Re: [R-pkg-devel] Debugging M1mac problems [solved]

On Sat, 27 Mar 2021 17:26:16 +0300 Ivan Krylov wrote: > I'm probably doing something stupid with the file names that usually > works but isn't guaranteed to work in all cases, but I cannot figure > it out. Long story short, the problem turned out to be that I called basename

Re: [R-pkg-devel] can't reproduce 'Additional issues' on CRAN with valgrind

On Mon, 2 Aug 2021 17:11:14 + Georgi Boshnakov wrote: > What am I missing? Do I need to have a separate library for the > instrumented R-devel version? It doesn't look to me like you're missing anything, unless you start seeing the errors when you start `R -d valgrind` and then run the tests

Re: [R-pkg-devel] Ongoing CXX17 woes

On Fri, 6 Aug 2021 15:51:37 -0500 Tim Keitt wrote: > CXX17=`${R_HOME}/bin/R CMD config --all | awk '{print $1}' | grep \ > "^CXX17$"` This seems to output "CXX17" on a machine with no C++17 support. On the other hand, running `${R_HOME}/bin/R CMD config CXX17` here gives me an empty string. --

Re: [R-pkg-devel] UX for "WARNING unable to translate to native encoding"?

On Mon, 16 Aug 2021 09:05:54 + David Norris wrote: > Unicode U+00d7 (times), U+00b1 (plus-minus) and U+03bc (mu) have > equivalents in Latin-1 encoding, and I have used these without > difficulty in strings, neither U+2206 (INCREMENT) nor U+0394 (Greek > Delta) does But not in some other loc

Re: [R-pkg-devel] http error handling in packages

On Wed, 8 Sep 2021 12:02:51 +1200 obrl soil wrote: > I just want to clarify whether the problem is an overly brief error > message, or my use of stop() in this context? I think it's neither: it's perfectly fine to use the R error system to signal being unable to establish function postcondition

Re: [R-pkg-devel] Internet resources and Errors

On Fri, 24 Sep 2021 07:49:44 -0700 Roy Mendelssohn - NOAA Federal via R-package-devel wrote: > All internet calls are wrapped in 'try()'. If that shows an error, > I write a message to the screen about the error, and call stop(), > perhaps with a further message in that call. Somehow this do

Re: [R-pkg-devel] Tests run without --as-cran and not with

On Fri, 24 Sep 2021 21:48:12 +0200 Jan van der Laan wrote: > my tests run fine when run with R CMD check, but not with R CMD check > --as-cran <...> > pandoc then calls R again with a script which is part of the package Part of R CMD check --as-cran is placing fake R and Rscript executables on

Re: [R-pkg-devel] multithreading in packages

В Thu, 7 Oct 2021 21:58:08 -0400 (EDT) Vladimir Dergachev пишет: >* My understanding from reading documentation and source code is > that there is no dedicated support in R yet, but there are packages > that use multithreading. Are there any plans for multithreading > support in future R vers

Re: [R-pkg-devel] Checking package in Windows fails

On Mon, 15 Nov 2021 17:15:14 +0100 Ben Engbers wrote: > I don't know why I have to explicitly include 'library("rex")' in > the code since I have added rex to the Imports in the DESCRIPTION Have you added the corresponding importFrom(...) [1] commands to your NAMESPACE file? > pi <- pingr::is_o

Re: [R-pkg-devel] Checking package in Windows fails

On Wed, 17 Nov 2021 00:20:44 +0100 Ben Engbers wrote: > I don't edit the NAMESPACE file by hand. It is created by roxygen2. Right. In that case, use an @importFrom tag: https://roxygen2.r-lib.org/articles/namespace.html#imports -- Best regards, Ivan ___

Re: [R-pkg-devel] CRAN submission error when running tests in testthat

On Wed, 24 Nov 2021 16:37:44 + (UTC) Nathan Green via R-package-devel wrote: > An irrecoverable exception occurred. R is aborting now ... It seems that some of your dependencies which use compiled code manage to crash the R process on CRAN Mac machines. Since testthat normally hides most out

Re: [R-pkg-devel] CRAN submission error when running tests in testthat

On Thu, 25 Nov 2021 12:33:01 +0100 Gábor Csárdi wrote: > Are you sure about this? I don't think testthat hides any output. R > CMD check on the other hand AFAICT only shows the last 13 lines by > default. See the _R_CHECK_TESTS_NLINES_ environment variable in > https://cran.r-project.org/doc/manu

Re: [R-pkg-devel] Cannot find source of devtool::check() warnings in R code

On Thu, 9 Dec 2021 11:10:36 -0500 Steve Gutreuter wrote: > Warning: replacing previous import ‘pROC::cov’ by ‘stats::cov’ > when loading ‘screenr’ > Warning: replacing previous import ‘pROC::var’ by ‘stats::var’ > when loading ‘screenr’ > Warning: replacing previous import ‘pR

