Re: [R-pkg-devel] NOTE: Installation took CPU time 3.5 times elapsed time

On Tue, 29 Jul 2025 07:25:46 -0500 Dirk Eddelbuettel wrote: > But note that my machine has no -flto=$N for > some N but rather '-flto=auto' which also results in the NOTE. > > So an extra check may be needed to not issue the nag if LTO is used? You're right, -flto=auto chooses the number of LTO

Re: [R-pkg-devel] NOTE: Installation took CPU time 3.5 times elapsed time

Dear Dirk, On Mon, 28 Jul 2025 06:45:06 -0500 Dirk Eddelbuettel wrote: > And I just validated it: removing that last line from DESCRIPTION > removes the compilation time NOTE. This must be the culprit. The 00install.out file [1] shows -flto=8 being used, which GCC documentation [2] describes as

Re: [R-pkg-devel] Mega2R CRAN submission: false positive

В Thu, 24 Jul 2025 09:48:58 -0700 Kevin Ushey пишет: > hopefully the issue will go away once the version of gcc > used on these CRAN check machines is updated Or when SQLite 3.51.0 comes out, containing the workaround for the compiler bug, and RSQLite is released with the updated version of SQLi

Re: [R-pkg-devel] `Warning in formals(fun) : argument is not a function`

В Thu, 24 Jul 2025 15:15:35 + Mark Clements пишет: > I am looking for guidance on how to debug a CRAN warning for a > package (rstpm2). The warning is: > > `Warning in formals(fun) : argument is not a function` Could you please provide some more information on where you encounter it and how

Re: [R-pkg-devel] [External] compact vignettes

В Wed, 23 Jul 2025 20:09:26 + "Richard M. Heiberger" пишет: > When I use > R_QPDF=/Library/Frameworks/R.framework/Resources/bin/qpdf > R_GSCMD=/usr/local/bin/Cellar/ghostscript/10.03.0/bin/gs > GS_QUALITY=ebook > echo $R_QPDF $R_GSCMD $GS_QUALITY > R CMD build --compact-vignettes=both micropl

Re: [R-pkg-devel] Package removed from CRAN without warning

В Thu, 17 Jul 2025 08:30:12 -0300 "Rafael H. M. Pereira" пишет: > both packages were passing all CRAN checks (see here > > and here >

Re: [R-pkg-devel] Should I ignore a remote-check NOTE on 'Author field differs from Authors@R'?

On Fri, 11 Jul 2025 18:50:44 + Daniel Kelley wrote: > My concern is with the last test, i.e. on system > > R version 4.4.3 (2025-02-28 ucrt) > > It produces one NOTE. Looking into this, I see the following in the > 00check.log file: > > * checking DESCRIPTION meta-information ... NOTE > A

Re: [R-pkg-devel] Help with CRAN Submission Feedback

В Sat, 5 Jul 2025 14:12:56 -0700 "Reed A. Cartwright" пишет: > `tools/config.Rtools/config/configure.R` is not a file in my package. > So I assume that this report is saying that it is being created during > installation, but I can't reproduce it. Proving a negative is hard. My guess is that th

Re: [R-pkg-devel] Depending on R 4.5.0 because a related package depends on it?

В Sun, 29 Jun 2025 13:56:36 +0800 Shu Fai Cheung пишет: > An R-CMD-check action on an old release of R, conducted by GitHub > action, failed, because Package C depends on R 4.5.0. However, I found > that several other packages that import Package C, including Package > B, do not require R 4.5.0.

Re: [R-pkg-devel] Help resolving Warning for Mega2R package

Dear Daniel E. Weeks, В Mon, 23 Jun 2025 13:29:52 + "Weeks, Daniel E" пишет: >vendor/sqlite3/sqlite3.c:80239:14: runtime error: load of address > 0x7faa31b1fa40 with insufficient space for an object of type 'struct > MemPage *' Thank you for pointing out that the issue is reproducible w

Re: [R-pkg-devel] CRAN 'blackswan' server configuration

В Fri, 20 Jun 2025 17:32:34 -0400 Tyler пишет: > You can see the failure logs here: > > https://www.stats.ox.ac.uk/pub/bdr/donttest/libdeflate.log > > And my configure script here : > > https://github.com/tylermorganwall/libdeflate/blob/main/tools/config/configure.R > > Note that I've exclude

Re: [R-pkg-devel] Tcl/Tk version difficulty building loon package on Unix ??

В Sun, 8 Jun 2025 22:24:11 + Wayne Oldford пишет: > As I understand it, the problem appears to be that package testing > under Unix uses an R built with Tcl/Tk version 9.0.1 <...> > I think I have excised the version number 8.6 everywhere in the > package and am only asking that the version >

Re: [R-pkg-devel] Check time > 10min

On Tue, 3 Jun 2025 15:36:09 +0200 Sebastian Meyer wrote: > It is indeed unfortunate and perhaps a bug that the Windows check log > shows no runtime for > > > * checking whether package 'secr' can be installed ... OK > > (which on the Debian check machine was reported with 164s) On the same

Re: [R-pkg-devel] [Extern] Re: Problem building package depending on third party c++ source library.

