Re: [R-pkg-devel] Trouble with dependencies on phyloseq and microViz

2024-05-06 Thread Ivan Krylov via R-package-devel
ream weak dependency for a CRAN package, the URL must be specified as https://david-barnett.r-universe.dev/src/contrib, not just https://david-barnett.r-universe.dev/. I am sorry for not getting it right the first time. -- Best regards, Ivan __________ R-package

Re: [R-pkg-devel] Cannot repro failing CRAN autochecks

2024-05-07 Thread Ivan Krylov via R-package-devel
В Tue, 7 May 2024 14:03:42 -0400 Josiah Parry пишет: > This NOTE does not appear in Ubuntu, Mac, or Windows checks > https://github.com/R-ArcGIS/arcgisutils/actions/runs/8989812276/job/24693685840 That's a bit strange. It fires for me in a local R CMD check for a test package even w

Re: [R-pkg-devel] Cannot repro failing CRAN autochecks

2024-05-07 Thread Ivan Krylov via R-package-devel
В Tue, 7 May 2024 21:40:31 +0300 Ivan Krylov via R-package-devel пишет: > It's too late for Makevars to exclude files from the source package > tarball. Use .Rbuildignore instead: Sorry, that was mostly misguided. .Rbuildignore won't help with the contents of the Rust vendor

Re: [R-pkg-devel] package removed from CRAN

2024-05-08 Thread Ivan Krylov via R-package-devel
ernet-related errors. This will make it possible for your examples and tests to catch them, as in: tests/*.R: tryCatch( , refseqR_internet_error = function(e) message("Caught Internet-related error") ) -- Best regards, Ivan ______

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

2024-05-08 Thread Ivan Krylov via R-package-devel
he PATH and then exec "${R_HOME}/bin/Rscript" tools/configure.R (in the regular, non-multiarch configure for Unix-like systems) or exec "${R_HOME}/bin${R_ARCH_BIN}/Rscript.exe" tools/configure.R (in configure.win, which you'll also need). You've already wrote the r

Re: [R-pkg-devel] flang doesn't support derived types

2024-05-09 Thread Ivan Krylov via R-package-devel
Dear Othman El Hammouchi, Welcome to R-package-devel! В Wed, 08 May 2024 16:52:51 + Othman El Hammouchi пишет: > However, upon submission I received an automatic reply shortly > afterwards saying the build had failed on CRAN's servers for Debian. > The log gives the f

Re: [R-pkg-devel] flang doesn't support derived types

2024-05-09 Thread Ivan Krylov via R-package-devel
better compiler or at least a better documented one, but instead of a list of features on their website, I can only see "Getting Involved [3] for tips on how to get in touch <...> and to learn more about the current status". There is only so many projects one can get involved in. -- B

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

2024-05-09 Thread Ivan Krylov via R-package-devel
ce. Guidance with > GitHub actions and ChatGPT is essentially a must for me since my bash > is remedial at best. Then you might like Kevin Ushey's configure <https://github.com/kevinushey/configure>, which is like autoconf redone in R. The only few lines of bash are the system-specifi

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

2024-05-10 Thread Ivan Krylov via R-package-devel
On Fri, 10 May 2024 15:12:17 +1200 Simon Urbanek wrote: > I wonder if it may be worth doing something a bit smarter and tag > officially a "reverse XDR" format instead - that way it would be > well-defined and could be made the default. Do you mean changing R so that

Re: [R-pkg-devel] clang-UBSAN

2024-05-13 Thread Ivan Krylov via R-package-devel
В Sun, 12 May 2024 14:43:18 -0400 Kaifeng Lu пишет: > /data/gannet/ripley/R/test-clang/Rcpp/include/Rcpp/internal/caster.h:30:25: > runtime error: nan is outside the range of representable values of > type 'int' On line 4618 of src/misc.cpp of the lrstat package, you have a

Re: [R-pkg-devel] An issue regarding the authors field in DESCRIPTION

2024-05-13 Thread Ivan Krylov via R-package-devel
В Mon, 13 May 2024 08:33:04 -0500 Ruwani Herath пишет: > This is what I entered in DESCRIPTION field. > > Authors@R: c(person(given = "Ruwani", family = "Herath", role = > c("aut","cre"), email = "ruwanirasanja...@gmail.com"), >