Re: [R-pkg-devel] Different behavior from devtools::check and install.packages() under Linux and Windows

On Tue, 14 Dec 2021 08:48:23 -0500 Steve Gutreuter wrote: > Error in set_makevars(.new, .path, makevars_file, assignment = > .assignment) : >   Multiple results for CXX11FLAGS found, something is wrong.FALSE set_makevars is a function from the "withr" package: https://github.com/r-lib/withr/bl

Re: [R-pkg-devel] Possible bug report/false positive

On Wed, 5 Jan 2022 17:15:20 -0300 Igor L wrote: > Found the platform-specific device: >'X11' > how to solve it? One of the tricks that work (in the sense that calls to functions using non-standard evaluation don't result in warnings about "Undefined global functions or variables") is to d

Re: [R-pkg-devel] should I increase the version number when resubmitting a package that failed incoming tests?

On Thu, 17 Feb 2022 20:53:50 + Daniel Kelley wrote: > My question is: should I retain the same version number, or should I > bump the number? CRAN policy currently says: "Increasing the version number at each submission reduces confusion so is preferred even when a previous submission was n

Re: [R-pkg-devel] table lacks "summary" attribute

On Sat, 5 Mar 2022 16:54:08 -0800 alexios galanos wrote: > * checking HTML version of manual ... NOTE > Found the following problems: > DCCfilter-class.Rd:7:1: Warning: lacks "summary" attribute > > Any pointers/documentation on this? This seems to be the new check for HTML documentation valid

Re: [R-pkg-devel] What is best practice for handling false negatives on CRAN submission tests?

On Sat, 19 Mar 2022 12:14:30 + Daniel Kelley wrote: > Would I be sensible to wait a couple of weeks for a reply? I agree with Duncan, I'd wait for days, not weeks. > I ask because the schedule would have oce being auto-removed from > CRAN early next month, and I worry a bit about that happe

Re: [R-pkg-devel] handling of byte-order-mark on r-devel-linux-x86_64-debian-clang machine

On Tue, 5 Apr 2022 20:20:37 +0200 Tomas Kalibera wrote: > I've rewritten the paragraphs, biasing towards users who have UTF-8 > as the native encoding as this is going to be the majority. Thank you! > But the level of detail I think needs to remain as long as these > features are supported - th

Re: [R-pkg-devel] Two problems with fda

On Mon, 25 Apr 2022 15:06:28 -0500 Spencer Graves wrote: > GitHub action reports, <<'"pdflatex"' not found>> with > vignettes. No personal experience with GitHub Actions, but have you tried following the advice by Gábor Csárdi from a few days ago? https://stat.ethz.ch/pipermail/r-package-devel

Re: [R-pkg-devel] Issue with HTML version of manual

В Thu, 28 Apr 2022 03:59:01 -0700 Arkajyoti Saha пишет: > Please let me know if this attachment works, It worked for me, but didn't work for anyone else: R-package-devel strips out most kinds of attachments. Is this the same file? https://github.com/ArkajyotiSaha/RandomForestsGLS/blob/main/man/R

Re: [R-pkg-devel] moving from C to C++ with Rcpp in R package

В Thu, 2 Jun 2022 15:06:44 +0200 THIOULOUSE JEAN пишет: > "object '_ade4_RVrandtestCpp' not found"). > static const R_CallMethodDef CallEntries[] = { > {"_ade4_RVrandtestCpp", (DL_FUNC) &_ade4_RVrandtestCpp, 3}, > {NULL, NULL, 0} > }; Almost there. Since you're using the fixes = 'C_' ar

Re: [R-pkg-devel] Warning: attribute "width" not allowed for HTML5

On Tue, 14 Jun 2022 12:56:27 -0500 Spencer Graves wrote: > Warning: escaping malformed URI reference This part is actually important. If you look at the generated HTML for nuclearWeaponStates.Rd, you can see that Tidy complains about the following link: https://www.americansecurityproject.org/

Re: [R-pkg-devel] URL checks

On Thu, 30 Jun 2022 10:00:53 +1000 Greg Hunt wrote: > With a little more experimenting, the 503 response from the wiley DOI > lookup does seem to come from CloudFlare, there is a "server: > cloudflare" header. Unfortunately, CloudFlare also returns the 503 status code with the "server: cloudflar

Re: [R-pkg-devel] URL checks

Greg, I realise you are trying to solve the problem and I thank you for trying to make the URL checks better for everyone. I probably sound defeatist in my e-mails; sorry about that. On Thu, 30 Jun 2022 17:49:49 +1000 Greg Hunt wrote: > Do you have evidence that even without the use of HEAD tha