On Sat, 24 May 2025 17:07:06 +0200 Nils Lüschow wrote: > Regarding the "mismatched-new-delete" warning I am also relatively > sure that this is actually a false positive. Taking a look into the > stack-trace, the new and delete operators are actually overloaded > with functions that internally us

Re: [R-pkg-devel] Advice for addressing CRAN rejection

В Tue, 13 May 2025 17:05:14 + smallepsilon пишет: > In many package tests, I want to verify that two ways of specifying > something lead to the execution of exactly the same calculations. Would you like to try tracing the linear algebra calculations themselves (together with their arguments)

Re: [R-pkg-devel] Failed test automatic checks CRAN

On Sat, 10 May 2025 16:48:16 +0200 Lorenzo Sostero wrote: > Flavor: r-devel-windows-x86_64 > Check: tests, Result: ERROR > Running 'testthat.R' > Running the tests in 'tests/testthat.R' failed. > Complete output: > > library(testthat) > > library(EmiR) > > test_check("EmiR")

Re: [R-pkg-devel] CRAN Submission xgboost 1.7.11.1

В Fri, 9 May 2025 04:22:52 + jiaming yuan пишет: > We are trying to resolve the test failures of XGBoost but so far no > one has managed to reproduce them locally. > https://github.com/dmlc/xgboost/issues/11431 One test failure really stands out: > Error ('test_feature_weights.R:17:5'): t

Re: [R-pkg-devel] Secondary Issues getting a package on cran

В Thu, 8 May 2025 12:01:47 -0400 Tracy Morrison Sweet пишет: > New submission > Package was archived on CRAN > > I’m not sure how to do anything to remove this note. This note is to be expected. > In process.txt and summary.txt, it says "File: HLSM-Ex.Rout > vendor/cigraph/src/constructors/ad

Re: [R-pkg-devel] Run Examples Not Found

В Wed, 7 May 2025 20:10:50 + (UTC) Mat Fok via R-package-devel пишет: > I want to be able to click "Run Examples" in my Help documentation > but I get the error /Example/olr not found. > I have searched online for this but the most relevant thing I have > found was > stackoverflow.com/quest

Re: [R-pkg-devel] Problem building package depending on third party c++ source library.

В Tue, 29 Apr 2025 14:43:40 +0200 Nils Lüschow пишет: > While we generally got this feature to work when Gecode is > pre-installed on the system, we would like to spare the users this > step and include it with the package It's probably a good idea to try to achieve both. If a system copy of the

Re: [R-pkg-devel] Check if any object pointing to a given address is locked

В Thu, 24 Apr 2025 12:36:57 + Tony Wilkes пишет: > One use-case for this is to check if it's save to modify an object by > reference. I think you might need NOT_SHARED() for that, except it's far from being simple, especially once you pass arbitrary expressions (not just variable names) as a

Re: [R-pkg-devel] How to resolve help files with \Sexpr{} warning?

В Sun, 13 Apr 2025 21:54:03 -0700 (PDT) adi...@pdx.edu пишет: > Package has help file(s) containing install/render-stage \Sexpr{} > expressions but no prebuilt PDF manual. This is a relatively recent change (r85348, October 2023). Previously, R CMD build detected non-build-time dynamic content i

Re: [R-pkg-devel] cran check about examples time

В Mon, 14 Apr 2025 08:53:38 +0200 Emanuele Cordano пишет: > CRAN check were OK (frorr Windows) whereas in Debian a function > example elapses 5.326 seconds. I need to fix this. Most lines in > the examples are within \donttest{} brackets, so they should not be > executed by CRAN checks. Nowad

Re: [R-pkg-devel] broken or outdaeted URLs

В Mon, 14 Apr 2025 08:57:49 +0200 Emanuele Cordano пишет: > R CMD check --as-cran on my machine did not help. Strange, it should be doing the same thing as 'urlchecker'. I've tried it with an old version of 'RMAWGEN' and saw the messages: >> * checking CRAN incoming feasibility ... [6s/526s] WA

Re: [R-pkg-devel] \linkS4class anchoring

В Fri, 11 Apr 2025 16:00:16 + "Killick, Rebecca" пишет: > All of the \link uses within my package are anchored except for the > \linkS4class{cpt} call so I think this is what it is referring to. > I've checked the writing R extensions "Cross-references" section and > it just says to use \link

