gábor Csárdi wrote: | On Fri, Sep 7, 2018 at 12:29 PM Dirk Eddelbuettel wrote: | > | > | > On 7 September 2018 at 09:27, Gábor Csárdi wrote: | > | When are users running tests for packages at all? The tests are by default | > | no even installed w

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 10:38, Hadley Wickham wrote: | On Fri, Sep 7, 2018 at 9:13 AM Iñaki Ucar wrote: | > El vie., 7 sept. 2018 a las 16:03, Ralf Stubner | > () escribió: | > > On 07.09.2018 15:52, Iñaki Ucar wrote: | > > Tests in 'inst/test' got deprecated later on: | > > | > > https://github

Re: [R-pkg-devel] Submission to CRAN when package needs personal data (API key)

On 7 September 2018 at 13:08, Gábor Csárdi wrote: | On Fri, Sep 7, 2018 at 12:29 PM Dirk Eddelbuettel wrote: | > | > | > On 7 September 2018 at 09:27, Gábor Csárdi wrote: | > | When are users running tests for packages at all? The tests are by default | > | no even installed w

Re: [R-pkg-devel] Package Etiquette

Hi Joseph, On 8 September 2018 at 21:11, Joseph Wood wrote: | I’m a new developer and this is my first post. I have a question regarding | package development with regards to duplication of functionality. I read | the posting guide (https://www.r-project.org/posting-guide.html) and didn’t | see

Re: [R-pkg-devel] RcppEigen and -Wno-ignored-attributes flag

On 10 September 2018 at 16:27, Τόλης Χαλκής wrote: | Dear all, | | I am developing a R package using RcppEigen on Ubuntu 18.04. Since update | 0.3.3.4.0 I get hundreds of warnings but if I add PKG_CXXFLAGS = | -Wno-ignored-attributes in Makevars the warnings disappear and the compile | time red

<    1   2   3   4   5   6   7   8   >