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Ivan Krylov via R-package-devel
Dear Zeinab, Welcome to R-package-devel! В Thu, 16 May 2024 03:22:56 + Zeinab Mashreghi пишет: > I recently submitted my R package to CRAN, and I received this note > from the CRAN teams: "checking CRAN incoming feasibility ... NOTE." Without a link to the full error log

Re: [R-pkg-devel] Altrep header, MSVC, and STRUCT_SUBTYPES macro

2024-05-16 Thread Ivan Krylov via R-package-devel
В Wed, 15 May 2024 18:54:37 +0200 David Cortes пишет: > The code compiles without errors under MSVC, but executing code that > involves returning Altrep objects leads to segfaults and memory > corruptions, even though it works fine under other compilers. > > I see the R Altrep

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Goldfeld, Keith via R-package-devel
Zeinab I have found that setting this system value to FALSE eliminates the issue: Sys.setenv("_R_CHECK_RD_VALIDATE_RD2HTML_" = FALSE) - Keith On 5/16/24, 12:02 PM, "R-package-devel on behalf of Zeinab Mashreghi" mailto:r-package-devel-boun...@r-project.org>

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-16 Thread Ivan Krylov via R-package-devel
В Thu, 16 May 2024 16:01:45 + Zeinab Mashreghi пишет: > checking HTML version of manual ... NOTE > Found the following HTML validation problems: > All.data.html:4:1 (All.data.Rd:10): Warning: inserting "type" > attribute > All.data.html:12:1 (All.data.Rd:10): Warning:

Re: [R-pkg-devel] Altrep header, MSVC, and STRUCT_SUBTYPES macro

2024-05-17 Thread Ivan Krylov via R-package-devel
ts than when using the STRUCT_SUBTYPES definition. So much for the hope for an easy solution. > May I ask: how would you go around getting R code into Godbolt? Definitely not much of it. I was assuming that the problem was due to passing structs by value (something that had been a p

Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note

2024-05-17 Thread Marc Girondot via R-package-devel
ssues. Thanks again! Zeinab From: Ivan Krylov Date: Thursday, May 16, 2024 at 12:27 PM To: Zeinab Mashreghi Cc: r-package-devel@r-project.org Subject: Re: [R-pkg-devel] Assistance Needed to Resolve CRAN Submission Note Notice: This is external email. Verify the sender and use caution wit

Re: [R-pkg-devel] [External] Re: [External] Re: Assistance Needed to Resolve CRAN Submission Note

2024-05-18 Thread Jeff Newmiller via R-package-devel
so... your suggestion is not for CRAN, but for R-Core, who makes changes to R On May 18, 2024 6:03:55 PM PDT, "Richard M. Heiberger" wrote: >exactly. when the --as-cran detects the need for that NOTE, it could prefix >the initial instance of that NOTE with information abo

Re: [R-pkg-devel] [External] Re: Assistance Needed to Resolve CRAN Submission Note

2024-05-18 Thread Ivan Krylov via R-package-devel
ng the patch from <https://stat.ethz.ch/pipermail/r-devel/2023-August/082763.html>? If you or someone else here has a computer running macOS, what exactly does it print when running `tidy --version` (1) with an old version of Tidy (that comes with macOS) and (2) with a new (>= 5) version

Re: [R-pkg-devel] [External] Re: Assistance Needed to Resolve CRAN Submission Note

2024-05-19 Thread Ivan Krylov via R-package-devel
~ /usr/bin/tidy --version > HTML Tidy for Mac OS X released on 31 October 2006 - Apple Inc. build > 9576 Thank you for providing the output! R CMD check only knows about "Apple Inc. build 2649" (not 9576) being old, which must be why the spurious NOTEs appeared on Zeinab's compu

[R-pkg-devel] handling documentation build tools

2024-05-21 Thread Boylan, Ross via R-package-devel
t's in inst/doc, which led to problems with the build system sometimes wiping it out. I've solved that problem. Thanks. Ross [[alternative HTML version deleted]] ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2024-05-21 Thread Boylan, Ross via R-package-devel
cated way to get the core pdf copied to inst/doc. Also, my main concern was how to automate production of the "core" pdf, using the language of the blog post. Ross From: Dirk Eddelbuettel Sent: Tuesday, May 21, 2024 2:15 PM To: Boylan,

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

2024-05-23 Thread Ivan Krylov via R-package-devel
g such a library, the operation fails unless the missing symbols are already present in the address space of the process (e.g. from a different shared library). A fresh process of R built without OpenMP support will neither link in the OpenMP runtime while running SHLIB nor have the OpenMP runtime lo