Re: [R-pkg-devel] broken or outdaeted URLs

В Thu, 10 Apr 2025 11:24:31 +0200 Emanuele Cordano пишет: > Is there an option in R CMD check that I can use on > my server to directly verify all URLs Does R CMD check --as-cran help? -- Best regards, Ivan __ R-package-devel@r-project.org mailing l

Re: [R-pkg-devel] URLs in DESCRIPTION file

В Mon, 7 Apr 2025 11:10:21 -0400 "Kevin R. Coombes" пишет: > But version R 4.5.0 RC comes back with; >     (possibly) invalid URL. Status: 403  Message: Forbidden > I copied the URL as reported in the error message, pasted it into my > browser, and it worked just fine. > > Can I assume that th

Re: [R-pkg-devel] proper way to cite an invalid URL

В Wed, 2 Apr 2025 21:20:19 -0400 Jason Cory Brunson пишет: > in case you're curious, www.ibge.Goiásv.br/ I went looking for links to this domain on the Web, found the link in the documentation for the 'ripserr' package, and then found what looks like a domain where the desired page could be foun

Re: [R-pkg-devel] Connection time-out when checking a package

В Tue, 1 Apr 2025 14:28:04 +0200 Thierry Onkelinx пишет: > Any suggestions how to fix this note without removing the > URL for the README? I think it should be possible to set the environment variable _R_CHECK_CRAN_INCOMING_REMOTE_=FALSE to disable the "remote" checks [*] (including checks for r

Re: [R-pkg-devel] NOTE about authors, no explanation

В Mon, 17 Mar 2025 13:38:50 + (UTC) Mark Webster пишет: > > Flavor: r-devel-windows-x86_64 > > Check: Overall checktime, Result: NOTE > >   Overall checktime 12 min > 10 min I think you'll have to reduce the test datasets further: https://win-builder.r-project.org/incoming_pretest/autodb_2.3

Re: [R-pkg-devel] NOTE about authors, no explanation

В Sun, 16 Mar 2025 22:06:16 + (UTC) Mark Webster via R-package-devel пишет: > I'm getting a NOTE on winbuilder, which doesn't come with much > information: > Build log: > * using log directory > 'd:/RCompile/CRANguest/R-devel/autodb.Rcheck' > > * using R version 4.5.0 alpha (2025-03-15 r87978

Re: [R-pkg-devel] How do you make it possible to run the example that requires a Conda environment?

В Wed, 26 Feb 2025 08:57:10 + KABILAN S пишет: > if I submit the package to CRAN, the example is not running and > returning an error message. Even if I mention \donttest{} to avoid > the automatic checking of example, the CRAN team members are not > allowing. Does it help to use if (reticul

Re: [R-pkg-devel] False positive antivirus reports on package vignettes

On Tue, 18 Feb 2025 08:11:15 -0600 Dirk Eddelbuettel wrote: > Maybe these do not tickle the silly anti-virsu tool. Looks like they don't, so no need to tinker with raw PDF bytes: https://www.virustotal.com/gui/url/2ef08a12060e046308afd6923b6447be10eafc36416b3af0734f724ce5127f22 (As they shouldn

Re: [R-pkg-devel] False positive antivirus reports on package vignettes

On Tue, 18 Feb 2025 07:31:59 -0600 Dirk Eddelbuettel wrote: > I have no idea. They have not communicated with me. I am only the > relevant author so why whould they. That's unfortunate. I've just fed the RcppArmadillo-sparseMatrix vignette to VirusTotal, and, indeed, there is one match: https:

Re: [R-pkg-devel] False positive antivirus reports on package vignettes

On Tue, 18 Feb 2025 07:05:06 -0600 Dirk Eddelbuettel wrote: > one of the two pdf vignettes (which I happen to create as a shallow > Rnw -> pdf wrapper around a pre-made pdf, here that inner pdf had not > changed in five years, sigh ...) now upsets one of these (idiotic, > but hey, I am sure that

Re: [R-pkg-devel] How to fix "attribute "id" has invalid value" when submitting new package to CRAN

Dear Han Zhang, Welcome to R-package-devel! В Mon, 17 Feb 2025 23:28:24 -0500 Han Zhang пишет: > Found the following > HTML validation problems: GraphicalTesting.html:114:1 > (GraphicalTesting.Rd:170): Warning: attribute "id" has invalid > value "method-Graphical Testing Procedure-new" Thank

Re: [R-pkg-devel] GPU programming in R packages

В Sun, 16 Feb 2025 13:00:55 + Wolfgang Rolke via R-package-devel пишет: > I am currently working on a project that requires calculations on > large matrices, for example calculating pairwise distances of points > in higher dimensions. How large are the matrices? Are CPU-side calculations (po

Re: [R-pkg-devel] R package submission - too many threads error

Dear Stephen Abrams, Welcome to R-package-devel! В Thu, 13 Feb 2025 22:20:50 -0500 Stephen Abrams пишет: > A secondary worry is that even if I resolve this, there might be > something else causing threads to spin up. Instead of using detectCores() [*] and creating cluster objects yourself, how

Re: [R-pkg-devel] Registering methods conditionally

В Sat, 8 Feb 2025 19:18:59 +0100 Lluís Revilla пишет: > Error in UseMethod("tidy") : no applicable method for 'tidy' applied > to an object of class "GeneSet" This seems to be a distant consequence of . The example for BaseSet::tidy starts

Re: [R-pkg-devel] How to solve this error while running python script in R environment?

