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

Did you seriously look for instructions and not find [1]? And why do you think the answer should not involve Rd files? Documentation in R packages is what Rd files are for. If you don't want to mess with Rd files then you have no choice but to use something like the Roxygen package to mess with

Re: [R-pkg-devel] Retrieving versioned csv datasets for use in an R package

Seconded... have the support for obtaining the desired file be completely initiated by the user, and explicitly pass the filename into the functions that use the data. It is also easier to trace which file was used in a past analysis this way... auto config seems convenient, but it is hard to re

Re: [R-pkg-devel] Failed: Future File Timestamp Check

e is just programmatically generated. > > >On Tue, Feb 4, 2025 at 14:54 Jeff Newmiller >wrote: > >> Packages are supposed to work when mounted in a read-only filesystem... >> using writeLines seems like a very bad idea since you can't assume the >> package install is

Re: [R-pkg-devel] Failed: Future File Timestamp Check

Packages are supposed to work when mounted in a read-only filesystem... using writeLines seems like a very bad idea since you can't assume the package install is writeable when it is run, and running code from tmp is a security hole. If you absolutely cannot think of a way around running code f

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

You should not use "library(anything)" in a package. You should rely on the Imports: field in the DESCRIPTION file along with importFrom() in your NAMESPACE file, or the Suggests: field in the DESCRIPTION file and if (requireNamespace("anypackage")) {anypackage::somefun} else {# avoid using an

Re: [R-pkg-devel] R-extension requirement about third-party random number generators (RNG)

You mention that you did not like putting the rstream in the user API but there is nothing forcing you to have the user call your cpp function directly... there are lots of packages that use R glue functions as the API. I have not dug into Dirk's code, but having the native R seed management is

Re: [R-pkg-devel] unregistered S3 methods in a package

I have been reluctant to pipe up on this because I am no expert on the dark corners of the S3 dispatch mechanism, but I think unregistered S3 methods in packages are verboten. Perhaps [1] will shed some light? [1] https://blog.r-project.org/2019/08/19/s3-method-lookup/ On September 4, 2024 11:2

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

I cannot/will not to help you do this, but there are people out there who disagree with me who put considerable effort into doing this... the search term you would need in order to find them is "monorepo". But please reconsider... the whole point of putting code into separate packages is to iso

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

with no further elaboration. I can't fix this >issue because I don't actually know what's wrong. > > >On Fri, Jun 28, 2024, 18:43 Jeff Newmiller wrote: > >> Google for "http 403 error"... likely win-builder has multiple packages >> with links to Pos

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

Google for "http 403 error"... likely win-builder has multiple packages with links to Posit, and the Posit web server is throttling automated hits. Theoretically this is just a warning and you can try submitting to CRAN, but CRAN may have even less luck accessing Posit than win-builder. Submitti

Re: [R-pkg-devel] NOTEs in packages using Rust

I am not connected to CRAN (by a long shot), but if I were I would not accept any of the arguments you are making here. I don't know what you are talking about with respect to excluding files in tarring... you should be using the package build processes as documented in Writing R Extensions. A

Re: [R-pkg-devel] No email with confirmation link on resubmission of package

Did you increment the version number? On June 5, 2024 1:19:27 AM PDT, Paul Kabaila wrote: >(1) Today, I submitted my R package to CRAN using >devtools::submit_cran() >which resulted in an email from >CRAN Package Submission Form >cransub...@xmbombadil.wu.ac.at

Re: [R-pkg-devel] different build tools

Duncan's point about options is key... the build options set by default in devtools etc are generally configured to minimize the time required to identify the next big issue to address. Options appropriate for preparing to submit to CRAN are slow and inconvenient for developing. I recommend tha

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

so... your suggestion is not for CRAN, but for R-Core, who makes changes to R On May 18, 2024 6:03:55 PM PDT, "Richard M. Heiberger" wrote: >exactly. when the --as-cran detects the need for that NOTE, it could prefix >the initial instance of that NOTE with information about >updating the ti

