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

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 already got an answer from Kurt. I think we're not seeing his mails to the list.)

Re: [Rd] confint Attempts to Use All Server CPUs by Default

В Tue, 21 May 2024 08:00:11 + Dario Strbenac via R-devel пишет: > Would a less resource-intensive value, such as 1, be a safer default > CPU value for confint? Which confint() method do you have in mind? There is at least four of them by default in R, and many additional classes could make

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

On Sun, 19 May 2024 09:52:08 + Daniel Kelley wrote: > In answer to the question about tidy version on macOS, I have the > latest version of that OS (Sonoma 14.5 release 23F79 -- a beta > release, unless the official has caught up in recent days) and I get > as follows. > $ ~ /usr/bin/tidy

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

On Sat, 18 May 2024 21:10:18 + "Richard M. Heiberger" wrote: > when checking a package and discovering these messages about html5, > can you generate an informational message about tidy with a link to > updating tidy? That's a useful suggestion. Would you mind testing the patch from

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

В Thu, 16 May 2024 21:32:24 +0200 David Cortes пишет: > Unfortunately, after some further testing, it seems this was just a > matter of getting lucky - using the alternative non-STRUCT_SUBTYPES > def. of Altrep still leads to memory corruptions and crashes, just at > different points than when

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

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: [Rd] FR: Customize background colour of row and column headers for the View output

The change suggested by Iago Giné Vázquez is indeed very simple. It sets the background colour of the row and column headers to the background of the rest of the dataentry window. With this patch, R passes 'make check'. As Duncan Murdoch mentions, the X11 editor already behaves this way. If it's

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

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 header has this

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

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 and, ideally, to

Re: [Rd] [External] R hang/bug with circular references and promises

On Mon, 13 May 2024 09:54:27 -0500 (CDT) luke-tierney--- via R-devel wrote: > Looks like I added that warning 22 years ago, so that should be enough > notice :-). I'll look into removing it now. Dear Luke, I've got a somewhat niche use case: as a way of protecting myself against rogue *.rds

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

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"), >person(given = "Leila", family = "Amiri", role =

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

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 suspicious default

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

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 when reading a "B\n"

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

В Wed, 8 May 2024 16:01:23 -0400 Josiah Parry пишет: >- I'll see if I can get the configure.ac to make the appropriate > Rscript call for configure.win. > - I think the idea of having a single `confgure.ac` file to > generate both configure and configure.win is nice. Guidance with >

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

В Thu, 09 May 2024 15:31:25 + Othman El Hammouchi пишет: > Do I understand it correctly that there is no way to specify a > Fortran standard in the SystemRequirements? It's possible (and even recommended) to describe the Fortran version requirement in SystemRequirements [1], but this field

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

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 following error: > >

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

В Wed, 8 May 2024 14:08:36 -0400 Josiah Parry пишет: > With ChatGPT's ability to write autoconf, I *think *I have something > that can work. You don't have to write autoconf if your configure.ac is mostly a plain shell script. You can write the configure script itself. Set the PATH and then

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

В Wed, 8 May 2024 17:30:46 +0200 "Jose V. Die Ramon" пишет: > Could anyone please help me understand the reasons behind this, or > suggest any steps I should take to resolve it? Here's what I could find in https://cran.r-project.org/src/contrib/PACKAGES.in: >> X-CRAN-Comment: Archived on

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

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 tarball.

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

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 without

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

On Tue, 7 May 2024 10:07:59 +1200 Simon Urbanek wrote: > That doesn't work - additional repositories are not allowed on CRAN > other than in very exceptional cases, because it means the package > cannot be installed by users making it somewhat pointless. I suppose that

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

В Sat, 4 May 2024 15:53:25 + Sharon Bewick пишет: > I have a dependency on phyloseq, which is available through GitHub > but not on the CRAN site. I have a similar problem with microViz, > however I’ve managed to make it suggested, rather than required. > There is no way to get around the

