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

2024-03-07 Thread Jeff Newmiller via R-package-devel
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

2024-03-05 Thread Jeff Newmiller via R-package-devel
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

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

2024-02-08 Thread Jeff Newmiller via R-package-devel
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

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

2024-02-03 Thread Jeff Newmiller via R-package-devel
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,

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

2023-12-13 Thread Jeff Newmiller via R-package-devel
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

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

2023-12-13 Thread Jeff Newmiller via R-package-devel
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

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

2023-11-07 Thread Jeff Newmiller via R-package-devel
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

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

2023-11-03 Thread Jeff Newmiller via R-package-devel
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

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

2023-10-31 Thread Jeff Newmiller via R-package-devel
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

2023-10-22 Thread Jeff Newmiller via R-package-devel
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

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

2023-10-09 Thread Jeff Newmiller via R-package-devel
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

2023-09-26 Thread Jeff Newmiller via R-package-devel
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,

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

2023-09-24 Thread Jeff Newmiller via R-package-devel
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?

2023-09-24 Thread Jeff Newmiller via R-package-devel
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

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

2023-09-21 Thread Jeff Newmiller via R-package-devel
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,

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

2023-09-21 Thread Jeff Newmiller via R-package-devel
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

2023-09-13 Thread Jeff Newmiller via R-package-devel
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

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

2023-09-06 Thread Jeff Newmiller
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

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

2023-09-02 Thread Jeff Newmiller
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

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

2023-08-25 Thread Jeff Newmiller
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] Trouble with long-running tests on CRAN debian server

2023-08-23 Thread Jeff Newmiller
performing 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 mis

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

2023-08-23 Thread Jeff Newmiller
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

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

2023-07-12 Thread Jeff Newmiller
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

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

2023-06-29 Thread Jeff Newmiller
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

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

2023-06-27 Thread Jeff Newmiller
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

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

2023-05-16 Thread Jeff Newmiller
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

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

2023-01-22 Thread Jeff Newmiller
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

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

2022-12-16 Thread Jeff Newmiller
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

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

2022-11-28 Thread Jeff Newmiller
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...

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

2022-10-28 Thread Jeff Newmiller
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

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

2022-10-10 Thread Jeff Newmiller
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

2022-10-09 Thread Jeff Newmiller
... 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

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

2022-10-04 Thread Jeff Newmiller
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

Re: [R-pkg-devel] Inquiry

2022-09-27 Thread Jeff Newmiller
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

2022-04-30 Thread Jeff Newmiller
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

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

2022-04-05 Thread Jeff Newmiller
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

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

2022-01-27 Thread Jeff Newmiller
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

2021-11-27 Thread Jeff Newmiller
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!

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

2021-11-27 Thread Jeff Newmiller
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

2021-11-27 Thread Jeff Newmiller
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

2021-11-15 Thread Jeff Newmiller
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

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

2021-10-09 Thread Jeff Newmiller
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

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

2021-10-01 Thread Jeff Newmiller
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

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

2021-09-30 Thread Jeff Newmiller
as a 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

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

2021-09-30 Thread Jeff Newmiller
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

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

2021-09-24 Thread Jeff Newmiller
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

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

2021-09-21 Thread Jeff Newmiller
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

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

2021-09-21 Thread Jeff Newmiller
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 to keep in on C

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

2021-09-21 Thread Jeff Newmiller
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

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

2021-09-17 Thread Jeff Newmiller
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

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

2021-09-11 Thread Jeff Newmiller
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

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

2021-09-07 Thread Jeff Newmiller
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

2021-07-16 Thread Jeff Newmiller
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

2021-06-22 Thread Jeff Newmiller
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

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

2021-06-18 Thread Jeff Newmiller
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

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

2021-06-03 Thread Jeff Newmiller
for their 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: > >Not

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

2021-06-02 Thread Jeff Newmiller
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

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

2021-06-01 Thread Jeff Newmiller
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

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

2021-05-11 Thread Jeff Newmiller
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'

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

2021-04-09 Thread Jeff Newmiller
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

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

2021-04-01 Thread Jeff Newmiller
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

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

2021-03-04 Thread Jeff Newmiller
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

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

2021-01-31 Thread Jeff Newmiller
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

2021-01-08 Thread Jeff Newmiller
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

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

2021-01-06 Thread Jeff Newmiller
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 >

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

2020-12-16 Thread Jeff Newmiller
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

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

2020-12-12 Thread Jeff Newmiller
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

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

2020-11-30 Thread Jeff Newmiller
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

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

2020-11-03 Thread Jeff Newmiller
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

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

2020-10-03 Thread Jeff Newmiller
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,

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

2020-10-02 Thread Jeff Newmiller
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

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

2020-09-14 Thread Jeff Newmiller
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

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

2020-09-12 Thread Jeff Newmiller
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.

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

2020-09-10 Thread Jeff Newmiller
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:

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

2020-08-07 Thread Jeff Newmiller
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.

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

2020-07-22 Thread Jeff Newmiller
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 >

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

2020-07-16 Thread Jeff Newmiller
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

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

2020-07-16 Thread Jeff Newmiller
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

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

2020-07-10 Thread Jeff Newmiller
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-

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

2020-06-29 Thread Jeff Newmiller
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

Re: [R-pkg-devel] package CatDataAnalysis

2020-06-28 Thread Jeff Newmiller
t;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 >book was

Re: [R-pkg-devel] package CatDataAnalysis

2020-06-28 Thread Jeff Newmiller
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

2020-06-14 Thread Jeff Newmiller
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

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

2020-06-02 Thread Jeff Newmiller
r copyleft 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

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

2020-06-02 Thread Jeff Newmiller
"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

Re: [R-pkg-devel] R_MAKEVARS_USER fail to pass down to sub-makes?