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

What is a "right side window"? Are you mixing up what R does and what RStudio does? I think I agree with Ivan that this is a question about the environment in which you are loading the package rather than anything in the package itself. On March 7, 2024 11:21:06 AM PST, "Ruff, Sergej" wrote: >

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

Remove leading periods from all file names in the tar.gz. Use .Rbuildignore to handle such files in your dev directory if you need them. Maybe also look at [1]. [1] https://stackoverflow.com/questions/40950799/r-cmd-check-error-how-to-get-rid-of-hidden-files-and-directory-in-devel-r-pack On M

Re: [R-pkg-devel] Changing package maintainers

Are you aware of this [1]? J. Random Lurker may not be a reliable source, and actual CRAN repo maintainers are probably a bit busy... [1] https://cran.r-project.org/web/packages/policies.html#Submission On February 8, 2024 8:37:50 AM PST, Josiah Parry wrote: >I intend to change the maintainer o

Re: [R-pkg-devel] Warnings from upstream C library in CRAN submission

Type conversions are always a bit risky... this one appears to be likely to corrupt data. If they actually intended to truncate values like this then they should have cast explicitly. Looks like you need to report this to the SUNDIALS maintainers. On February 3, 2024 7:38:35 AM PST, Satyaprakas

Re: [R-pkg-devel] Wrong mailing list: Could the 100 byte path length limit be lifted?

This is a narrow view of the world. As has been mentioned here by Tomas, the issue at this point is that a very widely-used operating system does not allow the absolute path to be longer than 254 characters unless users make possibly-breaking changes to their OS configuration. If a user is curre

Re: [R-pkg-devel] How to fix: non-standard things in the check directory: 'NUL' ?

Rhub is not CRAN. Please include a link to your source package if you want help. If there is actually a bug in Rhub then this NUL error may not reflect the response you will get from CRAN if and when you submit. On December 13, 2023 12:58:41 AM PST, Friedemann von Lampe wrote: >Hi, > >when try

Re: [R-pkg-devel] [External] circular suggested packages

Richard ... they are by different maintainers. They also are built with completely different underlying technologies... creating a bitmap is easy, deciphering one is difficult and may not be necessary in the same workflow and there may be different compiled code available optimized for different

Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

A code chunk does always begin with a triple backtick at the beginning of a line. The term for what you encountered is "inline code" used to embed computed results into the markdown text as though you had typed them directly. Check out https://www.r-bloggers.com/2017/12/how-to-show-r-inline-cod

Re: [R-pkg-devel] Fortune candidate Re: Issue with R Package on CRAN - OpenMP and clang17

ROFL! Seconded! The quote itself has a bit of greybeard smell to it, but the "ran out of stuff to delete at 100GB with 1000 out of 6000 targets compiled" had me in stitches. On October 31, 2023 10:16:10 AM PDT, Dirk Eddelbuettel wrote: > >On 31 October 2023 at 19:58, Ivan Krylov wrote: >| [...]

Re: [R-pkg-devel] Failing to write config file in linux

Installed packages may not be modified because they are permitted to be installed with read-only access. You have no option to proceed in this direction. Configuration files are normally stored in the user's working directory. Dotfiles are a common convention in *nix operating systems, but in W

Re: [R-pkg-devel] Problem persists, was Re: Problem compressing vignettes for CRAN

R could care less about what is in PATH... there is however a difference between Windows parsing PATH and how CMD lets you quote things interactively. The whole point of PATH is to let you or R provide simple program names like qpdf without knowing where they are... Windows takes over and looks

Re: [R-pkg-devel] Warning: a function declaration without a prototype is deprecated in all versions of C

This error arises because you are not declaring the function properly before you call it... likely because you have not included the appropriate header file or because you have typoed the function call. If you provide a link to your package someone may point you more precisely to your error, bu

Re: [R-pkg-devel] R_orderVector1 - algo: radix, shell, or another?

h is part of public R C >api. >Should I notice something relevant in the source of R's order? > >Best >Jan > >On Sun, Sep 24, 2023, 17:27 Jeff Newmiller wrote: > >> Have you read the output of >> >> order >> >> entered at the R console?