В Fri, 7 Feb 2025 06:51:27 + KABILAN S пишет: > > result <- TRANSFORMER(df = S_P_500_Close_data, study_variable = > > "Price") > Error: Valid installation of TensorFlow not found. > > Python environments searched for 'tensorflow' package: > C:\Users\CRAN\Documents\.virtualenvs\r-reticulat

Re: [R-pkg-devel] S3 generic/method consistency NOTE

В Wed, 5 Feb 2025 19:52:57 -0800 Zhian Kamvar пишет: > Mismatches for methods registered for non-generic: > is: > function(object, class2) > is.genind: > function(x) > > is: > function(object, class2) > is.genpop: > function(x) > > sample: > function(x, size, rep

Re: [R-pkg-devel] Additional issue clang-ASAN, gcc-ASAN

В Sun, 2 Feb 2025 22:56:47 + Bernd.Gruber пишет: > READ of size 16 at 0x518000697ff0 thread T0 > #0 0x7f2e873ccfdf in bytesToDouble > /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/src/snpbin.c:225:19 > #1 0x7f2e873ceca5 in snpbin2freq > /tmp/RtmpNNPUz9/R.INSTALL3cef1f2b1bd39c/adegenet/

Re: [R-pkg-devel] Issue with non-standard file 'vert.txt' in R CMD check

Dear Zahra Heidari Ghahfarrokhi, Welcome to R-package-devel! В Tue, 28 Jan 2025 18:17:06 +0330 zahra heidari gh пишет: >- Additional details: > - The package FD is used during package building. > - In a previous post on the r-h...@r-project.org mailing list, > I was advised that

Re: [R-pkg-devel] [SPAM Warning!]Re: CRAN Debian error installation time

В Tue, 28 Jan 2025 16:07:38 +0100 Guillermo Vinue пишет: > Thank you for your help, Ben and Ivan. Unfortunately, the note > persists: > https://win-builder.r-project.org/incoming_pretest/fawir_1.0_20250128_113725/Debian/00check.log > The public source repository from my package is here: > https:

Re: [R-pkg-devel] Assistance with 'Surv' and 'is.Surv' Error in check_win_devel

В Tue, 28 Jan 2025 10:01:00 + Gabriel Constantino Blain пишет: > When I run check_win_devel() on my package, I encounter the following > error: > > - > Error: objects 'Surv', 'is.Surv' are not exported by > 'namespace:survival' Execution halted Since Surv and is.Surv

Re: [R-pkg-devel] Is it possible to install a pre-compiled R package from Github?

В Tue, 28 Jan 2025 14:25:23 +0100 John Clarke пишет: > I'm wondering if there is a way to point an R package installer to a > pre-compiled release on Github rather than rely on CRAN. >From the point of view of install.packages(), a repository is a collection of package files plus an index file a

Re: [R-pkg-devel] CRAN Debian error installation time

Dear Guillermo, Welcome to R-package-devel! В Mon, 27 Jan 2025 19:26:10 +0100 Guillermo Vinue пишет: > I am writing to you because I am getting this NOTE from the CRAN > Debian machine that is not allowing CRAN acceptance: "Installation > took CPU time 2.9 times elapsed time". Uwe Ligges told m

Re: [R-pkg-devel] Reliably detecting FLIBS on source build of R (w.r.t Rust packages)

В Sat, 25 Jan 2025 08:54:45 -0800 Balasubramanian Narasimhan пишет: > (https://github.com/blas-lapack-rs/r-src/blob/966266425b1a21a1e979f767c6023e6bf00616fc/build.rs#L160). > Thank you for providing the link to the code! > The only thing I can think of is that FLIBS is being set outside > c

Re: [R-pkg-devel] Rcpp: how best to include source from another Github repository

В Tue, 21 Jan 2025 11:57:46 +0100 John Clarke пишет: > Ideally, it would be nice to be able to pull the files from the > source repo using a tag/hash so that the only code change in the Rcpp > repo would be that reference rather than all the changes to the > shared source. I've been using Git su

Re: [R-pkg-devel] Package builds on all systems except on Fedora with clang

В Sun, 19 Jan 2025 20:42:17 + Pepijn de Vries пишет: > I think I could write a similar test as used by `cpp11tesseract`: > > https://github.com/pachadotdev/cpp11tesseract/blob/2ea8287ef2c27901446bafa402728014d99904d4/configure#L66-L85 I should have replied to that thread too, but got swampe

Re: [R-pkg-devel] Package builds on all systems except on Fedora with clang

В Sun, 19 Jan 2025 17:07:51 + Pepijn de Vries пишет: > He also mentioned that I "need to check in your configure script that > the external library you need is available *and* usable with the > compilers used to compile R and packages." The Fedora-clang test fails with a symbol lookup error:

Re: [R-pkg-devel] Best practices for built version checking in packages LinkingTo others?