Re: [R-pkg-devel] Urgent Review of R Packages in Light of Recent RDS Exploit

On Sat, 4 May 2024 08:09:28 +0200 Maciej Nasinski wrote: > What do you think about promoting containers? Containers have an attack surface too, have user experience problems (how's Docker on Windows?) and may bring in more third-party code than what you're trying to protect against (whole

Re: [R-pkg-devel] Urgent Review of R Packages in Light of Recent RDS Exploit

On Fri, 3 May 2024 18:17:52 +0200 Maciej Nasinski wrote: > I found the https://github.com/hrbrmstr/rdaradar solution and ran it > on the 100 most downloaded R packages. > Happily, all data/inst rda files are safe/non-exposed to RDS exploit > (using the linked solution). This is a bit useful -

Re: [R-pkg-devel] Urgent Review of R Packages in Light of Recent RDS Exploit

Dear Maciej Nasinski, On Fri, 3 May 2024 11:37:57 +0200 Maciej Nasinski wrote: > I believe we must conduct a comprehensive review of all existing CRAN > packages. Why now? R packages are already code. You don't need poisoned RDS files to wreak havoc using an R package. On the other hand, R

Re: [R-pkg-devel] Extending proj with proj.line3d methods and overloading the methods

В Sun, 28 Apr 2024 15:15:06 + Leo Mada пишет: > This is why I intended to define a new method "proj.line3d" and > overload this method. But it seems that R interprets "line3d.numeric" > as a class - which originates probably from the "data,frame" class. It may help to call the original

Re: [Rd] max on numeric_version with long components

В Sat, 27 Apr 2024 13:56:58 -0500 Jonathan Keane пишет: > In devel: > > max(numeric_version(c("1.0.1.1", "1.0.3.1", > "1.0.2.1"))) > [1] ‘1.0.1.1’ > > max(numeric_version(c("1.0.1.1000", "1.0.3.1000", > "1.0.2.1000"))) > [1] ‘1.0.3.1000’ Thank

Re: [R-pkg-devel] Extending proj with proj.line3d methods and overloading the methods

27 апреля 2024 г. 00:49:47 GMT+03:00, Leo Mada via R-package-devel пишет: >Dear List-Members, > >I try to implement a proj.line3d method and to overload this method as follows: > >proj.line3d <- function(p, x, y, z, ...) > UseMethod("proj.line3d") > >proj.line3d.numeric = function(p, x, y, z,

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

On Fri, 26 Apr 2024 13:15:47 +0200 Gábor Csárdi wrote: > That's not how this worked in the past AFAIR. Simply, the packages in > the x.y.z/Recommended directories were included in > src/contrib/PACKAGES*, metadata, with the correct R version > dependencies, in the correct order, so that

Re: [Rd] R 4.4.0 has version of Matrix 1.7-0, but it's not available on CRAN

On Fri, 26 Apr 2024 12:32:59 +0200 Martin Maechler wrote: > Finally, I'd think it definitely would be nice for > install.packages("Matrix") to automatically get the correct > Matrix version from CRAN ... so we (R-core) would be grateful > for a patch to install.packages() to achieve this Since

Re: [R-pkg-devel] Some, but not all vignettes compressed

В Thu, 25 Apr 2024 11:54:49 -0700 Bryan Hanson пишет: > So my version of gs blows things up! The relatively good news is that GhostScript is not solely to blame. A fresh build of "GPL Ghostscript 10.03.0 (2024-03-06)" was able to reduce the files to 16..70% of their original size on my

Re: [R-pkg-devel] Some, but not all vignettes compressed

В Thu, 25 Apr 2024 08:54:41 -0700 Bryan Hanson пишет: > 'gs+qpdf' made some significant size reductions: > compacted 'Vig_02_Conceptual_Intro_PCA.pdf' from 432Kb to 143Kb > compacted 'Vig_03_Step_By_Step_PCA.pdf' from 414Kb to 101Kb > compacted 'Vig_04_Scores_Loadings.pdf' from

Re: [Rd] Big speedup in install.packages() by re-using connections

On Thu, 25 Apr 2024 14:45:04 +0200 Jeroen Ooms wrote: > Thoughts? How verboten would it be to create an empty external pointer object, add it to the preserved list, and set an on-exit finalizer to clean up the curl multi-handle? As far as I can tell, the internet module is not supposed to be

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, 24 Apr 2024 15:31:39 -0500 (CDT) luke-tierney--- via R-devel wrote: > We would be better off (in my view, not necessarily shared by others > in R-core) if we could get to a point where: > > all entry points listed in installed header files can be used in > packages, at least

Re: [Rd] View() segfaulting ...