Re: [R-pkg-devel] R_orderVector1 - algo: radix, shell, or another?

Have you read the output of order entered at the R console? On September 24, 2023 1:38:41 AM PDT, Jan Gorecki wrote: >Dear pkg developers, > >Are there any ways to check which sorting algorithm is being used when >calling `order` function? Documentation at >https://stat.ethz.ch/R-manual/R-deve

Re: [R-pkg-devel] roxygen style documentation for data sets

I thought roxygen supported documenting NULL constants for data. I do think roxygen ought to be able to co-exist with Rd files... but the claim that documenting data requires Rd files smells fishy to me. On September 21, 2023 1:30:11 PM PDT, Michael L Friendly wrote: >I am an RStudio user, and

Re: [R-pkg-devel] [Tagged] Re: roxygen style documentation for data sets

None of us here are lawyers, but a simple google search should take you to discussions such as [1]. There is a long history of debates about the upsides and downsides of restricting how people can use your source code. My short take is that a GPL license prevents anyone from stuffing your code

Re: [R-pkg-devel] is this expected behavior

Yes. Demo/test files need to use the library function to attach the package like any other user. On September 13, 2023 5:24:52 PM PDT, "Richard M. Heiberger" wrote: >I have a demo file that uses a function defined in the package. >when I force the demo to be run with >R CMD check --test-dir=de

Re: [R-pkg-devel] Fw: [CRAN-pretest-archived] CRAN Submission moodlequizR 1.0.1

I don't know how you can negotiate with CRAN regarding attach, but one approach is to return the data frame and instruct your students to write moodledata <- paste.data() instead of paste.data() since either is just as obscure as the other in the mind of a beginner and the former promotes

Re: [R-pkg-devel] R Package Development -- PDF Manual without Index

CRAN doesn't care about whether devtools is happy. R CMD check --as-cran needs to work, e.g. as in [1]. Devtools is a convenience tool to help put all of the necessary bits in the right places in your source code according to [2]. But if there is any disagreement about what works, devtools is n

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

You have a really bizarre way of twisting what others are saying, Dirk. I have seen no-one here saying 'limit R to 2 threads' except for you, as a way to paint opposing views to be absurd. What _is_ being said is that users need to be in control_, but _the default needs to do least harm_ until

Re: [R-pkg-devel] Re-building vignettes had CPU time 9.2 times elapsed time

Sanity seems to be in the eye of the beholder. FWIW I am certainly not CRAN or R Core, but I pretty strongly disagree with any package that defaults to using more than 2 cores. If I am using a shared HPC I can get in trouble if I over-consume cpu resources ... i.e. I may be given access to 10 co

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

forming if they link with compiled code that is supposed to make use of threads. On August 23, 2023 7:24:46 AM PDT, Uwe Ligges wrote: > > >On 23.08.2023 15:58, Jeff Newmiller wrote: >> To whom are you addressing this question? The OpenMP developers who define >> the missing

Re: [R-pkg-devel] Trouble with long-running tests on CRAN debian server

To whom are you addressing this question? The OpenMP developers who define the missing-OMP_THREAD_LIMIT behaviour and-or supply default config files? The CRAN server administrators who set the variable in their site-wide configuration intentionally or unintentionally? Or the package authors expe

Re: [R-pkg-devel] Package Load fails to find 3rd Party DLL

Use of precompiled code is not allowed in CRAN. This looks like your package needs to be distributed elsewhere... e.g. via GitHub. On July 12, 2023 6:41:11 AM PDT, Russell Almond wrote: >I have an R package (RNetica available at >https://ralmond.r-universe.dev/RNetica and >https://github.com/

