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

2022-10-30 Thread r
devel, r-hub and Github (there are some other issues on Gh and r-hub, but I don’t believe them to be relevant here). All I have to go on is: - A WARNING in “checking PDF version of manual”: LaTeX errors found: ! Package pdftex.def Error: File `...' not found: using draft setting. - An ERR

[R-pkg-devel] Using ggplot2 within another package

2021-04-22 Thread Kevin R. Coombes
Hi, I'm trying to help clean up an R package for someone else to submit to CRAN. He has used ggplot2 to implement a plotting function for the kinds of things that his packages generates. His plotting routine basically looks like (after changing names to protect the innocent): m

Re: [R-pkg-devel] Using ggplot2 within another package

2021-04-22 Thread Kevin R. Coombes
Thanks. Obviously, long. long ago, (in a galaxy not far enough away), Paul's suggestion of using "aes_string" was the correct one, since "aes" uses non-standard evaluation. (And to quote somebody from an R fortune cookie, "The problem with non-standard evaluati

[R-pkg-devel] Spelling and manual CRAN inspection

2021-07-16 Thread Kevin R. Coombes
Hi,  I have been updating a couple of R packages this morning. One of them triggered a manual inspection for "possibly mis-spelled words in DESCRIPTION" for my last name (Coombes) --- even though none of the other 20 packages that I maintain has ever triggered that particular NOTE

Re: [R-pkg-devel] Spelling and manual CRAN inspection

2021-07-16 Thread Kevin R. Coombes
n) should be the package author and maintainer, not the CRAN maintainers. Part of the issue is that the mis-spellings are reported from R CMD check as a NOTE, not a WARNING nor an ERROR. They don't affect the code in any way (unlike the consequences of trying to import the "grpahics"

Re: [R-pkg-devel] Spelling and manual CRAN inspection

2021-07-16 Thread Kevin R. Coombes
that commonly get > flagged as misspelled words when I submit updates. I generally just > put an explanation for each one in the "optional comment" section of > the submission form. It's pretty simple and seems to work out well. > > On Fri, Jul 16, 2021 at 9:08 AM Kevi

[R-pkg-devel] function name conflict

2022-04-12 Thread Kevin R. Coombes
s, and they are explicitly listed in importFrom directives in the NAMESPACE file. Thank in advance,   Kevin ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Rd cross-references ... NOTE, Undeclared packages ... in Rd xrefs

2022-06-14 Thread hugo . gruson+R
ote: >>>>> Hello, All: >>>>> >>>>> >>>>>How do I fix "Rd cross-references ... NOTE >>>>> Undeclared packages ‘EnvStats’, ‘drc’, ‘zoo’, ‘prodlim’, ‘plyr’, >>>>> ‘TRAMPR’, ‘raster’ in Rd x

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

2022-11-29 Thread hugo . gruson+R
is topic because the question of "how the Web should function" tends to result in pointlessly heated debates. ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2023-01-07 Thread Kevin R. Coombes
Hi, I am in the middle of developing a new package, which contains a markdown-knitr-html vignette. When I try to run R CMD build [mypackagedirectory] I get an error message Quitting from lines 330-336 Error: processing vignette  failed with diagnostics: invalid z limits If I run the same

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

2023-01-08 Thread Kevin R. Coombes
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 knitting the vign

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

2023-01-08 Thread Kevin R. Coombes
A very helpful answer. For some reason (probably because I have an ancient perl script that automates the steps i take when building and checking packages), I keep forgetting that the "tools" package let's me do these things from within R. I had already isolated the offending

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

2023-01-09 Thread Kevin R. Coombes
Did you have to split the packages to get the CI/CD tools to work? Because,to me, it looks as though I can install multiple different R packages from the same git project, using something like library(devtools) install_gitlab("krcoombes/[PROJECT]", "pkg/[PACKAGE]") Best,

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

2023-04-01 Thread Kevin R. Coombes
with --run-donttest ... [42s/42s] ERROR Running examples in ‘Monte.Carlo.se-Ex.R’ failed The error most likely occurred in: pairwise.se(hold,xcol=10:12,summary.f=cv) Error: object 'hold' not found Execution halted **

Re: [R-pkg-devel] Suppressing long-running vignette code in CRAN submission

2023-10-16 Thread Kevin R Coombes
cks the package or the check time will be excessive. The vignette is written as a .Rmd file to be compiled by knitr, producing an HTML vignette. The top of the .Rmd file looks like this: --- snip --- --- title: "Cross-validation of regression models" author: "John

[R-pkg-devel] re-exporting plot method?