On Wed, 24 Apr 2024 19:35:42 -0400 Ben Bolker wrote: > I'm using bleeding-edge R-devel, so maybe my build is weird. Can > anyone else reproduce this? > >View() seems to crash on just about anything. Not for me, sorry. If you have a sufficiently new processor, you can use `rr` [*] to

Re: [R-pkg-devel] [External] Re: Package submission to CRAN not passing incoming checks

В Wed, 24 Apr 2024 00:17:28 + "Petersen, Isaac T" пишет: > I included the packages (including the raw package folders and their > .tar.gz files) in the /inst/extdata folder. Would you prefer your test to install them from the source directories (as you currently do, in which case the

Re: [R-pkg-devel] Package submission to CRAN not passing incoming checks

Dear Isaac, В Mon, 22 Apr 2024 17:00:27 + "Petersen, Isaac T" пишет: > This my first post--I read the posting guidelines, but my apologies > in advance if I make a mistake. Welcome to R-package-devel! You're doing just fine. > 1) The first note <...> includes the contents of the LICENSE

Re: [R-pkg-devel] Old references in the Description file.

В Thu, 11 Apr 2024 11:57:00 + Gabriel Constantino Blain пишет: > The problem is that it is a paper from the 70's (Priestley and > Taylor, 1972) and its DOI has very uncommon symbols, such as <>. The > DOI is: 10.1175/1520-0493(1972)100<0081:OTAOSH>2.3.CO;2. Since the R CMD check function

Re: [R-pkg-devel] Question about CRAN submission resulting in 1 note

В Wed, 10 Apr 2024 14:11:53 + Chris Knoll пишет: > For "Package has VignetteBuilder field but no prebuilt vignette > index", how would this be resolved? The package at https://github.com/OHDSI/CirceR/ doesn't seem to have any vignettes. Without vignettes, there's no need for

Re: [Rd] Wish: a way to track progress of parallel operations

Dear Henrik (and everyone else): Here's a patch implementing support for immediateConditions in 'parallel' socket clusters. What do you think? I've tried to make the feature backwards-compatible in the sense that an older R starting a newer cluster worker will not pass the flag enabling

Re: [R-pkg-devel] Linking Tutorial Site to CRAN Package site.

В Sat, 6 Apr 2024 18:27:24 + "Ruff, Sergej" пишет: > The CRAN site > (https://cran.r-project.org/web/packages/RepeatedHighDim/index.html) > has a "documentation" part with the refrence pdf. > > Can I link to our tutorial site (https://software.klausjung-lab.de/.) > under documentation?

Re: [Rd] Bug in out-of-bounds assignment of list object to expression() vector

On Fri, 5 Apr 2024 08:15:20 -0400 June Choe wrote: > When assigning a list to an out of bounds index (ex: the next, n+1 > index), it errors the same but now changes the values of the vector > to NULL: > > ``` > x <- expression(a,b,c) > x[[4]] <- list() # Error > x > #> expression(NULL, NULL,

Re: [Rd] hand compile; link to MKL fails at BLAS zdotu

В Sat, 30 Mar 2024 20:31:25 +0300 Ivan Krylov via R-devel пишет: > It seems to crash inside MKL! Should have read some more about mkl_gf_lp64 before posting. According to the Intel forums, it is indeed required in order to work with the GFortran calling convention, but if you're linking agai

Re: [Rd] hand compile; link to MKL fails at BLAS zdotu

В Sat, 30 Mar 2024 10:55:48 + Ramón Fallon пишет: > In contrast to Dirk's solution, I've found R's configure script > doesn't recognise the update-alternatives system on debian/ubuntu, if > it's MKL. It ought to work if configured with --with-blas=-lblas --with-lapack=-llapack, but, as you

Re: [Rd] paths capability FALSE on devel?