Re: [R-pkg-devel] Public URLs for help for versions of base packages

Sure. On your computer. Install the old version of R and let it serve the relevant docs. Dunno of anyone doing this historical dive online for you though. Why would you want preformatted docs if you didn't have those old versions installed? On June 29, 2023 4:23:55 PM PDT, David Hugh-Jones wr

Re: [R-pkg-devel] Package broke with R 4.3.0

if (any(c( "alaska", "hawaii") %in% zoom)){} On June 27, 2023 9:11:09 AM PDT, "Göran Broström" wrote: > > >Den 2023-06-27 kl. 17:17, skrev Göran Broström: >> If(zoom %in% c(“alaska”, “hawaii”)… > >Wrong, maybe > >if (("alaska" %in% zoom) || ("hawaii" %in% zoom)){} > > >> >> Göran >> >>> 27 jun

Re: [R-pkg-devel] Problems with devtools::build() in R

Your mistake is confusing a tool designed for _iterative development_ for a tool designed for _delivery_. Use R CMD build the way WRE says you should. On May 16, 2023 9:07:05 AM PDT, Jarrett Phillips wrote: >Hi All, > >I'm trying to generate a `tar.gz` file on a Mac for R package submission to

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

Long build time for vignettes? On January 22, 2023 10:51:30 AM PST, Klaus Schliep wrote: > Dear all, > >I try to submit a new version of the package phangorn and got the mail back: > >"Dear maintainer, > >package phangorn_2.11.0.tar.gz does not pass the incoming checks >automatically, please see

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

Isn't the whole purpose of creating a new package to introduce new algorithms? That there is a history related to the modelsummary package is fine, but I think the request is for references to published discussion of why modelsummary needed to be augmented with new algorithms. It seems to me tha

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

Educating package authors about the semantics of URLs is not really something the CRAN maintainers should have to do. A slash at the end of a URL implies different URL construction for relative URLs based on the original one. [1] I am not sure why you think https is no more secure than http... t

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

This is definitely not a false positive. Find a way to not run long calcs during the CRAN build. There is no alternative. One way this can be done is by only running your examples when an environment variable of your choosing exists. Since CRAN machines won't configure that variable, you can ge

Re: [R-pkg-devel] Issue handling datetimes: possible differences between computers

zones (UTC and local civil are a common combination). Again, character import and manual conversion are needed. On October 10, 2022 9:40:42 AM PDT, Hadley Wickham wrote: >On Sun, Oct 9, 2022 at 9:31 PM Jeff Newmiller wrote: >> >> ... which is why tidyverse functions and Python da

Re: [R-pkg-devel] Issue handling datetimes: possible differences between computers

... which is why tidyverse functions and Python datetime handling irk me so much. Is tidyverse time handling intrinsically broken? They have a standard practice of reading time as UTC and then using force_tz to fix the "mistake". Same as Python. On October 9, 2022 6:57:06 PM PDT, Simon Urbanek

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

It looks like you are reading directly from URLs? How do you know the delay is not network I/O delay? Parallel computation is not a panacea. It allows tasks _that are CPU-bound_ to get through the CPU-intensive work faster. You need to be certain that your tasks actually can benefit from parall

Re: [R-pkg-devel] Inquiry

If you haven't settled on exactly which approach you want to use in accomplishing the main goals of your exported package functions, then hiding the gory details can make it easier to tell people later to sod off when you decide those gory details functions should act different or use different

Re: [R-pkg-devel] Rlang and Code Evalutation Within Aesthetics

Things like sensible legends are also impeded by using complex expressions in aesthetics mappings, so call it a workaround if you like but creating the data frame the way it should be _before_ giving it to ggplot has always been recommended. On April 30, 2022 5:09:51 AM PDT, Duncan Murdoch wr

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

Thanks to the ubiquity of Excel and its misguided inclusion of BOM codes in its UTF-8 CSV format, this optimism about encoding being a corner case seems premature. There are actually multiple options in Excel for writing CSV files, and only one of them (not the first one fortunately) has this "f

Re: [R-pkg-devel] Is using global assignment in package tests allowed?