2020-06-01 Thread Jeff Newmiller
AGS. >b) Syntax passed checkbashisms so I expect no problems due to that. > >On Mon, Jun 1, 2020 at 4:03 PM Jeff Newmiller > wrote: >> >> I don't know anything about the function of that environment >variable, but >> >> a) system() invokes a child process so

Re: [R-pkg-devel] R_MAKEVARS_USER fail to pass down to sub-makes?

2020-06-01 Thread Jeff Newmiller
I don't know anything about the function of that environment variable, but a) system() invokes a child process so environment variable changes made using it will only affect the child process created by that system call. b) The syntax you have used is shell-specific, so does not look portable.

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

2020-05-25 Thread Jeff Newmiller
Sorry, ESP not working today. Note that this list may or may not include the reviewer who last checked your submission. Perhaps re-read [1] and if you are still puzzled then consider pointing us to (or pasting into the body of the email) the DESCRIPTION file you are having difficulty with so

Re: [R-pkg-devel] Problems importing packages with SystemRequirements

2020-04-28 Thread Jeff Newmiller
Maybe your use of those packages represent use cases that are not tested by those packages. If you pare down your code that triggers these problems to small reproducible examples then you can contribute them to those packages? On April 27, 2020 11:05:49 PM PDT, fvaf...@mailbox.org wrote: >Dear

Re: [R-pkg-devel] /usr/bin/ld: cannot find -ludev

2020-04-26 Thread Jeff Newmiller
This is a highly OS-specific dependency. Are you sure you need this? Is it listed in your SystemRequirements entry in your DESCRIPTION file? On April 26, 2020 6:41:27 AM PDT, "Sameh M. Abdulah" wrote: >I am getting this error when trying to install my package on CRAN. Do I >need to contact

Re: [R-pkg-devel] Detritus in temp directory - Note from submission of R package in CRAN

2020-04-18 Thread Jeff Newmiller
I agree that my example was not optimal, but I was trying to duplicate the existing behaviour with the exception of use of global variables. On April 18, 2020 3:02:17 PM PDT, Duncan Murdoch wrote: >On 18/04/2020 5:55 p.m., Jeff Newmiller wrote: >> See below: >> >> On Sa

Re: [R-pkg-devel] Detritus in temp directory - Note from submission of R package in CRAN

2020-04-18 Thread Jeff Newmiller
olombia, Bogot? phone: +571 3165000 ext 13406 address: Av. NQS (Carrera 30) # 45-03, Hydraulics Lab (408-213) email: dazamo...@unal.edu.co [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-packa

Re: [R-pkg-devel] Appropriate keyword in help file.

2020-04-16 Thread Jeff Newmiller
You can get away with a lot if you are not distributing your package. But I usually try to satisfy R CMD check at least. On April 16, 2020 5:50:04 PM PDT, Rolf Turner wrote: > >On 17/04/20 12:14 pm, Duncan Murdoch wrote: > >> On 16/04/2020 8:12 p.m., Rolf Turner wrote: >>> >>> I'm writing a

Re: [R-pkg-devel] Add SystemRequirements of imported package in description file?

2020-04-09 Thread Jeff Newmiller
AFAIK, no, though if the upstream package cannot (or won't) be implemented without that system requirement and it really is a requirement for this package then you might want to indicate "libzzz via Package X" just to be clear for users. If it isn't a requirement for most of your functionality

Re: [R-pkg-devel] [FWD] [CRAN-pretest-archived] CRAN submission JuliaConnectoR 0.5.0

2020-04-07 Thread Jeff Newmiller
output on the command line. > > >ursprüngliche Nachricht- >Von: Jeff Newmiller [jdnew...@dcn.davis.ca.us] >An: r-package-devel@r-project.org, Duncan Murdoch >[murdoch.dun...@gmail.com], Stefan Lenz IMBI >[l...@imbi.uni-freiburg.de] >Datum

Re: [R-pkg-devel] About dataset in my own package

2020-04-07 Thread Jeff Newmiller
Either use the data() function to retrieve it or use the LazyData: true line in your DESCRIPTION file. On April 6, 2020 11:25:21 PM PDT, jared_wood wrote: >Dear all, > >I have three datasets (drugbank.rda edgar.rda mala.rda) in my package >and I put them in the document folder which called

Re: [R-pkg-devel] [FWD] [CRAN-pretest-archived] CRAN submission JuliaConnectoR 0.5.0

2020-04-06 Thread Jeff Newmiller
One could take the position that the library and require functions were a mistake to begin with and that all contributed packages should be accessed using ::... or one could recognize that these functions are an expected feature of R at this point and then it is not defensible to ban the

Re: [R-pkg-devel] packaging biosig for R

2020-03-15 Thread Jeff Newmiller
I am just a lurker (not representing CRAN) but I am having a hard time understanding your question. Binary packages are a convenience for users, not a method for submitting packages. When you have an R package accepted it is accepted in source format. If it doesn't exclude support for Windows

Re: [R-pkg-devel] [EXTERNAL] Re: slightly polemic question re R CMD check

2020-03-09 Thread Jeff Newmiller
from >the general, so that an lm is a glm, not a glm is an lm. It's way too >late to change this now, of course. > > >-Original Message- >From: R-package-devel On Behalf >Of David Hugh-Jones >Sent: Sunday, 8 March 2020 6:28 PM >To: Jeff Newmiller >Cc: R pac

Re: [R-pkg-devel] slightly polemic question re R CMD check

2020-03-08 Thread Jeff Newmiller
argument then we are back into the generic conundrum again and the user will experience the normal function failing to catch unused arguments. On March 8, 2020 10:14:49 AM PDT, Jeff Newmiller wrote: >R encourages the use of ... particularly in S3 generics, to avoid >over-dep

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