Re: [R-pkg-devel] Warning... unable to translate 'Ekstrm' to a wide string; Error... input string 1 is invalid

On Tue, 19 Jul 2022 12:32:20 -0500 Spencer Graves wrote: > Can someone provide me with a link to the correct development > version of help('iconv')? The current version includes the exact > offending "\x" strings that I have. http://svn.r-project.org/R/trunk/src/library/base/man/iconv.Rd I

Re: [R-pkg-devel] Misspelled words in descrition and tar.gz inside folder

On Tue, 9 Aug 2022 13:38:33 -0700 Edward Wei wrote: > 1. My misspelled words are just referencing names of packages and > programming terms etc. Is there a way to get around this or should I > omit them from my description and put them somewhere else. If you can, mention them in the comments to

Re: [R-pkg-devel] No package called 'scales' (r-oldrel-windows)

В Tue, 23 Aug 2022 12:39:33 -0500 Paul Hibbing пишет: > It has errored for r-oldrel-windows with "there is no package called > 'scales'" (see > https://www.r-project.org/nosvn/R.check/r-oldrel-windows-ix86+x86_64/PAutilities-00install.html). I think it's a hiccup on the testing machine. There do

Re: [R-pkg-devel] Error checking in an independent C code and printing (perror, printf, etc.)

Hello Jiří and welcome to the mailing list! On Tue, 6 Sep 2022 14:48:02 +1200 "Jiří Moravec" wrote: > That brings me to a problem: How to do error handling in C without > the use of various <...> R-specific print functions? (Assuming that's what you meant...) One way would be to introduce call

Re: [R-pkg-devel] Examples taking too long depend on object that takes a while to generate

On Wed, 14 Sep 2022 12:31:49 -0400 Duncan Murdoch wrote: > It's also possible to put .R files in the data directory, and they > are executed to create the data object. I think that happens at the > time when you call data() rather than at install time, so it might > not be helpful. Some time ag

Re: [R-pkg-devel] debian - how to replicate the error

On Tue, 20 Sep 2022 03:28:09 + "Zhang, Xueqiong" wrote: > I don’t have a linux box, and was not able to check it via > r-hub-linux-platforms since some of bioc dependencies are not > installed on r-hub. What should I do for the error check, any ideas? There are Debian builds for both x86_64

Re: [R-pkg-devel] Help - Shiny app on CRAN

В Mon, 26 Sep 2022 19:14:04 +0400 "Jahajeeah, Havisha" пишет: > * checking extension type ... ERROR > Extensions with Type 'Shiny application' cannot be checked. Since you're writing a package, you can either specify Type: Package in the DESCRIPTION file, or omit the field entirely: https://cran

Re: [R-pkg-devel] Unable to create manual

On Mon, 26 Sep 2022 10:50:01 -0700 Edward Wei wrote: > 1. Where do I run "make check"? In the directory where R is built from source. If you're using a binary build of R, this isn't applicable. > 3. I get this back when I run the "tools::testInstalledPackages(scope > = "base")" on my RGUI. > >

Re: [R-pkg-devel] Help - Shiny app on CRAN

It might be easier to help you if you show us your package by publishing the source code somewhere. On Mon, 26 Sep 2022 22:22:48 +0400 "Jahajeeah, Havisha" wrote: > CIvalue2: no visible global function definition for 'qt' > andgm11: no visible binding for global variable 'ParticleSwarm' > andgm1

Re: [R-pkg-devel] How to decrease time to import files in xlsx format?

On Tue, 4 Oct 2022 15:29:54 -0300 Igor L wrote: > The problem is that importing files in xlsx format is time consuming. Do the openxlsx or XLConnect packages fare any better? > plan(strategy = future::multicore(workers = 4)) As far as I understand the documentation, multicore only works on POS

Re: [R-pkg-devel] Identify Original Column Names of Model Matrix

On Mon, 10 Oct 2022 08:00:04 + Dario Strbenac wrote: > It requires input data to be in one-hot encoding, which is created by > Matrix::sparse.model.matrix. For further analysis, such as variable > importance, is there a way to identify which original feature each > column of a sparse.model.ma

Re: [R-pkg-devel] Problems with news in ‘NEWS’

В Wed, 12 Oct 2022 20:16:20 -0500 Spencer Graves пишет: > I copied NEWS to NEWS.md and tried to format it as described in: > > > https://r-pkgs.org/other-markdown.html#news > > > Sadly, I still get the same error. It seems to be ignoring > my NEWS.md file and continuing to tell me I

Re: [R-pkg-devel] Invalid UTF-8

В Mon, 17 Oct 2022 11:07:25 +0200 Göran Broström пишет: > warning: invalid UTF-8 in comment [-Winvalid-utf8] > (It's my name) > > So I wonder: How do I make valid UTF-8 in comment? The file GB_zeroin.c is saved in Latin-1 encoding. The warning should go away once you convert it to UTF-8. -- B