I don't know the answer to your question, but "beyond my ken" doesn't sound like a very convincing reason. Mucking with any environment that isn't yours is asking for trouble... the behavior you depend on today may come into conflict with the code you are coordinating with when you least expect

Re: [R-pkg-devel] socketConnection, delay when reading from

Google? https://developer.r-project.org/Blog/public/2020/03/17/socket-connections-update/ https://www.digitalocean.com/community/tutorials/understanding-sockets https://developer.ibm.com/tutorials/l-sockpit/ On November 27, 2021 2:36:48 PM PST, Ben Engbers wrote: >Hi, > >Looks promising! Where

Re: [R-pkg-devel] socketConnection, delay when reading from

Maybe time to learn it. At least to assemble complete messages. That said, the design of this protocol is intrinsically inefficient. Maybe they will upgrade if the software gets popular. On November 27, 2021 8:24:36 AM PST, Ben Engbers wrote: >Op 27-11-2021 om 17:03 schreef Jeff Newmil

Re: [R-pkg-devel] socketConnection, delay when reading from

This is a null-terminated message protocol [1]. It has to be processed one byte at a time. [1] https://docs.basex.org/wiki/Server_Protocol On November 27, 2021 7:45:31 AM PST, Gabor Grothendieck wrote: >Whether the length is variable or not isn't relevant. The point is >whether the message is

Re: [R-pkg-devel] Inconsistent available package dependencies

You should ALWAYS build with the latest stable AND the latest development versions of R before submitting. On November 15, 2021 6:33:12 PM PST, Michael Hellstern wrote: >Hi all, > >I maintain a package (netgsa) that has been on CRAN since september 2021 >and recently got an email about CRAN chec

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

Keep in mind that by embedding this decision into your package you may be consuming a resource (cores) that may be more efficiently allocated by an application-level partitioning. of available resources. I for one am not a fan of this kind of thinking, and it makes system requirements for your p

Re: [R-pkg-devel] Lists vs Attributes

Duncan has used the phrase "do regular operations on the object" to divide the use cases and emphasized that needing the attributes might be important, but he did not come out and remind you that if you _do_ perform regular operations on it then the outputs of those operations are likely to lose

Re: [R-pkg-devel] if statements in NAMESPACE file

way to identify a path, but if he covers all cases then my opinion is just an opinion. On September 30, 2021 2:34:48 PM PDT, Duncan Murdoch wrote: >On 30/09/2021 5:21 p.m., Jeff Newmiller wrote: >> What if you are on Windows but running R at the command prompt, or via >> cy

Re: [R-pkg-devel] if statements in NAMESPACE file

What if you are on Windows but running R at the command prompt, or via cygwin, or in the console window of RStudio? This seems unstable to me. On September 30, 2021 11:52:16 AM PDT, Andrew Simmons wrote: >Hello, > > >I'm updating my package 'this.path' which is supposed to retrieve the >absolu

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

Grace is in the eyes of the beholder. Using stop in your functions can be perfectly valid. But within the context of examples or tests you need to catch those errors because one key definition of success in normal building of a package is that no uncaught errors occur. So either don't call thos

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

I agree... but trouble is in the eyes of the beholder. If OP's approval process requires use of actively-maintained software, then use of code depending on one of these "retired"/"superceded" packages could indeed be a problem... for the OP. OP cannot expect to be able to impose those requiremen

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

ing hassled by is concerned about... not the label applied to that status. On September 21, 2021 8:50:32 AM PDT, "Lenth, Russell V" wrote: >... "I am not fixing this hot mess"??? To the contrary, the README contains a >clearly expressed intention to maintain plyr

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

There is nothing official about that term. However, the meaning as intended by the package authors seems pretty clear to me, and if some organization decides not to allow software that is not being maintained to be relied upon then that is their decision. I don't think slapping a different label