2024-04-30 Thread Kevin R. Coombes
remind the user to load the other package. But (in part because the plot function in Rgraphviz is actually an S4 method, which I don't need to alter in any way), I'm not sure exactly what needs to be imported or exported. Helpful suggestion would be greatly appreciated. Best,   Kevin

Re: [R-pkg-devel] re-exporting plot method?

2024-05-01 Thread Kevin R. Coombes
by calling the generic from Rgraphviz, but that sounds a little hacky even for my taste ;). Cheers, Simon On 1/05/2024, at 6:03 AM, Kevin R. Coombes wrote: Hi, I am working on a new package that primarily makes use of "igraph" representations of certain mathematical graphs, in o

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

2024-07-01 Thread Kevin R. Coombes
Hi, I have been maintaining packages in R-Forge for many tears. Last week I sent an email to r-fo...@r-project.org to report problems with the build process. It appears that any changes I have pushed to R-Forge over approximately the last two months have resulted in the package remaining in

[R-pkg-devel] Inherited methods

2024-08-16 Thread Kevin R. Coombes
go-rounds of changing the code, changing the NAMESPACE, and running "R CMD check" approximately an infinite number of times, I now have NAMESPACE: importMethodFrom("A", "hist") exportMethod("hist") R SCRIPT: setClass("D", slots = c(some_extra_st

[R-pkg-devel] R CMD check options

2024-08-16 Thread Kevin R. Coombes
mmon issues are * spelling (especially in the DESCRIPTION file), and * links in the documentation with missing package anchors. How do I enable these checks so that when I run "R CMD check --as-cran" it actually does behave like those CRAN machines do, so I can find and fix the issues befo

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

2024-08-17 Thread Kevin R. Coombes
Thank you! On 8/17/2024 9:24 AM, Ivan Krylov wrote: 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 Bu

[R-pkg-devel] Spell Check with Hunspell on Windows

2024-08-20 Thread Kevin R. Coombes
Hi, This is a follow-up to an earlier question where I asked about R CMD check on Windows to be able to check R packages in a manner closer to the checks on CRAN machines before i submit (new or updated) packages.  From the answers to the previous question, I learned the (magic) environment

[R-pkg-devel] Getting error: Installation failed: Unknown username with my package

2018-07-13 Thread R. Mark Sharp
ameSurgerySheets, and one public rmsharp/rmsutilityr both install fine. Does anyone know what I may have broken or how? Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-286

Re: [R-pkg-devel] Getting error: Installation failed: Unknown username with my package

2018-07-13 Thread R. Mark Sharp
. Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-2868 rmsh...@me.com > On Jul 13, 2018, at 7:17 PM, Gábor Csárdi wrote: > > Hi Mark, > > seems like you have "Remotes: covr"

Re: [R-pkg-devel] submitting to github

2019-01-25 Thread SMITH, MARTIN R.
. - Martin -- Martin R. Smith Assistant Professor in Palaeontology Department of Earth Sciences Durham University Mountjoy Site, South Road Durham DH1 3LE T: +44 191 334 2320 M: +44 774 353 7510 E: martin.sm...@durham.ac.uk<mailto:martin.sm...@durham.ac.uk> Skype: martin--smith durham.ac.uk/ear

Re: [R-pkg-devel] Change in normal random numbers between R 3.5.3 and R 3.6.0

2019-05-09 Thread R. Mark Sharp
I was dealing with a similar issue but in the context of getting the same unit test code to work on multiple versions of R in a Travis-CI build. It seems RNGkind(sample.kind="Rounding”) does not work prior to version 3.6 so I resorted to using version dependent construction of the argument