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

2024-05-27 Thread Ivan Krylov via R-package-devel
s.getenv("SHLIB_OPENMP_CXXFLAGS, ""))) } >From the documentation, it sounds like a good use for # variables will be pre-loaded from Makeconf Rcpp.plugin.maker(Makevars = ' PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS) PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) ') ...but I can&#

Re: [R-pkg-devel] Debian and Fedora clang segmentation faults

2024-05-27 Thread Ivan Krylov via R-package-devel
В Mon, 27 May 2024 13:29:56 -0500 Stephen Meyers пишет: > I'm updating the 'astrochron' R package, and I'm trying to resolve a > new segmentation fault that arises only with the Debian and Fedora > clang compilers. An example is the function 'asm', whi

[R-pkg-devel] different build tools

2024-05-28 Thread Boylan, Ross via R-package-devel
There are at least 4 ways to build a package: 1. R CMD build 2. pkgbuild::build(), which I believe calls 1. 3. devtools::build(), which calls 2. 4. RStudio GUI, which calls 3. I recently discovered these don't all behave the same. Invoking bootstrap.R at the start requires

Re: [R-pkg-devel] different build tools

2024-05-28 Thread Boylan, Ross via R-package-devel
-Original Message- From: Duncan Murdoch Sent: Tuesday, May 28, 2024 3:30 PM To: Boylan, Ross ; r-package-devel@r-project.org Subject: Re: [R-pkg-devel] different build tools On 2024-05-28 6:20 p.m., Boylan, Ross via R-package-devel wrote: > There are at least 4 ways to build a pack

Re: [R-pkg-devel] different build tools

2024-05-28 Thread Jeff Newmiller via R-package-devel
esent the official R-supported development process, and may become out-of-date during R version transitions. On May 28, 2024 3:29:41 PM PDT, Duncan Murdoch wrote: >On 2024-05-28 6:20 p.m., Boylan, Ross via R-package-devel wrote: >> There are at least 4 ways to build a package: >&

Re: [R-pkg-devel] different build tools

2024-05-28 Thread Boylan, Ross via R-package-devel
[Sorry: Outlook doesn't quote messages the "normal" way] -Original Message- From: Simon Urbanek Sent: Tuesday, May 28, 2024 4:10 PM Ross, R CMD build is the only offical way to build a (source) package in R. All other "tools" are just convenience wrappers

Re: [R-pkg-devel] Help with detritus on temporary directory note

2024-05-30 Thread Ivan Krylov via R-package-devel
В Thu, 30 May 2024 11:12:05 +0200 Héctor Meleiro Suárez пишет: > So why is this a problem? Is it that there are too many files aftes > examples and tests are run? or would this NOTE be an issue to CRAN > even if only one file was detected at the end? This problem has two sides. The si

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

2024-06-05 Thread Jeff Newmiller via R-package-devel
Did you increment the version number? On June 5, 2024 1:19:27 AM PDT, Paul Kabaila wrote: >(1) Today, I submitted my R package to CRAN using >devtools::submit_cran() >which resulted in an email from >CRAN Package Submission Form >cransub...@xmbombadil.wu.ac.at

[R-pkg-devel] warning: explicit assigning values of variable of type ....

2024-06-06 Thread Søren Højsgaard via R-package-devel
Dear all, From CRAN maintainers I recieve: Flavor: r-devel-linux-x86_64-debian-gcc Check: whether package can be installed, Result: WARNING Found the following significant warnings: grips_fit_ips.cpp:149:45: warning: explicitly assigning value of variable of type 'int' to itse

Re: [R-pkg-devel] warning: explicit assigning values of variable of type ....

2024-06-06 Thread Søren Højsgaard via R-package-devel
Thanks :) -Original Message- From: Iris Simmons mailto:iris%20simmons%20%3cikwsi...@gmail.com%3e>> To: Søren Højsgaard mailto:%3d%3fiso-8859-1%3fq%3fs%3df8ren_h%3df8jsgaard%3f%3d%20%3csor...@math.aau.dk%3e>> Cc: List r-package-devel mailto:list%20r-package-devel%20%3cr-pac

Re: [R-pkg-devel] Check errors for RMarkdown vignettes with error chunks

2024-06-07 Thread Ivan Krylov via R-package-devel
В Fri, 7 Jun 2024 09:10:03 +0200 "C.H." пишет: > RMarkdown vignettes are sometimes used to demonstrate errors and one > can write vignettes with `error` chunks. > > ```{r, error = TRUE} > stop() > ``` > But now CRAN also reports the same ERRORS for mac and linux