Re: [R-pkg-devel] NOTE related to Miniconda installation

I can't really see why it should be "recommended" to handle installing system requirements inside an R package. There are many ways to satisfy such requirements that would not involve miniconda. If you were determined to provide such support, doing so in a normal function documented in a vignett

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

This advice would apply if the errors were being generated on a computer under the package developer's control... but this looks like it is from a repo submission. That said, if the developer has installed packages not currently in BioC for R4.1.1 they may need to wait for those packages to pro

Re: [R-pkg-devel] Additional CRAN Checks

Exactly what errors do you think you found? It is not an error for a package to be compatible with a range of versions of R. On September 6, 2021 4:02:08 AM PDT, Colin Gillespie wrote: >Dear All, > >Sorry if this is the wrong mailing address. > >I was doing a little investigation of R versions

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

Spelling has different importance to different people. You are expressing a value judgement that differs from the values of R Core, but are presenting your opinion as if they are facts. My point is that your challenging attitude IMO makes having a conversation about those concerns difficult. (I

Re: [R-pkg-devel] Assignments to the global environment and use of on.exit

Just don't. E.g. https://stackoverflow.com/questions/12598242/global-variables-in-packages-in-r On June 22, 2021 1:47:56 AM PDT, Siddhanta Phuyal wrote: > Hello, > >A few weeks ago, I submitted a package to CRAN. The automated system >rejected the package showing the following note: > >Found th

Re: [R-pkg-devel] How to sent possible bug report to maintainer

This is a job for a detective, not a package developer mailing list participant. If this condition persists, CRAN will archive the package, as maintaining a valid email address is required. On June 18, 2021 5:29:20 PM PDT, mai zhou wrote: >Dear developers, > >I was trying to send an email to th

Re: [R-pkg-devel] Question about preventing CRAN package archival

non-free software tarpits, and transferring GPL2 code to MIT without the GPL2 author explicitly re-releasing as MIT would allow that. On June 2, 2021 11:51:01 PM PDT, Berwin A Turlach wrote: >G'day Jeff, > >On Wed, 02 Jun 2021 11:34:21 -0700 >Jeff Newmiller wrote: > >

Re: [R-pkg-devel] Question about preventing CRAN package archival

MIT is more permissive than GPL2, so there is a collision there. But you may be able to work it out with the author? On June 2, 2021 10:36:00 AM PDT, Ben Staton wrote: >My package uses the MIT license, so would that not meet the >compatibility >requirements? > >I will attempt to reach out to the

Re: [R-pkg-devel] \donttest{} and writing outputs to tempdir()

Make examples shorter so they can run faster. Wrapping everything in donttest means that running examples() does nothing, which is counterproductive. Techinically, vignettes are not tests or examples... but they do have the advantage that they don't have to run quickly. But that doesn't make a v

Re: [R-pkg-devel] Installed image not found in Debian

Why aren't you using system.file()? On May 11, 2021 1:45:37 PM PDT, Tiago Olivoto wrote: >Dear all, >I just submitted a new package 'pliman' ( >https://github.com/TiagoOlivoto/pliman) and it does not pass the >incoming >checks automatically. >I have some images that are under '/inst/tmp_images' t

Re: [R-pkg-devel] Package Vignette depends on Ensembl, server certificate issue?

Maybe use r.rsp? https://blog.r-hub.io/2020/06/03/vignettes/ How to include my pre-print / cheatsheet as a PDF vignette? On April 8, 2021 12:39:20 PM PDT, "Dr. Connie Brett" wrote: >Hello, >I have a package (DGEobj) that depends on the Ensembl service to look >up information used to build the

Re: [R-pkg-devel] Lazy data compression for packages without data folder

I don't think those settings apply to that file. Search for "sysdata.rda" in [1]. [1] https://cran.r-project.org/doc/manuals/r-release/R-exts.html On April 1, 2021 3:11:17 AM PDT, Peter Ruckdeschel wrote: >Hi, > >I just noticed that, last week-end, R CMD build was changed to remove >‘LazyDat

Re: [R-pkg-devel] Why .Rbuildignore doesn't ignore?