Re: [R-pkg-devel] R package build- C compilation issue related to math.h

On Wed, 19 Oct 2022 23:39:57 +0100 Vincent Plagnol wrote: > gcc-12 -I"/home/hornik/tmp/R/include" -DNDEBUG -I/usr/local/include > -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=2 -fpic -g -O2 -Wall > -Wstrict-prototypes -pedantic -mtune=native -c VP_gamma.c -o > VP_gamma.o > /usr/include/x86

Re: [R-pkg-devel] How ton print in the console from Rcpp

В Thu, 20 Oct 2022 12:43:30 +0200 Elysée Aristide пишет: > What I understood is that it is better to use Rcpp functions. So I > used: > > Rcpp::Rcout << "beta: \n"; > Rcpp::print(betacpp); > Rcpp::Rcout << "log-likelihood: " << llh << "\n"; This seems to be a right way of printing from Rcpp cod

Re: [R-pkg-devel] Latex issue on CRAN: Package pdftex.def Error

В Sun, 30 Oct 2022 14:48:05 +0100 r...@nbenn.ch пишет: > It seems like when building the PDF manual, an image that should be > included is not found and then things fall apart, causing both the > error and note. For all I know, the image should be there unter > `man/figures/`. Is it the following

Re: [R-pkg-devel] Best way to restore an archived CRAN package

В Sun, 30 Oct 2022 16:56:03 +0900 "Stefan Angrick" пишет: > Writing code to digest the new data format is straightforward, so I'd > like to bring the package back. Unfortunately I'm unable to reach the > original author, so I'm unsure how to proceed. > > Does CRAN allow for people other than the

Re: [R-pkg-devel] Examples with CPU time is greater than elapsed time.

On Sat, 5 Nov 2022 22:41:45 +0800 Jiaming Yuan wrote: >Examples with CPU time > 2.5 times elapsed time > I'm wondering what the note is trying to tell me and how can I > resolve it with confidence. Henrik Bengtsson already gave a good explanation of the problem. Not sure what exactly is th

Re: [R-pkg-devel] Error uploading file on CRAN

В Mon, 7 Nov 2022 12:30:35 +0400 "Jahajeeah, Havisha" пишет: > After loading the package on CRAN, when I try to upload file (xlsx or > xls) the following error appears: > > Error: cannot open the connection Do you mean uploading files into your Shiny application, or somewhere else? Have you tr

Re: [R-pkg-devel] Error uploading file on CRAN

В Mon, 7 Nov 2022 14:55:06 +0400 "Jahajeeah, Havisha" пишет: > The Greymodels package loads data from spreadsheets and each model > accepts a set of data and outputs the values. However, the package > is unable to do that because of the error: cannot open connection. Thank you for clarifying th

Re: [R-pkg-devel] vignettes - size of pdf

В Fri, 11 Nov 2022 12:54:52 + "Grose, Daniel" пишет: > * checking sizes of PDF files under 'inst/doc' ... WARNING > 'gs+qpdf' made some significant size reductions: > compacted 'cpop.pdf' from 805Kb to 547Kb > consider running tools::compactPDF(gs_quality = "ebook") on these > files

Re: [R-pkg-devel] How ton print in the console from Rcpp

В Sun, 13 Nov 2022 11:29:21 + Elysée Aristide пишет: > The only difference I saw is that all those packages put > > #define NDEBUG > > after #include . > I did the same thing without understanding :) Glad you got it working! If you're curious why it helped, see

Re: [R-pkg-devel] Too many processes spawned on Windows and Debian, although only 2 cores should be used

В Wed, 16 Nov 2022 07:29:25 +0100 Riko Kelter пишет: > if (nzchar(chk) && chk == "TRUE") { > # use 2 cores in CRAN/Travis/AppVeyor > num_workers <- 2L > } The check in parallel:::.check_ncores is a bit different: chk <- tolower(Sys.getenv("_R_CHECK_LIMIT_CORES_", "")) if (nzchar(chk) && (chk

Re: [R-pkg-devel] request to remove/archive package from CRAN

В Wed, 23 Nov 2022 13:50:01 + Kopperud пишет: > Is it possible to request for a package to be removed/archived from > CRAN? The policy implies it should be possible: >> Packages will not normally be removed from CRAN: however, they may >> be archived, including at the maintainer’s request.