Re: [R-pkg-devel] Change in normal random numbers between R 3.5.3 and R 3.6.0

2019-05-10 Thread R. Mark Sharp
Ulrike, RNGkind() worked on 3.4.1 and 3.6.0 but generated a warning on R 3.5.3. The message follows: checking whether package ‘nprcmanager’ can be installed ... WARNING Found the following significant warnings: Note: possible error in 'RNGkind(sample.kind = "Rounding")&#x

[R-pkg-devel] checking CRAN incoming feasibility NOTE

2019-10-05 Thread R. Mark Sharp
a CRAN submission we recommend that you fix all NOTEs, WARNINGs and ERRORs. ## Test environments - R-hub windows-x86_64-devel (r-devel) - R-hub ubuntu-gcc-release (r-release) - R-hub fedora-clang-devel (r-devel) ## R CMD check results ❯ On windows-x86_64-devel (r-devel), ubuntu-gcc-release (r-r

Re: [R-pkg-devel] checking CRAN incoming feasibility NOTE

2019-10-05 Thread R. Mark Sharp
Roy, Thank you for your guidance and advice. I ran usethis::use_cran_comments() shown below. > usethis::use_cran_comments() ✔ Setting active project to '/Users/msharp/Documents/Development/R/r_workspace/library/nprcmanager' ✔ Writing 'cran-comments.md' ✔ Adding &#

[R-pkg-devel] R-hub PREPERROR on Ubuntu Linux 16.04 LTS, R-release, GCC not on other platforms

2019-11-08 Thread R. Mark Sharp
not available for package ‘nprcmanager’ The following platforms have no errors or warnings and have only the “New submission” note. Windows Server 2008 R2 SP1, R-devel, 32/64 bit Fedora Linux, R-devel, clang, gfortran Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 75

[R-pkg-devel] compression of vignettes

2019-11-21 Thread R. Mark Sharp
I have been unsuccessful with all of the following attempts to have compression of dynamically generated vignettes during the build on travis-ci and within RStudio. Help is appreciated. I have tried the following travis-ci YAML to have vignettes compressed. script: - R -e 'r <- r

Re: [R-pkg-devel] Manual inspection of a new CRAN submission

2019-12-18 Thread R. Mark Sharp
mistake. Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-2868 rmsh...@me.com > On Dec 18, 2019, at 7:26 PM, Mauricio Zambrano-Bigiarini > wrote: > > Thank you very much Duncan for the

[R-pkg-devel] Examples for functions called by Shiny server

2020-03-15 Thread R. Mark Sharp
an Rd file that is to have the example. I cannot think of a meaningful example for a function that creates the content of a new Shiny tabpanel when an error is detected. Suggestions are eagerly sought. Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow

[R-pkg-devel] Fwd: [R] a question of etiquette

2020-06-01 Thread R. Mark Sharp
Adelchi, I have a similar situation where I had made all of the typical academic references within the code and documentation for a small but important function my package uses. I was asked by the CRAN reviewers to add the author of that function to the DESCRIPTION Authors@R section. I added

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread R. Mark Sharp
I strongly prefer. The GPL-2 and GPL-3 licenses are apparently sufficiently ambiguous in the legal community that some companies avoid them. Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-2868 rmsh

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread Kevin R. Coombes
For academics, aren't those citations the currency in which they are supposed to be paid (at least for R packages)?   Kevin On 6/2/2020 3:24 PM, Avraham Adler wrote: On Tue, Jun 2, 2020 at 5:04 PM Spencer Graves < spencer.gra...@effectivedefense.org> wrote: QUESTION: How much

Re: [R-pkg-devel] [R] a question of etiquette

2020-06-02 Thread R. Mark Sharp
defending their position and disagree with it. However, it is their position based on what I think is a conservative or overly cautious legal interpretation. I am not a lawyer, however, so my opinions are of no import. Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant

Re: [R-pkg-devel] [External] Re: Two packages with the same generic function

2020-06-23 Thread Kevin R. Coombes
conflict resolution options appropriately). Best, luke __________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] Debugging Clang ASAN errors

2020-07-03 Thread Martin R. Smith
a similar issue in the r-packages archives ( https://stat.ethz.ch/pipermail/r-package-devel/2018q3/002907.html). The suggestion in that case was that the issue may have been a false positive, a possibility that is consistent with a "HINT" in the output log. I optimistically suspect that

[R-pkg-devel] DOI for archived package?