Re: [R-pkg-devel] debugging R CMD build

2024-06-07 Thread Ivan Krylov via R-package-devel
В Fri, 7 Jun 2024 08:40:48 -0400 Vincent Carey пишет: > I wanted to know if anyone has a way of stepping through in a CMD > build task. On Linux, R CMD build launches file.path(R.home('bin'), 'build'), which is a short script. It should be possible to step into R C

Re: [R-pkg-devel] Seeking help with a phantom "re-building vignettes" error in 00check.log from CRAN

2024-06-09 Thread Ivan Krylov via R-package-devel
В Fri, 7 Jun 2024 12:03:23 -0700 Jeff Lewis пишет: > I am running into a perplexing issue that creates an error in the > Windows build when I submit the package to CRAN. The error does not > occur on: win-builder-devel, > Debian on CRAN, my mac, or in Docker using r-base on my m

Re: [R-pkg-devel] Vignette with error=TRUE chunks fails CRAN checks on r-oldrel-macos

2024-06-14 Thread Ivan Krylov via R-package-devel
В Fri, 14 Jun 2024 07:58:09 +0200 Roland Fuß пишет: > We have many code chunks with knitr option `error=TRUE`. A recent change required knitr to actually tangle the code for vignettes when requested by R CMD check, with the intent to make sure that the resulting *.R file runs without err

Re: [R-pkg-devel] CRAN check servers terminating on stanExports_*.o files

2024-06-20 Thread Ivan Krylov via R-package-devel
В Sat, 15 Jun 2024 15:11:36 + "Slager, Dave" пишет: > The r-patched-linux-x86_64 and/or r-release-linux-x86_64 CRAN check > servers seem to be erroring out on multiple packages, including > these, for similar reasons: > > bakR > baldur > bayes4psy > Bayes

Re: [R-pkg-devel] NOTEs in packages using Rust

2024-06-20 Thread Jeff Newmiller via R-package-devel
I am not connected to CRAN (by a long shot), but if I were I would not accept any of the arguments you are making here. I don't know what you are talking about with respect to excluding files in tarring... you should be using the package build processes as documented in Writing R Exten

Re: [R-pkg-devel] CRAN check servers terminating on stanExports_*.o files

2024-06-21 Thread Ivan Krylov via R-package-devel
.) __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2024-06-28 Thread Jeff Newmiller via R-package-devel
in-builder. Submitting anyway is recommended here [1]. [1] https://stackoverflow.com/questions/66078248/invalid_url_in_cran_checks On June 28, 2024 2:57:13 PM PDT, Iris Simmons wrote: >Hi, > > >I've got an update for my R package ready to go. It checks successfully on >my own mach

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'

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

2024-06-29 Thread Ivan Krylov via R-package-devel
? Also, it's best to put both knitr and rmarkdown in the VignetteBuilder field of the DESCRIPTION, because both packages are required to process the vignette successfully. -- Best regards, Ivan __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2024-06-29 Thread Ivan Krylov via R-package-devel
tly have available in the Git repository, but I did find this.path_2.5.0.tar.gz in the archive subdirectory on the CRAN FTP server, which crashes R-devel but not R-4.4.1 on Windows: * checking whether the namespace can be unloaded cleanly ...Rterm.exe caused an Access Violation at location 7FFCC43B2

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

2024-07-01 Thread Jeff Newmiller via R-package-devel
ages is to isolate their internals to make them less interdependent... putting all of them into a monorepo can lead you to forget that users experience them as distinct units. On July 1, 2024 3:04:40 PM PDT, "Kevin R. Coombes" wrote: >Hi, > >I have been maintaining packages in

[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] Help for understanding CRAN rejection

2024-07-09 Thread Ivan Krylov via R-package-devel
-- Best regards, Ivan [1] https://svn.r-project.org/R/trunk/share/licenses/license.db [2] https://creativecommons.org/faq/#can-i-apply-a-creative-commons-license-to-software ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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 dynam

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

2024-07-09 Thread Ivan Krylov via R-package-devel
mons license and 18 of those that use the non-FOSS "NonCommercial" clause, none use the "NoDerivatives" clause. Your users would probably appreciate being able to install binary builds of your package from CRAN. Does `R CMD INSTALL --build` count as creating a derivative work, o

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 ever

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 to

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

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:

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

2024-07-19 Thread Ivan Krylov via R-package-devel
y with perl -d, I can confirm this: main::(C:/Users/redacted/AppData/Local/R/win-library/4.5/WriteXLS/Perl/WriteXLS.pl:135): 135:my @FileNames = ""; DB<3> main::(C:/Users/redacted/AppData/Local/R/win-library/4.5/WriteXLS/Perl/WriteXLS.pl:136): 136:open (DFHANDLE, $Encode, &

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
its # [1] 0 However, I do not know how easy it is to convert from the mpfr format to the other format. Maybe the BH-team can add an mpfr constructor to the library. On a somewhat related topic, I did implement a very basic solver in native R (and based on Rmpfr). You can have a look on GitHub;

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

2024-07-29 Thread Ivan Krylov via R-package-devel
erhaps even options(device = \(file = myfilenamevar, ...) pdf(file = file, ...)) so that every plot would get the same treatment, though that requires re-implementing the dev.new() logic to guess an available file name. You can even misuse R_PROFILE_USER to inject the code into the R CMD

Re: [R-pkg-devel] LaTeX errors under MacOS on CRAN

2024-08-02 Thread Ivan Krylov via R-package-devel
emes or opts_knit$set('header'), you should be getting both \hlkwd and \hldef defined from themes/default.css via knitr::render_latex. Is there a way to inadvertently set the 'header' knitr option? -- Best regards, Ivan ______

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

2024-08-02 Thread Ivan Krylov via R-package-devel
> Now I want to build a Windoze binary of the package. If the vignette uses LaTeX packages unavailable on the computer (rhub2 virtual machine) running R CMD build or R CMD check, that would indeed not work. Not sure about CRAN. Since your package doesn't seem to contain any native co

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

2024-08-13 Thread Ivan Krylov via R-package-devel
В Mon, 12 Aug 2024 18:24:30 + David via R-package-devel пишет: > in the intel environment (provided by rhub), the intel fortran > compiler generates intermediary files from *.f -> *__genmod.f90. The > R check then complains that the genmod files are not portable. I > include

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

2024-08-16 Thread Ivan Krylov via R-package-devel
; build deps so I can't confirm it work. This may be worth reporting to the rhub developers. The error is really strange. It looks like the package at https://github.com/cran/igraph/releases/download/2.0.3/igraph_2.0.3_b1_R4.5_x86_64-pc-linux-gnu-fedora-38.tar.gz (referenced from https://github.

Re: [R-pkg-devel] R CMD check options

2024-08-17 Thread Ivan Krylov via R-package-devel
В Sat, 17 Aug 2024 09:17:40 -0400 Ben Bolker пишет: > does there exist/has someone compiled a list of > the environment variables that determine R CMD check's behaviour? https://cran.r-project.org/doc/manuals/R-ints.html#Tools But the _R_CHECK_CRAN_INCOMING_USE_ASPELL_ variable

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

2024-08-17 Thread Ivan Krylov via R-package-devel
uctor or pak issue. Could also be an rhub issue, although unlike the igraph problem below, I have no idea where to start diagnosing it. > > > igraph::sample_pref(10) > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared object > > &

Re: [R-pkg-devel] unregistered S3 methods in a package

2024-09-04 Thread Jeff Newmiller via R-package-devel
:21:22 AM PDT, Toby Hocking wrote: >I got this warning too, so I filed an issue to ask >https://github.com/r-lib/roxygen2/issues/1654 > >On Mon, Sep 2, 2024 at 2:58 PM John Fox wrote: >> >> As it turned out, I was able to avoid redefining coef.merMod(), etc., by >> m

Re: [R-pkg-devel] Error in creating virtual environment on Debian machines

2024-09-06 Thread Ivan Krylov via R-package-devel
Hello Taeyong and welcome to R-package-devel! В Thu, 5 Sep 2024 23:40:00 +0300 Taeyong Park пишет: > # Define paths > venv_path <- file.path(Sys.getenv("HOME"), ".virtualenvs", > "pytrends-in-r-new") > python_path <- file.path(venv_path, &q

Re: [R-pkg-devel] Justification and status of the 100-bytes path length limit.