Re: [R-pkg-devel] Note on submission Found the following files/directories: 'NUL'

В Fri, 25 Nov 2022 09:59:10 + "ROTOLO, Federico /FR" пишет: > When submitting my package parfm, I get the following note > Flavor: r-devel-linux-x86_64-debian-gcc > Check: for non-standard things in the check directory, Result: NOTE > Found the following files/directories: > 'NUL' > so

Re: [R-pkg-devel] Note on submission Found the following files/directories: 'NUL'

В Fri, 25 Nov 2022 13:10:39 +0300 Ivan Krylov пишет: > It also breaks the non-default sink, if any was set up by the user. That's not correct, I'm sorry. sink() maintains a stack of diversions and will automatically restore the user-chosen sink(), if any was set up, when you c

Re: [R-pkg-devel] Error uploading file on CRAN

On Sun, 27 Nov 2022 20:29:10 +0400 "Jahajeeah, Havisha" wrote: > The Greymodels package has been debugged and the updated package has > been published on Github. Congratulations on getting it working! > I would be very much grateful if the app could be updated on CRAN. Please do it the same w

Re: [R-pkg-devel] Missing link or links in documentation object

В Mon, 28 Nov 2022 15:34:53 +0100 Ibon Tamayo пишет: > \code{\link[R6::R6Class]{R6::R6Class}} I think you need only one colon in the first argument of \link[pkg:foo]{bar}: https://cran.r-project.org/doc/manuals/R-exts.html#Cross_002dreferences -- Best regards, Ivan ___

Re: [R-pkg-devel] Logical Inconsistency of check regarding URL?

Dear Michael, On Tue, 29 Nov 2022 08:19:40 +0100 "Dr. habil. Michael Thrun" wrote: > URL: https://www.deepbionics.org (moved to > https://mthrun.github.io/index) > From: DESCRIPTION > Status: 301 > Message: Moved Permanently > Please change http --> https, add trailing slashes, or follow moved

Re: [R-pkg-devel] Error uploading file on CRAN

В Wed, 30 Nov 2022 13:43:21 +0400 "Jahajeeah, Havisha" пишет: > but now I am getting the following error: > > An error has occurred! > > Couldn't normalize path in `addResourcePath`, with arguments: > `prefix` = 'AdminLTE-2.0.6'; `directoryPath` = > 'D:/RCompile/CRANpkg/lib/4.2/shinydashboard/A

Re: [R-pkg-devel] Error uploading file on CRAN

В Wed, 30 Nov 2022 14:17:54 +0400 "Jahajeeah, Havisha" пишет: > To run the app, we use: > > install.packages("Greymodels") > library(Greymodels) > run_app() > > The app worked fine on Monday. Today it is showing error. > > Please see below traceback() > > 13: execCallbacks(timeoutSecs, all,

Re: [R-pkg-devel] Error uploading file on CRAN

В Wed, 30 Nov 2022 16:10:22 +0400 "Jahajeeah, Havisha" пишет: > How do I fix this problem? Kindly advise. I think I know what could be the problem. Your run_app function calls shiny::shinyApp(ui, server, options = list(launch.browser = TRUE)). Here, `ui` is an object of class "shiny.tag". I thi

Re: [R-pkg-devel] Error uploading file on CRAN

On Mon, 5 Dec 2022 11:14:19 +0400 "Jahajeeah, Havisha" wrote: > Will a binary package resolve the above issue? Due to an interaction between the way R binary packages work and the way you have implemented the Greymodels:::ui variable, this binary package will only work on your computer. (And, we

Re: [R-pkg-devel] Package fails on Debian

On Fri, 9 Dec 2022 17:29:21 + Stephen Coleman wrote: > ``outlierComponentFactory.h:37:15: error: ‘unique_ptr’ in namespace > ‘std’ does not name a template type``. Does it help to explicitly #include in outlierComponentFactory.h in order to provide the definition of the template class uniqu

Re: [R-pkg-devel] Do you run R on Fedora or Debian?

On Sat, 10 Dec 2022 14:00:22 -0800 Roy Mendelssohn - NOAA Federal via R-package-devel wrote: > cache_setup(temp_dir = TRUE) Unfortunately, it prints a path under tempdir() for me on my Debian oldstable machine. I see that the error came from the "donttest" check from an extra test that's not on

Re: [R-pkg-devel] Do you run R on Fedora or Debian?