2020-09-10 Thread Kevin R. Coombes
Hi, I am in the process of submitting a "workflow" article about an R package (which is onCRAN) to F1000Research. The associate editor that I am dealing with wants a "DOI" for the source code of the package being described in the manuscript.  I have already explained tha

[R-pkg-devel] Licenses

2020-10-22 Thread Kevin R. Coombes
Hi, I am developing a package and getting a NOTE from R CMD check about licenses and ultimate dependencies on a restrictive license, which I can't figure out how to fix. My package imports flowCore, which has an Artistic-2.0 license. But flowCore imports cytolib, which has a license fro

[R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
les are: 1. Mercator depends on Thresher 2. Thresher imports moVMF 3. moMVF suggests flexmix On my Windows machine, the package builds and installs with no errors or warnings even if flexmix is not available (which I believe to be the correct behavior). On R-Forge, both the Windows and LIN

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
dency hierarchy? For building and installing the package (or running R CMD check ---as-cran), I tried on my machine when flexmix is not even installed, and got no errors or warnings. There is clearly something I don't understand about namespaces, and I'd like to learn it to avoid this k

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
Hi Duncan, Oops; I didn't realize I had forgotten to push updates to the OOMPA web site. The code for Mercator is contained as part of the Thresher project in the subversion repository on R-Forge. (https://r-forge.r-project.org/projects/thresher/) It's under pkg/Mercator belo

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
flexmix (and related objects) is listed, because the flexmix NAMESPACE has been attached. If I run the same code on an R system where flexmix is not installed, then, of course, neither the NAMESPACE nor the method is available. I suspect (but am by no means certain) that the combination of

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
ed by something several layers down the hierarchy should get attached and cause an issue like this one. (The attached NAMESPACE happens in current versions of R.) Thanks,   Kevin On 11/11/2020 1:07 PM, Duncan Murdoch wrote: Okay, I've tried testing on my Mac with R 4.0.3 and R-devel for the

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
Oh, I forgot to mention explicitly that checking (with --as-cran) on the development version of R on Windows also produces no errors or warnings. On 11/11/2020 1:39 PM, Kevin R. Coombes wrote: Hi Duncan, I just sent a longer version of this message, but it looks to me like the underlying

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-11 Thread Kevin R. Coombes
ugh stuff to check Mercator.) In the R-devel --as-cran checks, some checks are run with only strong dependencies of your package visible.  Somehow I think that .onLoad function sees flexmix and loads it, but then some other part of the check can't see it. A workaround is to add flexmix to

Re: [R-pkg-devel] Strange error from CRAN on package submission

2020-11-12 Thread Kevin R. Coombes
Hi Martin, I think you may be right that it is something odd about the configuration on the test machine, since I haven't been able to reproduce it anywhere else. But Duncan did say he could reproduce it in R-devel but not R-4.0.3, so there's that. The error message is buried de

[R-pkg-devel] Confusion about what should be in Imports for a package with a shiny app

2021-03-24 Thread R. Mark Sharp
me to place them in the Imports section and I now have multiple test environments (3 R-hub builder, 3 winbuilder, and 3 Travis-ci) that are showing no errors, warnings, or notes with that placement. However, the package check page https://cran.rstudio.com//web/checks

Re: [R-pkg-devel] Confusion about what should be in Imports for a package with a shiny app

2021-03-24 Thread R. Mark Sharp
interactively or in their own scripts and applications. I will modify the DESCRIPTION file accordingly. Mark R. Mark Sharp, Ph.D. Data Scientist and Biomedical Statistical Consultant 7526 Meadow Green St. San Antonio, TX 78251 mobile: 210-218-2868 rmsh...@me.com > On Mar 24, 2021, a

[R-pkg-devel] Case of package name

2024-12-30 Thread Kevin R. Coombes
the similarly named component of the blood instead. Is there any simple way (that won't burden or confuse the CRAN maintainers excessively) to make this change? Thanks,   Kevin __________ R-package-devel@r-project.org mailing list https://stat.ethz.c