В Wed, 27 Mar 2024 11:28:17 +0100 Alexandre Courtiol пишет: > after installing R-devel the output of > grDevices::dev.capabilities()$paths is FALSE, while it is TRUE for R > 4.3.3 Your system must be missing Cairo development headers, making x11() fall back to type = 'Xlib': $ R-devel -q -s -e

Re: [Rd] Wish: a way to track progress of parallel operations

Henrik, Thank you for taking the time to read and reply to my message! On Mon, 25 Mar 2024 10:19:38 -0700 Henrik Bengtsson wrote: > * Target a solution that works the same regardless whether we run in > parallel or not, i.e. the code/API should look the same regardless of > using, say,

[Rd] Wish: a way to track progress of parallel operations

Hello R-devel, A function to be run inside lapply() or one of its friends is trivial to augment with side effects to show a progress bar. When the code is intended to be run on a 'parallel' cluster, it generally cannot rely on its own side effects to report progress. I've found three approaches

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

В Mon, 25 Mar 2024 11:12:57 +0100 Jairo Hidalgo Migueles пишет: > Specifically, this data consists of regression and random forest > models crucial for making predictions within our R package. Apologies for asking a silly question, but is there a chance that these models are large by accident

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

В Thu, 21 Mar 2024 18:32:59 + Annaig De-Walsche пишет: > If ever I condition the use of OpenMD directives, users will indeed > be capable of installing the package, but they wont access to a > performant version of the code, as it necessitates the use of OpenMD. > Is there a method to

Re: [R-pkg-devel] help diagnosing win-builder failures

Hi, This may need the help of Uwe Ligges to diagnose. I suspect this may be related to the Windows machine having too much memory committed (as Uwe has been able to pinpoint recently [*] about a package that failed to compile some heavily templated C++), but there is not enough information to

Re: [Rd] Spurious warning in as.data.frame.factor()

On Fri, 15 Mar 2024 11:24:22 +0100 Martin Maechler wrote: > I think just adding > > removeGeneric('as.data.frame') > > is appropriate here as it is self-explaining and should not leave > much traces. Thanks for letting me know! I'll make sure to use removeGeneric() in similar cases in

Re: [R-pkg-devel] Removing import(methods) stops exporting S4 "meta name"

On Thu, 14 Mar 2024 16:06:50 -0400 Duncan Murdoch wrote: > Error in xj[i] : invalid subscript type 'list' > Calls: join_inner -> data.frame -> [ -> [.data.table -> [.data.frame > Execution halted And here's how it happens: join_inner calls xi[yi,on=by,nomatch=0] on data.tables xi and yi.

Re: [Rd] Spurious warning in as.data.frame.factor()

On Thu, 14 Mar 2024 10:41:54 +0100 Martin Maechler wrote: > Anybody trying S7 examples and see if they work w/o producing > wrong warnings? It looks like this is not applicable to S7. If I overwrite as.data.frame with a newly created S7 generic, it fails to dispatch on existing S3 classes:

Re: [Rd] Spurious warning in as.data.frame.factor()

В Tue, 12 Mar 2024 12:33:17 -0700 Hervé Pagès пишет: > The acrobatics that as.data.frame.factor() is going thru in order to > recognize a direct call don't play nice if as.data.frame() is an S4 > generic: > >     df <- as.data.frame(factor(11:12)) > >    

Re: [R-pkg-devel] confusion over spellchecking

В Sun, 10 Mar 2024 13:55:43 -0400 Ben Bolker пишет: > I am working on a package and can't seem to get rid of a NOTE about > > Possibly misspelled words in DESCRIPTION: >glmmTMB (10:88) >lme (10:82) > > on win-builder. Do you have these words anywhere else in the package (e.g. in the