On Sat, 10 Dec 2022 14:00:22 -0800 Roy Mendelssohn - NOAA Federal via R-package-devel wrote: > CRAN has sent me a notice about the following: > > https://www.stats.ox.ac.uk/pub/bdr/donttest/rerddapXtracto.out > > I can not reproduce it. I test on my Mac, the cache space is > properly handled

Re: [R-pkg-devel] Question on Description/Citing Feedback

On Fri, 16 Dec 2022 10:06:44 -0800 Michael Topper wrote: >- I understand the Description portion of the DESCRIPTION file > needs to be edited, but I'm a little confused as to what I am > supposed to add and how. Do I need to include a citation to the > published paper of modelsummary Yes, ex

Re: [R-pkg-devel] How do I enable to show data in inst/extdata in data() || lazy load

On Mon, 19 Dec 2022 20:59:27 +0530 Sanjeev Sariya wrote: > ... I have created a .Rd file. > I'm interested in listing this file in data() ... My understanding is that data() is for R-level objects, and so is help(), most likely. One way to solve this could be to write a script that imports the

Re: [R-pkg-devel] How do I enable to show data in inst/extdata in data() || lazy load

В Tue, 20 Dec 2022 05:28:49 +0530 Sanjeev Sariya пишет: > I need to provide an external data/file in the R package. This has > come as a request from F1000 journal editors. Would the journal editors agree to have this data in the form of an R object? Is it a strict requirement to have this file

Re: [R-pkg-devel] Help with fixing problems for new R package

В Tue, 20 Dec 2022 10:45:38 +1300 Anna Carolina Resende пишет: > * checking CRAN incoming feasibility ... [5s/25s] NOTE > Maintainer: ‘Anna Carolina Resende ’ > > I read online that it's a note for CRAN so they can check that the > maintainer made changes, could you confirm that that is the case

Re: [R-pkg-devel] Suppress R pop up message when using package OpenCL

(Sorry about the previous message.) В Thu, 22 Dec 2022 10:10:42 +0100 Quirin Stier пишет: > Any ideas how to get rid of the message popping up? You seem to be right that it's a package development question. Currently, as long as there's a non-empty build log, OpenCL will show it using R_ShowMes

Re: [R-pkg-devel] Current recommendations re. GitHub Action?

On Mon, 2 Jan 2023 19:18:33 -0600 Spencer Graves wrote: > However, Ubuntu failed with devel and oldrel1, complaining, > "there is no package called ‘rcmdcheck’". If we start from the error message and work backwards, it's easy to see that `rcmdcheck` fails to install because it depends o

Re: [R-pkg-devel] S3 generic/method consistency false positive when dplyr imported

On Wed, 4 Jan 2023 15:54:52 -0500 "Aaron A. King" wrote: > Why does inclusion of *dplyr* in the import list appear to trigger > these warnings when they were not there before? I think that's because dplyr itself contains an S3 generic named "filter", and having a package namespace loaded (not ev

Re: [R-pkg-devel] S3 generic/method consistency false positive when dplyr imported

On Thu, 5 Jan 2023 17:58:47 -0500 "Aaron A. King" wrote: > However, since the S3 dispatch system is not itself confused, I > suppose it must be the case that the S3 generic/method consistency > checker itself is confused. I wonder, how does the checker decide > when to throw a NOTE? Is it a sim

Re: [R-pkg-devel] S3 generic/method consistency false positive when dplyr imported

(Sorry for the unfinished message. I've got to do something about my mailer to make it harder to send them accidentally.) On Fri, 6 Jan 2023 11:21:49 +0300 Ivan Krylov wrote: > to see where 'filter' appears in the list of generics and where the filter.traj function gets

Re: [R-pkg-devel] Problem with NEWS file

On Sat, 7 Jan 2023 15:02:18 +0700 Thierry Denoeux wrote: > The NEWS file is a text file created by TextEdit on Mac with UTF-8 > encoding, so I don’t see how there could be hidden special characters > in it. The problem is that the NEWS files are supposed to have a certain format (documented in h

Re: [R-pkg-devel] Mysterious "invalid z limit"

On Sat, 7 Jan 2023 20:43:10 -0500 "Kevin R. Coombes" wrote: > (1) How is it possible that the same code works error > free in the RStudio contexts, but fails in the attempt to build the > package? When knitting the vignette from RStudio, it uses the package you already have installed. When knit

Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN

В Fri, 13 Jan 2023 08:54:50 + Chris Brien пишет: > I am getting the following response when I try to upload > growthPheno_2.1.17.tar.gz: > > Detected package information [non-editable] > In case of errors reupload the package or contact cran team That's not an error. This message is to info

Re: [R-pkg-devel] Failed CRAN tar.gz upload to CRAN

On Fri, 13 Jan 2023 21:51:01 + Chris Brien wrote: > the package files is being dropped as well. It replaces my file name > with "No file chosen". Consequently I cannot continue submit the > package. I understand that this behaviour is counter-intuitive, but that seems to be the way it's sup

Re: [R-pkg-devel] corrupted NAMESPACE file

В Fri, 20 Jan 2023 08:41:25 -0600 Spencer Graves пишет: > ** byte-compile and prepare package for lazy loading > Error in parse(nsFile, keep.source = FALSE, srcfile = NULL) : >1:1: unexpected input tools::showNonASCIIfile('https://raw.githubusercontent.com/JamesRamsay5/fda/master/NAMESPACE')