[R-pkg-devel] test script output

2025-01-31 Thread Kevin R. Coombes
uot;summary" to hide the differences). the only one that remains yields this R CMD check report: Comparing ‘testDiff.Rout’ to ‘testDiff.Rout.save’ ...52c52 < 2.600e-06 1.328e-01 4.666e-01 1.060e+00 1.369e+00 1.091e+01 --- > 0.03 0.132800 0.466600 1.06 1.369000 10.91000

Re: [R-pkg-devel] test script output

2025-01-31 Thread Kevin R. Coombes
Thanks for the quick (detailed) response. On 1/31/2025 12:23 PM, Martin Maechler wrote: Kevin R Coombes on Fri, 31 Jan 2025 11:48:33 -0500 writes: > Hi, > I have a package that has been in CRAN for years and is now failing > checks because some of the output

[R-pkg-devel] URLs in DESCRIPTION file

2025-04-07 Thread Kevin R. Coombes
Hi, I am systematically going through the packages that I maintain on CRAN to clean up some administrative details. Specifically, I am (1) changing all DESCRIPTION files to use Authirs@R, (2) updating the links in man files to include package anchors, and (3) making sure that the output of

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

2025-04-07 Thread Kevin R. Coombes
going to have a significantly longer stable lifetime than the NCBI URL. So, for now at least, I think I will leave them both. Best,    Kevin On 4/7/2025 11:35 AM, Ivan Krylov wrote: В Mon, 7 Apr 2025 11:10:21 -0400 "Kevin R. Coombes" пишет: But version R 4.5.0 RC comes back with;

Re: [R-pkg-devel] How and where do I document sysdata.rda

2025-03-20 Thread Kevin R. Coombes
If it is *only *in sysdata.Rda, then it is accessible to your package code but is not available to users. (They can't, for example, use the "data" function to load it themselves.) So, there is no reason to document it. Just like there is no reason to document functions in your

Re: [R-pkg-devel] DESCRIPTION file question

2023-07-24 Thread Taylor R. Brown via R-package-devel
okay I'm on board now. I think we're both looking at the same passage in Writing R Extensions, too. I had some grammatical confusion. When I read "Specifying a package in ‘LinkingTo’ suffices if these are C/C++ headers containing source code or static linking is done at installation&q

[R-pkg-devel] Problems runing a example (shiny App) within a package

2017-07-28 Thread Kévin A . S . R .
Problems running a example (shiny App) within a package #main code runclt = function(){ shiny::runApp(system.file("shinyCLT", package="CLT")) } #example \examples{ runclt() } #Problem R CMD check breaks in "checking examples ..." and don't c

[R-pkg-devel] Coordination Needed: Update in ast2ast affecting paropt

2023-11-29 Thread Konrad via R-package-devel
tions on how Ican smoothly navigate this transition with minimal disruption. Thanks a lot in advance. Best Konrad [[alternative HTML version deleted]] ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-pa

Re: [R-pkg-devel] Update timing of machines on CRAN?

2023-12-04 Thread andrew--- via R-package-devel
I do think that its a reasonable ask that the test machines be running operating systems within their vendor support periods. -Andrew Robbins From: R-package-devel on behalf of Josiah Parry Sent: Monday, December 4, 2023 11:34 AM To: Tomas Kalibera Cc: R

[R-pkg-devel] Flex missing in win-builder

2024-05-28 Thread drc via R-package-devel
with `pacman`. Flex can also be installed via `pacman`, so why are the other two available? I can't find much on how the `SystemRequirments` is used in "Writing R Extensions" either, is this used to tell CRAN what is needed to build the package? Or is it just a hint to end users?