Re: [R-pkg-devel] Submission after archived version

В Mon, 11 Mar 2024 23:45:13 +0100 Nils Mechtel пишет: > Despite R CMD check not giving any errors or warnings, the package > doesn’t pass the pre-tests: If your question was more about the reasons for the difference between your R CMD check and the pre-tests, most of it is due to --as-cran:

Re: [R-pkg-devel] Submission after archived version

В Mon, 11 Mar 2024 23:45:13 +0100 Nils Mechtel пишет: > Debian: > > Status: 3 NOTEs >> * checking CRAN incoming feasibility ... [4s/6s] NOTE >> Possibly misspelled words in DESCRIPTION: >>

Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation

В Mon, 11 Mar 2024 14:57:58 + "Ruff, Sergej" пишет: > I uploaded the old version of the package to my repo: > https://github.com/SergejRuff/boot After installing this tarball, running RStudio and typing: library(bootGSEA) ?bootGSEA ...I see the help page in RStudio's help tab, not in the

Re: [R-pkg-devel] RFC: C backtraces for R CMD check via just-in-time debugging

Vladimir, Thank you for the example and for sharing the ideas regarding symbol-relative offsets! On Thu, 7 Mar 2024 09:38:18 -0500 (EST) Vladimir Dergachev wrote: > unw_get_reg(, UNW_REG_IP, ); Is it ever possible for unw_get_reg() to fail (return non-zero) for UNW_REG_IP? The

Re: [R-pkg-devel] [EXTERN] Re: [EXTERN] Re: @doctype is deprecated. need help for r package documentation

В Thu, 7 Mar 2024 20:27:29 + "Ruff, Sergej" пишет: > I am refering to Rstudio. I checked the settings and type is set to > "htlm", not text. And I was wondering why the package documentation > opened in a browser when I used @doctype. Do you still have the source package .tar.gz file for

Re: [R-pkg-devel] @doctype is deprecated. need help for r package documentation

В Thu, 7 Mar 2024 10:37:51 + "Ruff, Sergej" пишет: > I noticed that when I try _?bootGSEA_ it goes to the help page in R > itself but not to the html page That's up to the user to choose. help(bootGSEA, help_type = 'html') should get you to the HTML documentation; help(bootGSEA, help_type =

Re: [R-pkg-devel] RFC: C backtraces for R CMD check via just-in-time debugging

On Tue, 5 Mar 2024 18:26:28 -0500 (EST) Vladimir Dergachev wrote: > I use libunwind in my programs, works quite well, and simple to use. > > Happy to share the code if there is interest.. Do you mean that you use libunwind in signal handlers? An example on how to produce a backtrace without

Re: [R-pkg-devel] [External] [External] RcmdrPlugin.HH_1.1-48.tar.gz

On Wed, 6 Mar 2024 13:46:55 -0500 Duncan Murdoch wrote: > is this just a more or less harmless error, thinking that > the dot needs escaping I think it's this one. You are absolutely right that the dot doesn't need escaping in either TRE (which is what's used inside exportPattern) or PCRE. In

[Rd] Never exporting .__global__ and .__suppressForeign__?

Hello, (Dear Richard, I hope you don't mind being Cc:'d on this thread in R-devel. This is one of the ways we can prevent similar problems from happening in the future.) Sometimes, package authors who use both exportPattern('.') and utils::globalVariables(...) get confusing WARNINGs about

Re: [R-pkg-devel] RcmdrPlugin.HH_1.1-48.tar.gz

В Tue, 5 Mar 2024 22:41:32 + "Richard M. Heiberger" пишет: > Undocumented code objects: >'.__global__' > All user-level objects in a package should have documentation > entries. See chapter 'Writing R documentation files' in the 'Writing R > Extensions' manual. This object is not

Re: [R-pkg-devel] RFC: C backtraces for R CMD check via just-in-time debugging

On Sun, 3 Mar 2024 19:19:43 -0800 Kevin Ushey wrote: > Would libSegFault be useful here? Glad to know it has been moved to and not just removed altogether after the upstream commit