В Fri, 17 Jan 2025 10:21:27 + Pavel Krivitsky via R-package-devel пишет: >1. What is the best way to save this information? I have a > rudimentary implementation [1] For now, this is the best way we have. Export the ABI version as an include-time constant and as a registered callab

Re: [R-pkg-devel] Help with clang-san warnings for package "tidyfit"

В Wed, 15 Jan 2025 22:13:36 +0100 Johann Pfitzinger пишет: > I have, so far, failed to reproduce this or to find any useful > information on how to fix it. My best guess based on the output.txt > is that it originates in "purrr" (which I depend on). This is, indeed, a purrr bug: https://github.

Re: [R-pkg-devel] Replacement for SETLENGTH

On Wed, 15 Jan 2025 15:30:36 + "Merlise Clyde, Ph.D." wrote: > For memory limited machines, the alloc/copy was a problem for memory > usage - and if I recall was one of the reasons in 2008 I switched to > SETLENGTH, which doesn't seem to do an allocation ??? If there is > going to be an abso

Re: [R-pkg-devel] SystemRequirements & configure check for FFTW with single precision support

В Sat, 11 Jan 2025 10:37:20 +0100 Lukas Schneiderbauer пишет: > I was told to add "fftw-s" since I require the fftw-s package on > MacOS. > * Can someone explain the reason behind this request to me? While the SystemRequirements: field currently contains free-form text, eventually we might be a

Re: [R-pkg-devel] [SPAM Warning!] addressing a CRAN submission pre-test clang-san warning

В Fri, 10 Jan 2025 07:45:00 -0700 Kent Riemondy пишет: > cleancall.c:110:46: runtime error: call to function cb_progress_done > through pointer to incorrect function type 'void (*)(void *)' This is a (mostly harmless) error in the purrr package: https://stat.ethz.ch/pipermail/r-package-devel/2

Re: [R-pkg-devel] long user + system time with CRAN special checks clang 19

В Fri, 20 Dec 2024 11:30:04 +0300 Ivan Krylov via R-package-devel пишет: > Unfortunately, it's still a puzzle why the function > tesseract::TessBaseAPI::GetVariableAsString(char const*, std::string*) > const fails to load from libtesseract. That's because libtesserac

Re: [R-pkg-devel] long user + system time with CRAN special checks clang 19

В Fri, 20 Dec 2024 08:00:08 + Mauricio Vargas Sepulveda пишет: > > https://win-builder.r-project.org/incoming_pretest/cpp11tesseract_5.3.5_20241220_042113/specialChecks/clang19/outputs.txt > >checking cpp11tesseract_5.3.5.tar.gz ... > >Timings: > user system

Re: [R-pkg-devel] Non-reproducible ASAN flagged issue

В Tue, 17 Dec 2024 20:26:01 +0100 David Cortes пишет: > I am seeing a curious error in an ASAN package check which is not > reproducible in the r-debug containers > (https://github.com/wch/r-debug), and which I'm suspecting might be a > compiler bug. r-debug differs from the gcc-ASAN special che

Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN Submission NMRphasing 1.0.6

Dear Aixiang, Welcome to R-package-devel! В Tue, 17 Dec 2024 09:47:26 + Aixiang Jiang пишет: > I am really confused by the error, which did not happen in the > previous versions. > > Since I have not changed my code at all, the possible reason is that > the external function is changed. T

Re: [R-pkg-devel] truncating strings on purpose

Dear Brad, Kurt, В Fri, 13 Dec 2024 18:08:27 + Brad Eck пишет: > The bad news is that following the gcc docs on avoid the warning did > not seem to work: I have asked on Libera.Chat's #gcc and was told that the "middle-end" warnings [1] (which include -Wstringop-truncation) should not count

Re: [R-pkg-devel] duplicating gcc-UBSAN warning

В Thu, 12 Dec 2024 14:46:08 + Brad Eck пишет: > The flag appears in 00install.out, but the warning doesn't get raised. > > Any ideas on how to duplicate? In my experiments with gcc 14.2.0-8 on Debian for amd64 (the debian:testing container), the warning only appears when all of the followin