Re: [R-pkg-devel] Pretest failed and I fail to find out what's the problem

On Sun, 22 Jan 2023 19:51:30 +0100 Klaus Schliep wrote: > package phangorn_2.11.0.tar.gz does not pass the incoming checks > automatically, please see the following pre-tests: Is this the whole e-mail? There may be a list of problems at the end of the message, right after the signature ("Best re

Re: [R-pkg-devel] strange errors (non-ascii symbols) on win-builder R-devel

On Tue, 24 Jan 2023 17:33:10 + Maxim Nazarov wrote: > this seems to come from the C code I'm 99% sure this comes from the following changes to the package: --- minpack.lm_1.2-2/src/fcn_message.c 2020-03-23 10:54:03.0 +0300 +++ minpack.lm_1.2-3/src/fcn_message.c 2023-01-17 09:30:05

Re: [R-pkg-devel] reproducing cran warnings

On Fri, 3 Feb 2023 16:28:23 + Brad Eck wrote: > For example R-devel-debian-gcc is ok on rhub > https://builder.r-hub.io/status/epanet2toolkit_0.6.1.tar.gz-58c1ce1e316317307679f58450a5e17a > > But not on CRAN: > https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/epanet2to

Re: [R-pkg-devel] How to update "SystemRequirements: C++11"?

В Mon, 6 Feb 2023 14:46:16 -0600 Winston Chang пишет: > 1. Remove "SystemRequirements: C++11" entirely. The problem with this > is that on systems with older versions of R (3.6 and below, I > believe), it may try to compile the package with an older C++ > standard, which will fail. > 2. Update it

Re: [R-pkg-devel] Problem with package containing spatial data

В Wed, 8 Feb 2023 11:32:36 -0300 Igor L пишет: > spatial_aisp <- sf::st_read('data-raw/shp_aisp/lm_aisp_2019.shp') > > plot(spatial_aisp) # works > > # Same data from .rda file after use usethis::use_data(spatial_aisp, > overwrite = TRUE) > > x <- ispdata::spatial_aisp > > plot(x) # do not wo

Re: [R-pkg-devel] Unable to load Windows NETIO.SYS and WINSPOOL.DRV DLLs

On Sat, 11 Feb 2023 11:19:42 + David Sterratt wrote: > WinDbg output reveals errors loading "NETIO.SYS" and "WINSPOOL.DRV" > when running "library(RGtk2)": > >0c64:0640 @ 44312812 - LdrpProcessWork - ERROR: Unable to load DLL: > "NETIO.SYS", Parent Module: "C:\Users\David > Sterratt\AppD

Re: [R-pkg-devel] Sanitize Input Code for a Shiny App

On Sun, 26 Feb 2023 14:36:22 -0500 wrote: > What I'd like to be able to do is to sanitize the inputs to ensure > that it won't to things including installing packages, running system > commands, reading and writing to the filesystem, and accessing the > network. I'd like to allow the user to do

Re: [R-pkg-devel] CRAN submission - Specified C++11

В Mon, 27 Feb 2023 10:25:55 +0100 Riccardo Di Francesco пишет: > Specifying C++11 is necessary to make my package work. How can I solve > this? Is it C++11 exactly or C++ ≥ 11? If the former, you're 100% right to specify this (but may have problems in unspecified future when someone decides to s

Re: [R-pkg-devel] URL timeout in win-builder check: suggestions?

В Mon, 13 Mar 2023 10:28:13 -0400 Ben Bolker пишет: > Found the following (possibly) invalid URLs: >URL: https://phdcomics.com/comics/archive.php?comicid=905 > From: man/pvalues.Rd > Status: Error > Message: Operation timed out after 60010 milliseconds with 0 > bytes received

Re: [R-pkg-devel] Checking timings of packages

В Tue, 14 Mar 2023 13:52:13 + Chris Brien пишет: > The difficulty I am having is that I cannot be sure that the timings > for r-devel-linux-x86_64-debian-gcc and r-devel-windows-x86_64 will > be under 10 s, as seems to be required, if I were to resubmit the > package to CRAN with the reduced

Re: [R-pkg-devel] CRAN submission - Specified C++11

[I am taking the liberty of Cc-ing the list again because this kind of advice could be useful for other people too.] Dear Riccardo Di Francesco, В Wed, 15 Mar 2023 08:41:01 +0100 Riccardo Di Francesco пишет: >> Please ensure that your functions do not write by default or in >> yourexamples/vign

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Thu, 16 Mar 2023 11:09:16 + "Ruff, Sergej" пишет: > The Check-Function in R shows no Notes, Warnings or Errors, but I am > not sure if that means that limma will install when installing my > package from CRAN. > Currently I am declaring limma like this: > > Suggests: > > limma insta

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On Thu, 16 Mar 2023 17:01:55 + "Ruff, Sergej" wrote: > Last question: How does CRAN work with Bioconductor Dependencies? > Will CRAN accept limma as a dependency or will my submission be > rejected? It's not explicitly spelled out in the CRAN policy

Re: [R-pkg-devel] Should 'methods' be in Imports?