2024-09-14 Thread Ivan Krylov via R-package-devel
d 1607 and exists in modern versions of R [*], it's not enabled by default on many current systems: d <- tempfile(); dir.create(d); setwd(d); d "C:\\Users\\[SNIP]\\AppData\\Local\\Temp\\3\\RtmpodtJLb\\file3fec5fce5feb" (path <- paste( sample( c('/', letters, LETTE

[R-pkg-devel] Latex error during compilation

2018-03-06 Thread michael tsagris via R-package-devel
o legal \end found) ! ==> Fatal error occurred, no output PDF file produced! * checking PDF version of manual without hyperrefs or index ... ERROR * DONE [[alternative HTML version deleted]] --- End Message --- __ R-package-devel@r-project.o

[R-pkg-devel] Σχετ: Latex error during compilation

2018-03-07 Thread michael tsagris via R-package-devel
--- Begin Message --- Hi Richard, Cheers for the answer. I had a problem with missing "}". I corrected all of them. However, when I compile it in many different computers everything is fine. 0 errors. When I upload it to r-devel it finds errors. Στις 5:08 μ.μ. Τρίτη, 6 Μαρτί

[R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object

2018-04-21 Thread David Hervás via R-package-devel
--- Begin Message --- Hi, I have sent my package "clickR" to CRAN and was asked to fix the following NOTE: * checking dependencies in R code ... NOTE Missing or unexported object: 'lmerTest::summary' I'm not sure what's going on, here is the Imports section of

Re: [R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object

2018-04-21 Thread David Hervás via R-package-devel
mespace:lmerTest' On the other hand summary(fm) works just fine. lmerTest defines the S3 method 'summary' for 'lmerModLmerTest' objects, so if you change  sx <- lmerTest::summary(x)  to  sx <- summary(x) you should be fine assuming that x is of class 'lmerModLme

[R-pkg-devel] Running R CMD CHECK on different architectures

2018-07-19 Thread Stuart Lacy via R-package-devel
ult of the check on the previous release is available here https://cran.r-project.org/web/checks/check_results_multistateutils.html However, the errors and warnings are in architectures that I don't have available, i.e. r-devel on fedora, r-patched solaris, r-release osx, r-oldrel osx.

[R-pkg-devel] Extending/adding to an R6 class from another package: qns

2018-10-19 Thread Hong Ooi via R-package-devel
--- Begin Message --- I'm writing a family of packages for talking to Azure (Microsoft's cloud service) from R. The basic architecture is AzureRMR: the "base" package, provides a number of R6 classes AzureVM: a "child" package that extends classes from AzureRMR wit

Re: [R-pkg-devel] Extending/adding to an R6 class from another package: qns

2018-10-19 Thread Hong Ooi via R-package-devel
x$set() calls to a secondary function, rather than having them directly in .onLoad(). -Original Message- From: Hadley Wickham Sent: Saturday, 20 October, 2018 2:42 AM To: Hong Ooi Cc: R Package Development Subject: Re: [R-pkg-devel] Extending/adding to an R6 class from another package

Re: [R-pkg-devel] SystemRequirements: Berkeley DB STL

2018-10-23 Thread Hong Ooi via R-package-devel
--- Begin Message --- This looks like a similar situation to the C++ Boost headers, which are packaged up for easy R consumption in the boost package. You could try doing that with BerkeleyDB. There's another issue though: looking at your FAQ page, you seem to rely on a bunch of tools wr

[R-pkg-devel] package 'corpus' not available?

2018-12-05 Thread Dalthorp, Daniel via R-package-devel
the package on CRAN, and it installs and runs fine on my machine. Since its last release, my package has not had any changes that involve 'corpus' functions, the 'corpus' package at CRAN has not changed, and R is still 3.5.1. Any ideas about what might be going on? Any h

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission vioplot 0.3.0

2018-12-26 Thread Hong Ooi via R-package-devel
ry permissive license. While I'm not a lawyer, I don't think there would be any conflicts if you changed it to, say, the MIT license which is also very permissive. -Original Message- From: R-package-devel On Behalf Of Tom Kelly Sent: Wednesday, 26 December, 2018 7:01 P

Re: [R-pkg-devel] R CMD INSTALL succeeds while R CMD BUILD fails

2019-01-11 Thread Hong Ooi via R-package-devel
--- Begin Message --- It looks like the ".rdata" in your package name is confusing R CMD BUILD into thinking there is a .rdata file involved. Consider renaming it to "bcmaps.data" or something similar. -Original Message- From: R-package-devel On Behalf Of Sam Alb

Re: [R-pkg-devel] vignette problems: invisible

2019-02-01 Thread Hong Ooi via R-package-devel
--- Begin Message --- The various devtools::install_* functions don't install vignettes by default; to do so, add the build_vignettes=TRUE argument. -Original Message- From: R-package-devel On Behalf Of Troels Ring Sent: Friday, 1 February, 2019 10:15 PM To: package-develop Su