[R-pkg-devel] RFC: C backtraces for R CMD check via just-in-time debugging

Hello, This may be of interest to people who run lots of R CMD checks and have to deal with resulting crashes in compiled code. Every now and then, the CRAN checks surface a particularly nasty crash. The R-level traceback stops in the compiled code. It's not obvious where exactly the crash

Re: [R-pkg-devel] Additional issues: Intel segfault

В Sat, 2 Mar 2024 02:07:47 + Murray Efford пишет: > Gabor suggested https://github.com/r-hub/rhub2 and that worked like a > charm. A check there on the Intel platform found no errors in my > present version of secrdesign, so I'll resubmit with confidence. Thank you for letting me know!

Re: [R-pkg-devel] Additional issues: Intel segfault

В Fri, 1 Mar 2024 07:42:01 + Murray Efford пишет: > R CMD check suggests it is most likely in the Examples for > 'validate', but all code there is wrapped in \dontrun{}. The crash happens after q('no'), suggesting a corruption in the heap or in the R memory manager. At least it's a null

Re: [R-pkg-devel] Unexpected multi-core CPU usage in package tests

В Tue, 27 Feb 2024 11:14:19 + Jon Clayden пишет: > My testing route is to install the packages within the > 'rocker/r-devel' Docker container, which is Debian-based, then use > 'time' to evaluate CPU usage. Note that, even though 'RNifti' does not > use OpenMP, setting OMP_NUM_THREADS

[Rd] How to avoid the Markdown code block bug on R Bugzilla

Hello, There's a rare but annoying bug in Bugzilla 5.1.2...5.3.2+ where a Markdown code block inside a comment may be replaced by U+F111 or U+F222, and then the following code blocks may end up being replaced by the preceding ones. For example, the problem can be seen in PR16158:

Re: [R-pkg-devel] CRAN Package Check Note: Warning: trimming empty

В Fri, 23 Feb 2024 17:04:39 + Sunmee Kim пишет: > Version: 1.0.4 > Check: HTML version of manual > Result: NOTE This may not be immediately obvious in the e-mail from CRAN, but I think this is a reminder of a warning from the previous version of the package. Haven't you just uploaded

Re: [Rd] Tcl socket server (tcltk) does not work any more on R 4.3.2

В Wed, 21 Feb 2024 08:01:16 +0100 "webmail.gandi.net" пишет: > Since the {tcltk} package was working fine with "while > (Tcl_DoOneEvent(TCL_DONT_WAIT) && max_ev) max_ev—;", unless there is > a clear performance enhancement with "while (i-- && > Tcl_ServiceAll())", it would perhaps be wise to

Re: [R-pkg-devel] Conversion failure in 'mbcsToSbcs'

В Wed, 21 Feb 2024 12:29:02 + Package Maintainer пишет: > Error: processing vignette 'ggenealogy.Rnw' failed with diagnostics: > chunk 58 (label = plotCBText) In order to use the non-standard graphics device, the chunk must set the option fig=TRUE. Otherwise, when something calls

Re: [Rd] Tcl socket server (tcltk) does not work any more on R 4.3.2

В Tue, 20 Feb 2024 12:27:35 +0100 "webmail.gandi.net" пишет: > When R process #1 is R 4.2.3, it works as expected (whatever version > of R #2). When R process #1 is R 4.3.2, nothing is sent or received > through the socket apparently, but no error is issued and process #2 > seems to be able to

Re: [R-pkg-devel] Conversion failure in 'mbcsToSbcs'

В Mon, 12 Feb 2024 16:01:27 + Package Maintainer пишет: > Unfortunately, I received a reply from the CRAN submission team > stating that my vignette file is still obtaining the "mbcsToSbcs" > ERROR as is shown here >

Re: [Rd] certain pipe() use cases not working in r-devel

В Wed, 14 Feb 2024 14:43:12 -0800 Jennifer Bryan пишет: > But in r-devel on macOS, this is silent no-op, i.e. "hello, world" > does not print: > > > R.version.string > [1] "R Under development (unstable) (2024-02-13 r85895)" > > con <- pipe("cat") > > writeLines("hello, world", con) I can