[R-pkg-devel] Properly referencing copied code

2024-07-11 Thread DRC via R-package-devel
. What roles to supply to authors of external software? After my last submission, I got the note: > Has copyright holders of included software in a [ctb] role only >From the CRAN Repository Policy file: >Where code is copied (or derived) from the work of others (including from R >itself),

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

2024-07-12 Thread DRC via R-package-devel
or?  - DRC On Friday, July 12th, 2024 at 3:07 AM, Ivan Krylov 'ikrylov at disroot.org' wrote: > > В Thu, 11 Jul 2024 20:58:53 +0000 > DRC via R-package-devel r-package-devel@r-project.org пишет: > > > 1. How does linking to external libs differ from providing the sou

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

2024-07-15 Thread DRC via R-package-devel
y own simple external C library. I wrote the C lib outside of the R package specifically so it would be possible to integrate the algorithm into multiple high level interfaces (i.e. python, matlab, in addition to R) otherwise the C would have been directly written into the R package. I don'

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

2024-08-12 Thread David via R-package-devel
I'm working on a package that uses some fortran copied from elsewhere. It compiles and build fine everywhere but exclusively in the intel environment (provided by rhub), the intel fortran compiler generates intermediary files from *.f -> *__genmod.f90. The R check then complains that th

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

2024-08-15 Thread David via R-package-devel
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't confirm it work. I was also unable to successfully bui

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

2024-08-16 Thread David via R-package-devel
I locally ran the rhub intel docker and that was much easier to set up. So I can now confirm the change to Makevars does work. > I experimented with the "ghcr.io/r-hub/containers/intel:latest" container and > was able to find out that the option -[no]gen-interfaces controls the

Re: [R-pkg-devel] gcc-asan replication for armadillo

2025-05-21 Thread andrew--- via R-package-devel
If this were the case I don't think that I'd be having problems replicating it. From: Serguei Sokol Sent: Wednesday, May 21, 2025 9:21 AM To: and...@robbinsa.me ; R Package Development Subject: Re: [R-pkg-devel] gcc-asan replication for

[R-pkg-devel] gcc-asan replication for armadillo

2025-05-21 Thread andrew--- via R-package-devel
both my shared object and the Rcpp binding library-which seems like something that shouldn't be raising any issues. Dirk, you wouldn't happen to have seen this before? -Andrew Robbins __ R-package-devel@r-project.org mailing list https

[R-pkg-devel] A package that traces base functions

2017-02-26 Thread brodie gaslam via R-package-devel
--- Begin Message --- Apologies, this is a cross post from 'R-devel', where I sent this message a few months ago when I did not realize there was an 'r-package-devel' list.  So here it is again in the correct list: I'm working on a package that implements a REPL.  A

Re: [R-pkg-devel] CRAN check FAIL due to pragmas in headers and code

2017-12-13 Thread brodie gaslam via R-package-devel
e error on the clang and gcc 64 bit debian checks: * diffobj: (my package) https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/diffobj-00check.html* xts: https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/xts-00check.html* backports: https://www.r-p

Re: [R-pkg-devel] Problems with too much testing

2021-04-16 Thread brodie gaslam via R-package-devel
testthat version 3.  I'd like ideas for something more robust.) Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Unable to get past CRAN submission checks for package cubature

2021-05-11 Thread brodie gaslam via R-package-devel
ce. Any suggestions? -Naras Forwarded Message Subject:     Re: [CRAN-pretest-archived] CRAN submission cubature 2.0.4.2 Date:     Thu, 6 May 2021 12:51:37 -0700 From:     Balasubramanian Narasimhan To:     cran-submissi...@r-project.org, na...@stat.stanford.edu Dear CRAN,

[R-pkg-devel] OpenMP on MacOS

2021-06-07 Thread Konrad Krämer via R-package-devel
code? Or is there a better way to cope with this problem? Many thanks in advance for your help. Regards, Konrad  [[alternative HTML version deleted]] __________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] package test returns error when R version 4.1.0

2021-07-06 Thread brodie gaslam via R-package-devel
and they obviously need to set the entry. > > But clearly Gm has a different problem.  He has now tried "LazyData: true", > "LazyData: false", and removing the LazyData entry entirely.  And he is > still getting this error: > > * installing *source* package

Re: [R-pkg-devel] Scrapping R CRAN website from package

2021-07-19 Thread Maëlle SALMON via R-package-devel
Could pkgsearch http://r-hub.github.io/pkgsearch/ help with what you're doing, as it can queries all versions of CRAN packages? See http://r-hub.github.io/pkgsearch/reference/cran_package_history.html for the docs of the function cran_package_history(). It does not scrape CRAN pages, it

[R-pkg-devel] FW: [EXTERNAL] [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