Don't run check against your development directory. Run it against the tar.gz file. On March 4, 2021 5:09:07 AM PST, Jose Barrera wrote: >Dear all, > >devtools::check() gives me the following NOTE: > >* Non-standard files/directories found at top level: > ‘README.Rmd’ ‘miclust.Rproj’ > >I ge

Re: [R-pkg-devel] Advice on R-forge to Github migration

Technically, git does not record file history... it records commit history, and reconstructs file history as needed. The contents of a file identify it uniquely among all commits ever made regardless of which directory it was ever in. IMO this is the main reason why git is superior and I put up

Re: [R-pkg-devel] Package used unconditionally only in testing

This is normally where the Suggests field is used. On January 8, 2021 6:17:58 AM PST, Greg Freedman Ellis wrote: >Hi all, > >I'm trying to update a package to conform to pass tests given >`_R_CHECK_DEPENDS_ONLY_=TRUE`. > >In this package, we only use the package `httptest` during testing, but >t

Re: [R-pkg-devel] Sweave vignette and bibtex

Sheepish grins may be good for character building, but MREs are good for solving problems. You can choose which you want first! ;-) On January 6, 2021 9:50:13 AM PST, Jarrod Hadfield wrote: >Dear Duncan and Michael, > >Thank you for the quick replies. When trying to generate a reproducible > >e

Re: [R-pkg-devel] Accessing features in R4.0.

For "obvious" reasons? I don't see this kind of avoidance as "obviously" correct at all. You have a dependency... it should be declared. There are various ways to proceed, with Imports or Depends or Suggests or pulling the code into your package... but trying to subvert the dependency management

Re: [R-pkg-devel] CRAN packages suggesting other packages but not using them conditionally

Examples should use dontrun to avoid calling functions that call stop. On December 12, 2020 8:24:50 AM PST, Michael L Friendly wrote: >I got the email below concerning 3 of my packages but wonder if they >are false alarms or >if not, how to locate & fix the problem. > >This concerns packages

Re: [R-pkg-devel] Conditional timeout for httr request when running R CMD check

Don't test against a live website for most of your testing... use recorded or simulated input. If your package functional interface doesn't allow for that, then re-factor it so it does. For those tests that actually have to interact with the live website, only run them if you know you are not o

Re: [R-pkg-devel] URLencode at DESCRIPTION file and citation()

Section 2.1 of the Writing R Extensions manual points out that percent symbols must (practically) always be escaped in Rd files. This includes within URLs. On November 3, 2020 2:08:05 AM PST, "Maëlle SALMON via R-package-devel" wrote: >Hello, > >1) I found (via GitHub search for DOIs in DESCRIP

Re: [R-pkg-devel] best practices for handling a mixed-licensed package

You are addressing interpretation of "a license", while my concern is not with the licenses themselves but with the identification of which code goes with which license. Assuming that you will need to retain lawyers to decide how to handle a license in a particular use case may be reasonable, bu

Re: [R-pkg-devel] best practices for handling a mixed-licensed package

Hadley offers what you _can_ do, but if you want clarity in the minds of _users_ I would beg you to split the code into two packages. People will likely either be afraid of the GPL bogey man and refrain from utilizing your MIT code as permitted or fail to honor the GPL terms correctly if both ar

Re: [R-pkg-devel] Use of `:::` in a package for code run in a parallel cluster

As Duncan said, if you are calling FROM a function in your package, and the function you are CALLING is in the same package, then you do NOT need any colons at all, whether exported or not. On September 14, 2020 7:30:12 AM PDT, "Wang, Zhu" wrote: >In mypkg, I want to call a function foo from pk

Re: [R-pkg-devel] failing on win and debian -- because of new submission?