On Thu, 16 Mar 2023 11:29:33 -0400 Noah Greifer wrote: > Is including these packages filling the DESCRIPTION with unnecessary > dependencies that are automatically satisfied, or is it being > helpfully explicit about the packages your package relies on? Here's a comment from the part of R CMD ch

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Fri, 17 Mar 2023 10:19:37 + "Ruff, Sergej" пишет: > Thats the source of my worries. Will the same error appear when CRAN > checks the examples of my package? Or should I not be worried? Yes, part of CRAN checks is running your package without the packages listed under Suggests: https://www

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Fri, 17 Mar 2023 11:02:18 + "Ruff, Sergej" пишет: > I would like to ask, if I need to add something to the > DESCRIPTION-file when declaring Bioconductor dependencies for CRAn > Submission. Strictly speaking, no. Once you list limma under Suggests, it's possible and proper to install your

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Fri, 17 Mar 2023 12:29:51 + "Ruff, Sergej" пишет: > The problem is that a local installation of my package (via USB-stick > for example) can´t install the dependencies from CRAN. > > The package works perfectly fine, if the dependencies are > preinstalled. This is a similar, but different

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

В Mon, 20 Mar 2023 08:38:41 + "Ruff, Sergej" пишет: > When Limma is üre-installed, I get the following Note: > > > "Package suggested but not available for checking: 'limma'". > > > Seems like the functions isnt installing limma. > > Is there something I am missing? No, this is exactly

Re: [R-pkg-devel] How to declare Bioconductor Dependencies in the Description File of my R Package

On Mon, 20 Mar 2023 19:32:03 + "Ruff, Sergej" wrote: > but I thought Notes will also cause rejection when submitting a > package to CRAN. Won´t that be a problem? True, a NOTE during an automatic check may cause a rejection, but you won't get this NOTE there. Automatic CRAN pre-tests are don

Re: [R-pkg-devel] Check: Rd \usage sections, Result: The \usage entries for S3 methods should use the \method markup and not their full name.

On Tue, 21 Mar 2023 23:08:43 +0100 Yohann Foucher wrote: > Check: Rd \usage sections, Result: NOTE > S3 methods shown with full name in documentation object 'nnet.time': >'nnet.time' > > The \usage entries for S3 methods should use the \method markup and > not their full name. I have down

Re: [R-pkg-devel] How to identify what flags "Additional Issues" for UBSAN

В Wed, 22 Mar 2023 15:51:54 + "Kenny, Christopher" пишет: > Is there an easy way to identify what is causing the flag? Unfortunately, it's _all_ the sanitizer errors. > wilson.cpp:165:34: runtime error: signed integer overflow: > -2147483648 * -1 cannot be represented in type 'int' > Howev

Re: [R-pkg-devel] correcting errors in an existing package

On Fri, 31 Mar 2023 16:51:40 -0400 Dennis Boos wrote: > Also, I keep getting the message in the Rstudio check > > WARNING >'qpdf' is needed for checks on size reduction of PDFs > > > but I got the latest versions of R and Rstudio and was able to get > qpdf to install and loaded with librar

Re: [R-pkg-devel] What checks are required before uploading a package to CRAN?

On Tue, 4 Apr 2023 14:28:52 -0600 John Lawson wrote: > ERROR: Access to the path > 'C:\Inetpub\ftproot\R-devel\daewr_1.2-9.tar.gz' is denied. (perhaps > you uploaded already and the file has not been processed yet?) > > It has been 4 days since I uploaded the file to R-release, and I get > autom

Re: [R-pkg-devel] package not passing automatic checks: no clue as to what is causing 2 notes

В Wed, 12 Apr 2023 10:05:32 +0200 Gianmarco Alberti пишет: > 'CreateProcess' failed to run > 'd:\rtools43\x86_64-w64-mingw32.static.posix\bin\tidy.exe -language > en -qe --drop-empty-elements no D:\temp\Rtmp29JsRe\file2426857b24734' This is a (transient?) problem on the machine running the check

Re: [R-pkg-devel] katex

On Mon, 24 Apr 2023 18:17:22 +0200 Göran Broström wrote: >cannot open file '/usr/lib/R/doc/html/katex/katex.js': No such > file or directory > I still get the error with R CMD check --as-cran. What am I > missing? Obviously /usr/lib/R/doc/html/katex/katex.js (no 'doc'), but > ... > > I am i

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