Re: [R-pkg-devel] failing CRAN checks due to problems with dependencies

В Wed, 7 Feb 2024 08:40:44 -0600 Marcin Jurek пишет: > Packages required but not available: 'Rcpp', 'FNN', > 'RcppArmadillo' Packages suggested but not available for checking: > 'fields', 'rmarkdown', 'testthat', 'maptools' One of the machines running the incoming checks was having problems. If

Re: [Rd] Difficult debug

On Wed, 07 Feb 2024 14:01:44 -0600 "Therneau, Terry M., Ph.D. via R-devel" wrote: > > test2 <- mysurv(fit2, pbc2$bili4, p0= 4:0/10, fit2, x0 =50) > ==31730== Invalid read of size 8 > ==31730==    at 0x298A07: Rf_allocVector3 (memory.c:2861) > ==31730==    by 0x299B2C: Rf_allocVector

Re: [R-pkg-devel] r-oldrel-linux- not in CRAN checks?

В Tue, 6 Feb 2024 18:27:32 +0100 Vincent van Hees пишет: > For details see: > https://github.com/RfastOfficial/Rfast/issues/99 GitHub processed your plain text description of the problem as if it was Markdown and among other things ate the text that used to be there between angle brackets: >

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

Dear Uwe Ligges, On Mon, 22 Jan 2024 15:50:44 +0100 Uwe Ligges wrote: > So we are looking for a person volunteering to take over 'XML'. > Please let us know if you are interested. Unless someone else has been discussing this with CRAN in private or had a package depending on XML and was

Re: [Rd] Advice debugging M1Mac check errors

On Sun, 4 Feb 2024 20:41:51 +0100 Holger Hoefling wrote: > I wanted to ask if people have good advice on how to debug M1Mac > package check errors when you don´t have a Mac? Apologies for not answering the question you asked, but is this about hdf5r and problems printing R_xlen_t [*] that

Re: [R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

Thank you Georgi Boshnakov, Ben Bolker, and Diego Hernangómez Herrero for introducing me to `revdepcheck`! On Tue, 30 Jan 2024 12:38:57 -0500 Ben Bolker wrote: > I have had a few issues with it > but overall it's > been very helpful. Indeed

Re: [R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

On Tue, 30 Jan 2024 16:24:40 + Martin Morgan wrote: > BiocManager (the recommended way to install Bioconductor packages) at > the end of the day does essentially install.packages(repos = > BiocManager::repositories()), ensuring that the right versions of > Bioconductor packages are installed

Re: [R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

Dear Dirk, Thank you very much for your help here and over on GitHub! I have finally managed to get the reverse dependency checks working. It took some additional disk space and a few more system dependencies. If not for r2u, I would have been stuck for much longer. I really appreciate the work

[R-pkg-devel] Bioconductor reverse dependency checks for a CRAN package

Hello R-package-devel, What would you recommend in order to run reverse dependency checks for a package with 182 direct strong dependencies from CRAN and 66 from Bioconductor (plus 3 more from annotations and experiments)? Without extra environment variables, R CMD check requires the Suggested

Re: [R-pkg-devel] Possible malware(?) in a vignette

There used to be a long analysis in the draft of this e-mail [*], but let me cut to the chase. Even something as simple as replacing the four-byte comment [**] at the beginning of the file ("%\xd0\xd4\xc5\xd8" -> "%") that keeps the file fully readable (!) results in the same behaviour but

Re: [R-pkg-devel] Possible malware(?) in a vignette

Apologies for being insufficiently clear. By "a file straight from NOAA" I meant a completely different PDF, , that gives the same SHA-256 hash whether downloaded by VirusTotal

Re: [R-pkg-devel] Possible malware(?) in a vignette

В Sat, 27 Jan 2024 03:52:01 -0500 Bob Rudis пишет: > Two VT sandboxes used Adobe Acrobat Reader to open the PDF and the PDF > seems to either had malicious JavaScript or had been crafted > sufficiently to caused a buffer overflow in Reader that then let it > perform other functions on those