I would not read anything into this. Does [1] help? [1] https://jef.works/blog/2018/06/18/get-your-package-on-cran-in-10-steps/ On September 12, 2020 1:58:15 PM PDT, Simit Patel wrote: >hello, > >  >i am submitting my first package for CRAN, but am failing pre-check on >windows and debian. below

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

If your article is published with a DOI and read by anyone actually interested in it then it will be likely be accessed, so "never" seems rather pessimistic of you. You could simply not argue with your editor and acquiesce. On September 10, 2020 9:14:12 AM PDT, "Kevin R. Coombes" wrote: >Hi,

Re: [R-pkg-devel] NOTE in r-devel-linux-x86_64-fedora-clang

The whole point of the Suggests package relationship is that you don't actually have to have it installed to use the package. It does have to be installed to check the package, which allows the link to be tested at least once before being released. On August 7, 2020 8:02:47 AM PDT, "Brian G. Pe

Re: [R-pkg-devel] Error in CHECK caused by dev.off()

I suspect your foo and bar variables are not logical anymore... insufficient info. However, why aren't you using short-circuit && and || operators? On July 22, 2020 5:36:06 AM PDT, "Helmut Schütz" wrote: >Dear all, > >I have two variables, foo and bar. The first is TRUE if a png should be > >cr

Re: [R-pkg-devel] [External] Re: Interpret feedback: not write testthat-tests in examples

Looks like 187 opportunities to improve clarity. On July 16, 2020 11:30:37 AM PDT, Ben Bolker wrote: >FWIW/in defense of the OP, this is a *very* common idiom in the base R >code base.  There may be some false positives, but > > find . -name "*.Rd" -exec grep -Fl "stopifnot(" {} \; | grep -v doc

Re: [R-pkg-devel] Interpret feedback: not write testthat-tests in examples

The point of an example is to provide an illustration of how the function should be used for people who are not software developers. IMO any use of any other functions should be absolutely minimized to reduce the cognitive overload ("you need to understand 13 other concepts before you can unders

Re: [R-pkg-devel] Getting two independent packages with identical S3 generics to dispatch each other's methods

Perhaps: https://cran.r-project.org/web/packages/generics/index.html On July 10, 2020 4:51:52 PM PDT, "Pavel N. Krivitsky" wrote: >Dear All, > >I would like to have two packages that do not depend on each other that >have an identical generic to be able to dispatch to each other's (non- >confl

Re: [R-pkg-devel] data and load version 3

Your choice. Do you want to support people using older versions of R, or not? On June 29, 2020 1:55:02 PM PDT, "Göran Broström" wrote: >I added two data sets (.rda) to my package eha, but when I build the >new >version I get: > > WARNING: Added dependency on R >= 3.5.0 because serialized objects

Re: [R-pkg-devel] package CatDataAnalysis

t;Wiley >says. > >So like I said in my original posting, good idea in an alternative >universe >where copyright law does not exist. > >On Sun, Jun 28, 2020 at 1:13 PM Jeff Newmiller > >wrote: > >> Just describe the nature of the data sets literally as though the >

Re: [R-pkg-devel] package CatDataAnalysis

Just describe the nature of the data sets literally as though the book was inaccessible. They are not asking you to describe how one should analyze the the data, so there really shouldn't be any conflict with the book content that your agreement with the author has not already resolved. If you

Re: [R-pkg-devel] Problem with test data folder. R package develpoment

Use a different name than "data" such as "rawdata" within "inst" to put files that your code refers to using the system.name() function. The directory name "data" is used for a specific purpose as described in the Writing R Extensions manual [1], and if you want to put files in that directory fo

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

license. If there is a >term >which reflects that mechanism from a discipline other than biology, >please let me know. > >Thanks, > >Avi > >On Tue, Jun 2, 2020 at 8:25 PM Jeff Newmiller > >wrote: > >> "Viral" is has connotations that reflect the

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

"Viral" is has connotations that reflect the biases of the person using the term. A less loaded perspective is that some people don't want you to take their contributions out of circulation by using it as the foundation of your proprietary work. If you want to close it up, build from scratch or

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