Re: [R-pkg-devel] CRAN review

2019-03-13 Thread Maëlle SALMON via R-package-devel
ne will start like > > > [This was generated from CRAN.R-project.org/submit.html] > > > > The following package was uploaded to CRAN: > > === > > > > Package Information: > > Package: rgl > > A while later you should get a thir

Re: [R-pkg-devel] CRAN review

2019-03-13 Thread Maëlle SALMON via R-package-devel
--- Begin Message --- Sorry, the link was removed (by my copy-pasting it wrongly): https://itsalocke.com/cransays/articles/dashboard Den onsdag 13 mars 2019 08:54:00 CET, Maëlle SALMON via R-package-devel skrev: We at Locke Data have made an hourly updated dashboard based on the FTP

Re: [R-pkg-devel] How to debug CRAN errors?

2019-03-14 Thread Maëlle SALMON via R-package-devel
--- Begin Message --- To follow up on the great answers regarding R-hub,- to use R-hub Linux Docker images you can use this brand-new rhub function  https://r-hub.github.io/rhub/reference/local_check_linux.html (untested on Windows)- here's WIP R-hub docs entry about choosing a platfo

[R-pkg-devel] Installing Additional "Packages" During Tests

2019-03-18 Thread brodie gaslam via R-package-devel
--- Begin Message --- My package unitizer has recently gained a new set of errors that look like: [[alternative HTML version deleted]] --- End Message --- __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

[R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread brodie gaslam via R-package-devel
--- Begin Message --- Sorry, previous e-mail got pre-maturely sent due to fat finger... My package unitizer[1] has recently gained the following type of error: Warning in install.packages(pkg, repos = NULL, type = "src") : 'lib = "/home/hornik/tmp/R.check/r-de

Re: [R-pkg-devel] Installing "Additional" Packages During Tests

2019-03-18 Thread brodie gaslam via R-package-devel
the library is writeable. It is not in many network installations. Best, Uwe Ligges On 18.03.2019 16:48, brodie gaslam via R-package-devel wrote: > > Subject: > Installing "Additional" Packages During Tests > From: > brodie gaslam > Date: > 18.03.2019, 16:48 &

Re: [R-pkg-devel] active bindings in package namespace

2019-03-24 Thread Hong Ooi via R-package-devel
ode could be exactly the same, and your local environment exactly the same, and yet running the code at different times can yield different results because the remote data has been updated. -Original Message- From: R-package-devel On Behalf Of Jack Wasey Sent: Sunday, 24 March 201

Re: [R-pkg-devel] Re :Re: Re :Re: package cartograflow_0.0.0.9000.tar.gz

2019-03-27 Thread Maëlle SALMON via R-package-devel
--- Begin Message --- Hi, To be able to run R CMD check on R devel, on top of your local checks, you might want to have a a look at the R-hub package builder that allows you to run R CMD check on several platforms (R versions, OS) for free. You can use the rhub package for that, https://r

Re: [R-pkg-devel] Re :Re: Re :Re: package cartograflow_0.0.0.9000.tar.gz

2019-04-04 Thread Maëlle SALMON via R-package-devel
--- Begin Message --- I'd recommend reading https://r-pkgs.org/description.html#dependencies (and the rest of the book is very good as well), it'll help you understand why and how to declare dependencies. Den torsdag 4 april 2019 17:05:02 CEST, cartograf...@gmail.com skrev:

[R-pkg-devel] Blog post about R-package-devel

2019-04-11 Thread Maëlle SALMON via R-package-devel
--- Begin Message --- Dear R-package-devel subscribers, We've just published a post about how to get help with R package development on R-hub blog. https://blog.r-hub.io/2019/04/11/r-package-devel/ It features this mailing list and its archives quite prominently. Thanks to the maintainer

[R-pkg-devel] CRAN Debian File Handling Differences?

2019-04-23 Thread David Blodgett via R-package-devel
--- Begin Message --- Dear R Package Development Community, I'm working on some CRAN Debian test failures (https://win-builder.r-project.org/incoming_pretest/ncdfgeom_1.0.0_20190423_031452/). The tests all pass on rhub Debian, CRAN windows, local OSX, and Travis Ubuntu. The tests tha

Re: [R-pkg-devel] [EXTERNAL] Re: CRAN Debian File Handling Differences?