Re: [R-pkg-devel] truncating strings on purpose

В Wed, 11 Dec 2024 12:12:11 + Brad Eck пишет: > Found the following significant warnings: > input2.c:863:5: warning: ‘__builtin_strncpy’ output may be > truncated copying 225 bytes from a string of length 255 > [-Wstringop-truncation] > Where the truncation warnings appear, I am truncati

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN Submission sidra 0.1.3

В Mon, 18 Nov 2024 16:31:21 -0300 Rodrigo Borges пишет: > The only note that is left is: > >* checking CRAN incoming feasibility ... NOTE >Maintainer: 'Rodrigo Emmanuel Santana > Borges' > >New submission > > I did online research, and it seems this could be ignored. Is it so? Yes

Re: [R-pkg-devel] update.packages Error in if (any(diff)) { : missing value where TRUE/FALSE needed

В Sun, 17 Nov 2024 14:04:56 +0100 Patrick Giraudoux пишет: > trying URL > 'https://pbil.univ-lyon1.fr/CRAN/bin/windows/contrib/4.4/xfun_0.49.zip' > Content type 'application/zip' length 568935 bytes (555 KB) > downloaded 555 KB > > Error in if (any(diff)) { : missing value where TRUE/FALSE need

Re: [R-pkg-devel] update.packages Error in if (any(diff)) { : missing value where TRUE/FALSE needed

В Sun, 17 Nov 2024 14:45:58 +0100 Patrick Giraudoux пишет: > Then I get x = a character of 658 elements, same for xx, same for nmxx Thank you for providing the information! The problem is that the following code: diff <- xx[nmxx] != x[nmxx] ...somehow gives missing values. What's in 'diff'? W

Re: [R-pkg-devel] update.packages Error in if (any(diff)) { : missing value where TRUE/FALSE needed

В Sun, 17 Nov 2024 15:12:58 +0100 Patrick Giraudoux пишет: > Running under: Windows 10 x64 (build 19045) > locale: > [1] LC_COLLATE=French_France.utf8  LC_CTYPE=French_France.utf8 > [3] LC_MONETARY=French_France.utf8 LC_NUMERIC=C > [5] LC_TIME=French_France.utf8 Your system is new enough to use

Re: [R-pkg-devel] Is this an issue with the package submission?

В Thu, 14 Nov 2024 12:27:02 -0500 Shail Choksi пишет: > The process.txt here: > https://win-builder.r-project.org/incoming_pretest/ToxicR_24.10.1.4_20241113_200016/specialChecks/clang-san/process.txt > > gives an error. Is this a win-builder issue or a package issue? How > do I go about debuggin

Re: [R-pkg-devel] Possible false negative for compiled C++ code in CRAN checks

В Thu, 14 Nov 2024 16:24:16 + Mauricio Vargas Sepulveda пишет: > After enabling the SAN flags, I cannot reproduce the gcc-san error > [2]. Can you use the rocker/r-devel-san container? It reproduces the problem for me. When reading galapagos/cg15.dic, FuzzyEntityParser::ParseEntities() keep

Re: [R-pkg-devel] New package with C++ code causes R abort in RStudio, not in R console.

В Thu, 14 Nov 2024 13:08:13 + Luc De Wilde пишет: > At last, with checking of the program with address sanitizer in > Visual Studio, I found an "off by 1 error" in my code. Now all tests > pass without problems in Rstudio. Congratulations on being able to solve the problem yourself! It took

Re: [R-pkg-devel] New package with C++ code causes R abort in RStudio, not in R console.

В Tue, 12 Nov 2024 21:09:54 + Luc De Wilde пишет: > I have attached a debugger (from Visual Studio) to the R process, > which gives me the message "A breakpoint instruction (__debugbreak() > statement or similar call) was executed in rsession-utf8.exe. > > When I go to the dll module in the

Re: [R-pkg-devel] Possible false negative for compiled C++ code in CRAN checks

В Tue, 12 Nov 2024 17:37:40 + Mauricio Vargas Sepulveda пишет: > I re-sent my package and I still see: > > 1. > https://win-builder.r-project.org/incoming_pretest/redatam_2.0.3_20241112_165458/specialChecks/clang-san/outputs.txt I understand this doesn't feel like progress, but this time

Re: [R-pkg-devel] New package with C++ code causes R abort in RStudio, not in R console.