2021-08-16 Thread Pooja Gangras via R-package-devel
istribution is strictly prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. -Original Message- From: lig...@statistik.tu-dortmund.de Sent: Monday, August 16, 2021 10:32 AM To: Pooja Gangras Cc: cra

Re: [R-pkg-devel] [EXTERNAL] Re: FW: [CRAN-pretest-archived] CRAN submission surfaltr 1.0.0.9000

2021-08-16 Thread Pooja Gangras via R-package-devel
contact the sender by reply email and destroy all copies of the original message. -Original Message- From: Sebastian Meyer Sent: Monday, August 16, 2021 2:49 PM To: Pooja Gangras ; r-package-devel@r-project.org Subject: [EXTERNAL] Re: [R-pkg-devel] FW: [CRAN-pretest-archived] CRAN

Re: [R-pkg-devel] (R-devel unknown warning: 'memory.limit()' is no longer supported)

2021-09-03 Thread brodie gaslam via R-package-devel
There was a recent changed made to R to remove that option. There is documentation visible in the patch that explains it: https://github.com/r-devel/r-svn/commit/795fb3fe60d35734750afbc34cc7d36b19290b9c Presumably you would have to remove any uses of the now unsupported functions.  After the

Re: [R-pkg-devel] (R-devel unknown warning: 'memory.limit()' is no longer supported)

2021-09-03 Thread brodie gaslam via R-package-devel
Or you might need to make their use conditional on the R version.  It is possible that the call is still needed if your package is run on older versions of R.  I am not familiar with the general use of this though.  I only noticed the change in R-devel and linked it to your question. Best, B

Re: [R-pkg-devel] system.file duplicates the path

2021-09-05 Thread brodie gaslam via R-package-devel
mpile/CRANincoming/R-devel/uFTIR.Rcheck/d:/RCompile/CRANincoming/R-devel/lib/uFTIR/extdata/tile.bsp' and fed it to your function from the prior version of your package and was able to produce a doubled up path as above. Best, B. PS: with this type of thing it is always helpful if you can provide a

[R-pkg-devel] Packages required but not available

2021-09-11 Thread Danielle Maeser via R-package-devel
Hello, I received the following output from my package, oncoPredict. However, I don't understand how to correct this error. I've tested the advice here: https://stackoverflow.com/questions/14358814/error-in-r-cmd-check-packages-required-but-not-available without success. Any thoughts

Re: [R-pkg-devel] Packages required but not available

2021-09-11 Thread Danielle Maeser via R-package-devel
Hi David, Yes. I did recently upgrade R. On Sat, Sep 11, 2021 at 4:28 PM wrote: > Danielle: > > Did you recently upgrade to R 4.1.1? > > David > > > -Original Message- > From: R-package-devel On Behalf > Of Danielle Maeser via R-package-devel > Sent:

[R-pkg-devel] Good practice for database with utf-8 string in package

2021-09-17 Thread Marc Girondot via R-package-devel
I have posted this question first to r-h...@r-project.org and Bert Gunter informs me that it was better for this discussion list that I didn't know. Hello everyone, I am a little bit stucked on the problem to include a database with utf-8 string in a package. When I submit it to CRA

Re: [R-pkg-devel] Good practice for database with utf-8 string in package

2021-09-17 Thread Maëlle SALMON via R-package-devel
: On Fri, 17 Sep 2021, Marc Girondot via R-package-devel writes: > I have posted this question first to r-h...@r-project.org and Bert Gunter > informs me that it was better for this discussion list that I didn't know. > > Hello everyone, > > I am a little bit stucked on t

Re: [R-pkg-devel] [External] Re: What is a "retired"package?

