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

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

В Thu, 15 Aug 2024 18:58:41 + anj5x...@nilly.addy.io пишет: > This seems like it should work. Unfortunately my rhub github actions > is failing to get past the setup deps step which has been occuring > inconsistently in the past but right now it's consistently failing to > build deps so I can'

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

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 removal of the fi

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

В Fri, 2 Aug 2024 11:10:59 + Rolf Turner пишет: > The advice was to the effect that if the vignette was actually just a > *.tex file, one could (after putting in some preparatory code, in the > form of comments, before the documentclass command) pre-process the > file (with pdflatex) and the

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

В Thu, 1 Aug 2024 10:53:56 -0400 Ben Bolker пишет: >! Undefined control sequence. >l.176 \hlkwd{library}\hldef > {(}\hlsng{"glmmTMB"}\hldef{)} Very strange. This may be related to https://github.com/yihui/knitr/issues/2345 (no diagnosis) and possibly https:

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

On Sun, 28 Jul 2024 15:27:33 -0500 Dirk Eddelbuettel wrote: > If we cannot (or do not want to) modify the given main.R, I would > suggest something along the lines of > > Rscript -e 'pdf(myfilenamevar); source("main.R"); dev.off()' | tee > 2024-07-28.log Perhaps even options(device = \(file =

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Correction: Kurt Hornik says that the installation most likely times out due to the hardware running the checks being more than a decade old. The problems should disappear once the new hardware, already received, is up and running. (Something prevents him from replying directly to the list.) __

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