В Tue, 12 Nov 2024 14:06:53 + Luc De Wilde пишет: > The package with C++ code is in https://github.com/lucdw/lavaanC.  > > When testing with a bunch of models, there is one model that causes > an abort of the R session in RStudio (on Windows), but in the R > console or in a batch job it cau

Re: [R-pkg-devel] Possible false negative for compiled C++ code in CRAN checks

В Tue, 12 Nov 2024 04:02:17 + Mauricio Vargas Sepulveda пишет: > For v2.0.3 I implemented a full refactor, where I simplified the code > considerably while trying to solve what looks to be a false positive. > > Now I implemented a "patch" based on the suggestion: I see the change on GitHub

Re: [R-pkg-devel] Found the following HTML validation problems: in R CMD check --as-cran

В Tue, 12 Nov 2024 01:53:08 -0600 Spencer Graves пишет: > In running "R CMD check --as-cran Ecfun_0.3-5.tar.gz" on my > local macOS 15.0.1 system, 00check.log contains "Found the following > HTML validation problems:" followed by 501 lines like the following When you run `tidy --version`

Re: [R-pkg-devel] Possible false negative for compiled C++ code in CRAN checks

Dear Mauricio Vargas Sepulveda, Welcome to R-package-devel! В Sat, 9 Nov 2024 17:34:07 + Mauricio Vargas Sepulveda пишет: > CRAN reported memory leaks for: > > CLAN/ASAN: > https://www.stats.ox.ac.uk/pub/bdr/memtests/clang-ASAN/redatam/00check.log > CLANG/UBSAN: > https://www.stats.ox.ac.u

Re: [R-pkg-devel] Alternative to ifeq for Makevars

В Fri, 8 Nov 2024 11:44:15 -0800 Josiah Parry пишет: > Do you know of any good documentation on the use of Makevars.in with > configure? A configure script for an R package could be any POSIX-compatible shell script, including a hand-written one that substitutes strings using sed [*], or even on

Re: [R-pkg-devel] Alternative to ifeq for Makevars

В Fri, 8 Nov 2024 11:21:16 -0800 Josiah Parry пишет: > I want to conditionally set the value of CRAN_FLAGS like so in my > Makevars files > > ifeq ($(NOT_CRAN), false) > CRAN_FLAGS = -j 2 --offline > else > CRAN_FLAGS = > endif Unless a better approach surfaces (detect the environment varia

Re: [R-pkg-devel] Warnings related to functions from the survival package

On Fri, 1 Nov 2024 09:56:01 +0100 Tomas Kalibera wrote: > isn't there a finer-grained way to suppress reports just > of this particular issue, ideally at finer granularity than a > function? The line saying "function:do_dotCode" in the suppression file will suppress errors just for mismatched f

Re: [R-pkg-devel] Warnings related to functions from the survival package

On Thu, 31 Oct 2024 17:59:01 +0100 Tomas Kalibera wrote: > for now, if you know an elegant, minimal way how to suppress > this, and have the time and energy, a patch would be welcome A fresh R-4.4.2 build compiled with clang-19 -fsanitize=function gives the error: $ bin/R -q -s -e 'library(surv

Re: [R-pkg-devel] HTML validation error in roxygen2 generated documentation

В Thu, 31 Oct 2024 18:04:47 +0100 Nikos Bosse пишет: >  Found the following HTML validation problems: >  ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning: > inserting implicit > ae_median_quantile.html:79:1 (ae_median_quantile.Rd:41): Warning: > trimming empty Thank you for pro

Re: [R-pkg-devel] Warnings related to functions from the survival package

В Thu, 31 Oct 2024 12:06:25 -0400 Kaifeng Lu пишет: > /home/hornik/src/R/src/main/dotcode.c:1978:2: runtime error: call to > function coxph_wtest through pointer to incorrect function type 'void > (*)(void *, void *, void *, void *, void *, void *)' > /home/hornik/src/R/src/main/dotcode.c:199

Re: [R-pkg-devel] clang-san issue with R vignettes using ggplot2

В Tue, 29 Oct 2024 22:21:16 -0400 Kaifeng Lu пишет: > ==1429888==ERROR: LeakSanitizer: detected memory leaks > > Direct leak of 7680 byte(s) in 12 object(s) allocated from: > #0 0x55b3e7ff95d0 in realloc > (/home/hornik/tmp/R-d-clang-xtra/bin/exec/R+0xc65d0) (BuildId: > 71b7cc9351bcc02

Re: [R-pkg-devel] *** caught segfault *** address (nil), cause 'unknown'

В Sat, 26 Oct 2024 12:18:07 -0400 jérémy Gelb пишет: > *** caught segfault *** > address (nil), cause 'unknown' > > It seems that the error is happening when loading a c++ module of my > package > > Traceback: > 1: Module(module, mustStart = TRUE, where = env) > 2: doTryCatch(return(expr), n

Re: [R-pkg-devel] Installation error when submitting package to CRAN

On Thu, 17 Oct 2024 10:33:33 +0200 Uwe Ligges wrote: > I looked, and farver is not declared in your DESCRIPTION file as any > dependency. Is it used by another package you depend on? It's a transitive dependency via hhmR's Imports: patchwork, which in turn Imports: farver. > Please only ship t