2021-09-22 Thread Avi Gross via R-package-devel
included functions may be available in base R or another commonly used package (such as the tidyverse collection) and just using the new one, perhaps with some alteration in how it is called, might help guide existing users away to something more likely to be maintained. And sometimes, it might be

Re: [R-pkg-devel] ERROR (re)building vignettes

2021-09-22 Thread Maëlle SALMON via R-package-devel
Dear Christine, Looking at the chunk that causes the error https://github.com/cran/SleepCycles/blob/141186934418af387f0af257e3079af588e72844/vignettes/introduction.Rmd#L50-L56 (via the CRAN mirror maintained by R-hub): * You should not install packages from a vignette. You can add "eval=

Re: [R-pkg-devel] Namespace is imported from in YAML header, but attracts Note that is is not imported from

2021-09-23 Thread Maëlle SALMON via R-package-devel
eed to worry about this? John Maindonald ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel   ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2021-09-24 Thread Maëlle SALMON via R-package-devel
We've summarized some advice around graceful packages in this chapter of the HTTP testing in R book: https://books.ropensci.org/http-testing/graceful.html I hope this can help too!  Le ven., sept. 24, 2021 à 17:03, Ben Bolker a écrit:   I think you're not supposed to stop

Re: [R-pkg-devel] Package submission to CRAN

2021-10-19 Thread Brodie Gaslam via R-package-devel
AN, and I have resubmitted my package. There have been no changes to my package and I resubmitted the same version with the same version number. I noted this in my submission. All checks passed, but I received the following from log CRAN-pretest: Flavor: r-devel-linux-x86_64-debian-gcc, r-deve

Re: [R-pkg-devel] R feature suggestion: Duplicated function arguments check

2021-11-08 Thread Avi Gross via R-package-devel
ways to get this result but probably not as simple. And note this can go several layers deep as various functions call each other and each has a different need and even meaning for a=something. Avi -Original Message- From: R-package-devel On Behalf Of Duncan Murdoch Sent: Monday, November

Re: [R-pkg-devel] R feature suggestion: Duplicated function arguments check

2021-11-08 Thread Avi Gross via R-package-devel
Vincent, But is the second being ignored the right result? In many programming situations, subsequent assignments replace earlier ones. And consider the way R allows something like this: func(a=2, b=3, a=4, c=a*b) Is it clear how to initialize the default for c as it depends on one value of &q

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

2021-11-25 Thread Nathan Green via R-package-devel
llel = parallel) 45: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 46: test_check("BCEA") An irrecoverable exception occurred. R is aborting now ... See: <https://www.r-project.org/nosvn/R.check/r-release

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

2021-11-26 Thread Nathan Green via R-package-devel
erious bug in rstan - apparently they only do that on macOS which explains why other platforms don't see it: .onLoad <- function(libname, pkgname) { [...]   ## the tbbmalloc_proxy is not loaded by RcppParallel which is linked   ## in by default on macOS; unloading only works under R >=

[R-pkg-devel] Cannot submit package due to false-positive rejection

2022-10-28 Thread Ying Li via R-package-devel
...@r-project.org<mailto:cran-submissi...@r-project.org>) but did not receive any message after 9 days. I am looking for suggestions on what to do in this case: should we continue waiting for CRAN team�s reply? Or is it necessary to eliminate those notes and then submit the package again? Bel

Re: [R-pkg-devel] Package submission error due to vignette

2022-11-22 Thread Dirk Eddelbuettel via R-package-devel
d may want to contact Robin about his timeline) or (at least for a while) skip 'rje' in your vignette. Dirk -- dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org ______ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

[R-pkg-devel] Inconsistent R CMD Check results

2023-01-24 Thread Ying Li via R-package-devel
Dear all, Hope you are well! Recently, in the check before a re-submission, I got an unexpected note when doing R CMD Check using rhub::check_for_cran(), saying that "Examples with CPU (user + system) or elapsed time > 5s". I didn't expect this note to appear because the sa

Re: [R-pkg-devel] Inconsistent R CMD Check results

2023-01-25 Thread Ying Li via R-package-devel
That makes sense, thanks very much for your explanation and advice, Tomas and Uwe! Best, Ying From: Uwe Ligges Sent: Wednesday, January 25, 2023 9:52 To: Tomas Kalibera ; Ying Li ; r-package-devel@r-project.org Cc: Arindam RoyChoudhury Subject: [EXTERNAL] Re

[R-pkg-devel] DESCRIPTION file question

2023-07-22 Thread taylor brown via R-package-devel
Hi everyone, I have a question about the DESCRIPTION file of an R package that has some c++ dependencies. This package of mine builds c++ code during an interactive R session, but does not contain any source c++ in itself. The c++ files make reference to some dependencies that are made

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