2019-04-23 Thread David Blodgett via R-package-devel
pr 23, 2019, at 10:16 AM, Iñaki Ucar wrote: > > On Tue, 23 Apr 2019 at 15:57, David Blodgett via R-package-devel > wrote: >> >> I'm working on some CRAN Debian test failures >> (https://win-builder.r-project.org/incoming_pretest/ncdfgeom_1.0.0_20190423_031

Re: [R-pkg-devel] [EXTERNAL] Re: CRAN Debian File Handling Differences?

2019-04-23 Thread David Blodgett via R-package-devel
icy: > > - Packages should not write in the user’s home filespace (including > clipboards), nor anywhere else on the file system apart from the R > session’s temporary directory (or during installation in the location > pointed to by TMP

Re: [R-pkg-devel] Package dependency graphs of packages in development (local)

2019-05-09 Thread Maëlle SALMON via R-package-devel
want to identify packages which I should leave out to reduce the number of (indirect) dependencies. Rainer > On 9 May 2019, at 11:24, Gábor Csárdi wrote: > > You can do something like this with https://github.com/r-lib/pkgdepends: > > pr <- pkgdepends::remotes()$new(&

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

2019-05-15 Thread Hong Ooi via R-package-devel
--- Begin Message --- I had a similar experience with a couple of my package updates needing changes. The background is that I have a family of packages for talking to Microsoft's Azure cloud service from R, and my examples are all marked \dontrun because they need an Azure subscription to

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

2019-05-16 Thread Hong Ooi via R-package-devel
Cc: R Package Development Subject: Re: [R-pkg-devel] CRAN student assistants Thanks for the excellent comparable package, Hong. Today's rejection of gargle instructs me to use \donttest{} instead of \dontrun{}. Most of the affected functions create, load, and/or refresh service account t

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

2019-10-01 Thread Hong Ooi via R-package-devel
, who approved the other packages in the first place -- the other reviewer probably just wasn't aware that I'd cleared things with Uwe previously. -Original Message- From: R-package-devel On Behalf Of Jim Hester Sent: Wednesday, 2 October 2019 3:37 AM To: R Package Development

Re: [R-pkg-devel] R package which creates a directory in the user home dir

2019-10-17 Thread Hong Ooi via R-package-devel
Also, consider using the rappdirs package to write to a location that follows standard practice on each platform. -Original Message- From: R-package-devel On Behalf Of Martin Maechler Sent: Thursday, 17 October 2019 11:44 PM To: Sigbert Klinke Cc: r-package-devel@r-project.org

[R-pkg-devel] New Package olr 4 NOTES

2019-12-04 Thread Mat Fok via R-package-devel
g for hidden files and directories ... NOTE Found the following hidden files and directories: .Rhistory .gitignore .Rproj.user These were most likely included in error. See section 'Package structure' in the 'Writing R Extensions' manual. 6. Lastly, I do not know how to fi

Re: [R-pkg-devel] New Package olr 4 NOTES

2019-12-04 Thread Mat Fok via R-package-devel
04/12/2019 1:02 p.m., Mat Fok via R-package-devel wrote: > Hi All, > This is the first time I am trying to upload a package. It is fun learning > this stuff. > Thank you all for kindly looking at the NOTES. > This is the log I recevied from CRAN volunteers:  > https://win-bui

Re: [R-pkg-devel] New Package olr 4 NOTES

2019-12-05 Thread Mat Fok via R-package-devel
I meant .Rbuildignore. Sent from Yahoo Mail for iPhone On Thursday, December 5, 2019, 3:19 AM, Martin Maechler wrote: >>>>> Mat Fok via R-package-devel >>>>>    on Wed, 4 Dec 2019 22:25:47 + writes:     > Hi,     > Thank you. I am wondering why the

Re: [R-pkg-devel] New Package olr 4 NOTES

2019-12-05 Thread Mat Fok via R-package-devel
Hi Max, Following your comment about, ".Rbuildignore is used by R CMD build to exclude some files from the bundled package. If you created the tar.gz file manually, then .Rbuildignore was, well, ignored. And .Rproj.user would then have been included in the tarball." I assume that i

[R-pkg-devel] Update on olr package

2019-12-08 Thread Mat Fok via R-package-devel
Hi, MatHatter/olr_r Thank you all for helping! It has lead me in the right direction. I have resolved a lot of the previous .Rbuildignore problems, because I have been using R CMD to build the tarball or in other words, I have been using the batch files to run the build and checks. R CMD -as

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