Re: [R-pkg-devel] Installation took CPU time elapsed time for rust-based package

В Wed, 16 Oct 2024 17:38:27 + D Z пишет: > if [ -n "$_R_CHECK_LIMIT_CORES" ]; then \ >   export BUILDFLAGS="-j 2 --offline"; \ This environment variable is spelled with an extra underscore: https://cran.r-project.org/doc/manuals/r-devel/R-ints.html#index-_005fR_005fCHECK_005fLIMIT_005fCORES_

Re: [R-pkg-devel] Help with 2 NOTES

В Thu, 10 Oct 2024 13:10:39 + Jaime Salvador пишет: > * The \dontrun in examples. To run the examples, we need a > database, the package doesn't include a sample database, so the code > can't be run. I remove \dontrun in functions that can run without a > database (for example redatam_ver

Re: [R-pkg-devel] Help with 2 NOTES

Dear Jaime Salvador, Welcome to R-package-devel! В Wed, 9 Oct 2024 20:42:24 + Jaime Salvador пишет: > New submission This one is expected for new packages. > Possibly misspelled words in DESCRIPTION: > DICX (12:67) > RXDB (12:59) > Redatam (2:34, 12:40) Wrap the abbreviations and s

Re: [R-pkg-devel] Deprecating apparent S3 method, changing name

В Tue, 1 Oct 2024 09:00:24 +0200 Jan van der Laan пишет: > S3method(esa, plot, esaplotmethod) > > To register `esaplotmethod` as the method that is called when using > `esa` with an object of type `plot`. This would prevent this issue. > However, this probably (can't test as the note doesn't h

Re: [R-pkg-devel] Deprecating apparent S3 method, changing name

В Wed, 25 Sep 2024 05:13:31 + Murray Efford via R-package-devel пишет: > When I deprecate the old functions (by exporting a shell function > that calls .Deprecated and the new function), I get a package check > note for e.g. esa.plot "* checking S3 generic/method consistency ... > NOTE Appare

Re: [R-pkg-devel] help with CRAN failures (broom.mixed, rstan-related)

В Wed, 25 Sep 2024 16:57:55 -0400 Ben Bolker пишет: > Next question, is this (in your opinion) worth escalating to > r-devel ? I think so, yes. Hopefully there will be a way to temporarily re-enable the S4 dispatch for primitive operators in methods:::.requirePackage (that lives in R/RClassUtil

Re: [R-pkg-devel] help with CRAN failures (broom.mixed, rstan-related)

В Wed, 25 Sep 2024 12:28:25 -0400 Ben Bolker пишет: >What is your current estimate of the probability that this is > something that I've done wrong vs. exposing something wonky elsewhere > (i.e. at the level of testthat, brms, rstan, Rcpp, R-devel, ...) ? I didn't have a good answer (the m

Re: [R-pkg-devel] help with CRAN failures (broom.mixed, rstan-related)

Hmm, so it's *not* a machine-specific problem after all [1,2] and can now be reproduced on a regular R-devel build on Debian Sid. I'm sorry for jumping to conclusions. Why would Rcpp::loadModule() (called from rstan's .onLoad) end up trying to apply a non-function, but only when being called from

Re: [R-pkg-devel] help with CRAN failures (broom.mixed, rstan-related)

В Tue, 24 Sep 2024 10:27:34 -0400 Ben Bolker пишет: >Weirdly, I can't get this to fail on my local system even if I > remove rstan -- maybe rstan needs to be present for brms at install > time but not at runtime ... ??? I'm noticing that despite broom.mixed having Suggests: rstan and it bein

Re: [R-pkg-devel] Rolling Back an Archived Package

В Mon, 23 Sep 2024 16:15:28 + Eric Giunta пишет: > Recently I submitted a large update to the package I maintain and was > unable to resolve the testing errors prior to it being archived. I've > been unable to reproduce the errors, so I expect to have to setup my > own fedora_clang virtual ma

Re: [R-pkg-devel] flang-new-18 complains: incompatiple object shapes

В Fri, 20 Sep 2024 13:44:44 +0200 Göran Broström пишет: > It is of course easy (but tedious) to cut the Gordian knot by > explicitly writing out the loops that defines 'daxpy', but is it > necessary? Definitely not. I think that flang will be satisfied if you provide an explicit interface for DA

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

В Fri, 13 Sep 2024 15:00:06 +0200 Iago Bonnici пишет: >     - Is the 100-bytes paths limitation only supposed to ensure > compatilbility with pre-POSIX.1-1998 `tar` files? There are also the Windows systems. While support for paths longer than 260 characters appeared in Windows 10 build 1607 a

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

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, "bin", "python") Please don't require placing the v

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

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/10202337528/job/28226219457"; > where several containers failed at the setup-deps st

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

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 that Kevin would

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