Re: [R-pkg-devel] How to deal with issues when using devtools::check_rhub(), rhub::check(), and web form

В Wed, 24 Jan 2024 16:14:05 -0800 Carl Schwarz пишет: > I tried using the web interface at https://builder.r-hub.io/ to > select the denebian machines, and it returns a message saying > > We're sorry, but something went wrong. > If you are the application owner check the logs for more

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

On Mon, 22 Jan 2024 17:14:04 +0100 Tomas Kalibera wrote: > Yes, inside a bigger email, reports can get overlooked, particularly > when in a thread with a rather different subject. It wasn't > overlooked this time thanks to Martin. Then additional thanks goes to Martin, and I'll make sure to

Re: [R-pkg-devel] lost braces note on CRAN pretest related to \itemize

В Tue, 23 Jan 2024 19:39:54 +0100 Patrick Giraudoux пишет: >   \itemize{ >   \item{.}{lm and glm objects can be passed directly as the upper > scope of term addition (all terms added). Inside the \itemize and \enumerate commands, the \item command doesn't take any arguments:

Re: [R-pkg-devel] Cannot see the failure output on Fedora clang/gcc falvor (page not found)

On Sun, 21 Jan 2024 16:51:39 + Sameh Abdulah wrote: > However, we cannot access the webpage (page not found) to identify > and address the failures on Fedora systems. > > https://cran-archive.r-project.org/web/checks/2024/2024-01-12_check_results_MPCR.html > > How can we see the failures

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

On Mon, 22 Jan 2024 12:30:46 +0100 Tomas Kalibera wrote: > Thanks, ported now to R-patched. Thank you! Is it fine to mention problems like this one in the middle of an e-mail, or should I have left a note in the Bugzilla instead? -- Best regards, Ivan

Re: [R-pkg-devel] Assistance Needed for Resolving Submission Issues with openaistream Package

Hello Li Gen and welcome to R-package-devel! В Mon, 22 Jan 2024 17:50:33 +0800 пишет: > The specific areas of concern are:License Information: There's a note > indicating that the license stub is an "invalid DCF". I've used 'MIT > + file LICENSE' as the licensing terms. I would appreciate

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

В Sat, 20 Jan 2024 20:28:00 -0500 Johann Gaebler пишет: > most likely there’s some error on my part in how I’ve set up cpp11, > but it also seems possible that cpp11 should have detected that that > header needs to be included and added it automatically Upon further investigation, it's more

Re: [R-pkg-devel] New Package Removal because Shared Library Too Large from Debugging Symbols

В Sat, 20 Jan 2024 14:38:55 -0500 Johann Gaebler пишет: > The issue is that the compiled libraries are too large. Was it in the e-mail? As you quite correctly observed, many other packages get the NOTE about shared library size. It may be not exactly obvious, but the red link saying "LTO" on

Re: [R-pkg-devel] Inquiry Regarding Package Organization in CRAN

Hello Andriy and welcome to R-package-devel! On Fri, 19 Jan 2024 14:34:25 + Protsak Andriy via R-package-devel wrote: > to achieve this the initial focus is on exploring the possibility of > renaming the packages so that they share a common prefix, making it > easier for uses to locate them

Re: [Rd] [External] Re: Choices to remove `srcref` (and its buddies) when serializing objects

On Thu, 18 Jan 2024 09:59:31 -0600 (CST) luke-tier...@uiowa.edu wrote: > What does 'blow up' mean? If it is anything other than signal a "bad > binding access" error then it would be good to have more details. My apologies for not being precise enough. I meant the "bad binding access" error in

Re: [Rd] Choices to remove `srcref` (and its buddies) when serializing objects

В Tue, 16 Jan 2024 14:16:19 -0500 Dipterix Wang пишет: > Could you recommend any packages/functions that compute hash such > that the source references and sexpinfo_struct are ignored? Basically > a version of `serialize` that convert R objects to raw without > storing the ancillary source

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