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 the

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' t

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 v

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 the

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

2021-06-03 Thread Jeff Newmiller
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] 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 th

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 th

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] 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] 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 pro

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 vignett

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 label

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

2021-09-21 Thread Jeff Newmiller
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] [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 requiremen

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 thos

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 >absolu

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

2021-09-30 Thread Jeff Newmiller
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] 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 lose

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 p

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 chec

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] 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
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] 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] 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 "f

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 wr

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] 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 parall

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 Urbanek

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] 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 ge

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... t

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 tha

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 see

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 to

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 jun

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 wr

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 >https://github.com/

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 expe

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

2023-08-23 Thread Jeff Newmiller
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] Re-building vignettes had CPU time 9.2 times elapsed time

2023-08-25 Thread Jeff Newmiller
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] 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] 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 n

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 promotes

Re: [R-pkg-devel] NOTE for a suggested package

2019-02-23 Thread Jeff Newmiller
Remove the library function call... On February 23, 2019 3:43:15 PM PST, Mohammad Ali Nilforooshan wrote: >I'm struggling to stop receiving a NOTE about a suggested package, and >it >seems to be the problem for many people. Your help is really >appreciated. > >In the function, I have: > >if(requ

Re: [R-pkg-devel] problems with .mod files

2019-02-28 Thread Jeff Newmiller
Don't run R CMD check against your working directory... only run it against your tar.gz source file. The devtools package will do this for you automatically from within R for convenience. On February 28, 2019 4:50:18 AM PST, "Rampal S. Etienne" wrote: >Dear Remi, > >The mod files are not in th

Re: [R-pkg-devel] regarding solution of these warning and note

2019-03-03 Thread Jeff Newmiller
Do you have a question? If so, please read the Posting Guide and follow its recommendations. (e.g. What did you do to trigger these errors in enough detail that we could trigger them? What is your desired outcome?) On March 3, 2019 1:11:45 PM PST, Krishan Gupta wrote: >Original: no visible bind

Re: [R-pkg-devel] Calls not declared

2019-03-11 Thread Jeff Newmiller
I did not see any mention of the distinction between Depends and Imports in the DESCRIPTION file... which is always a risk when duplicating existing documentation in an email. Imports is preferred because the user does not have to put definitions only needed inside your package into their public

Re: [R-pkg-devel] Calls not declared

2019-03-11 Thread Jeff Newmiller
0:07:12 AM PDT, Duncan Murdoch wrote: >On 11/03/2019 11:32 a.m., Jeff Newmiller wrote: >> I did not see any mention of the distinction between Depends and >Imports in the DESCRIPTION file... which is always a risk when >duplicating existing documentation in an email. Imports is pr

Re: [R-pkg-devel] Re :Re: Re :Re: Re :Re: package cartograflow_0.0.0.9000.tar.gz

2019-04-07 Thread Jeff Newmiller
don't you think other.ot...@gmail.com is inappropriate? On April 7, 2019 12:01:59 PM PDT, "cartograf...@gmail.com" wrote: >Thanks!So, I've already check and I didn't see the descrption of the >note in 00check.log.The only thing I can say is that there's a problem >with Author. >I tried to put Au

Re: [R-pkg-devel] read-only mirror of the CRAN R package repository on GitHub

2019-04-11 Thread Jeff Newmiller
I don't think "CRAN" (R Core) _ever_ did this... it was a volunteer effort by someone independently. On April 11, 2019 4:16:47 PM PDT, Mohammad Ali Nilforooshan wrote: >Hi, > >In the past, there were read-only mirrors of the CRAN R packages on >GitHub >(i.e., https://github.com/cran/). >I cann

Re: [R-pkg-devel] long file names in tar

2019-04-18 Thread Jeff Newmiller
You could go down this rabbit hole if you like, but I suspect it has something to do with maintaining compatibility with multiple operating systems and I doubt R Core will explore the consequences of this change for you. Windows, for example, allows long file names but has some nasty corners tha

Re: [R-pkg-devel] Writing to files without altering working directory in R package

2019-05-06 Thread Jeff Newmiller
You cannot go littering the user directories with sample files. Such examples would have to be dontrun, but in order to make some of the example runnable as is you would also need examples that use system.file paradigm. If you store the temporary file name in a variable then the user can retriev

Re: [R-pkg-devel] Writing to files without altering working directory in R package

2019-05-07 Thread Jeff Newmiller
I find the idea of using setwd in examples disturbing, because I try to avoid using setwd at all as a way to delegate my choice of working directory to the operating system actions taken when starting R. In other words, I recommend to beginners that they start R in their working directory and l

Re: [R-pkg-devel] noL

2019-05-16 Thread Jeff Newmiller
It pays to read the archives before posting https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003941.html On May 16, 2019 6:31:19 AM PDT, "Goldfeld, Keith" wrote: >Good morning - > >I have one final issue that is preventing me from a successful >submission of my package simstudy to CRAN

Re: [R-pkg-devel] note

2019-06-04 Thread Jeff Newmiller
Regarding the global variables... I found [1] illuminating, in particular the comments on the solution. [1] https://stackoverflow.com/questions/41954302/where-to-create-package-environment-variables On June 4, 2019 11:07:20 AM PDT, Duncan Murdoch wrote: >On 04/06/2019 8:36 a.m., Bernd JAGLA

Re: [R-pkg-devel] try() in R CMD check --as-cran

2019-06-07 Thread Jeff Newmiller
>> any(is.infinite(fval)) || any(is.na(fval)) > >a little typo here: it should be '|', not '||', right ? Since `any` collapses the vectors to length 1 either will work, but I would prefer `||`. On June 7, 2019 6:51:29 AM PDT, Serguei Sokol wrote: >On 07/06/2019 15:31, Sebastian Meyer wrote: >>

Re: [R-pkg-devel] Link compiled C object to internal package file

2019-06-19 Thread Jeff Newmiller
What do you mean by "call an external text file" ? Text files are data... do you want to open it and read it? Are you familiar with the system.file() function? On June 19, 2019 5:45:51 AM CDT, mark padgham wrote: >Dear All, > >I'm developing a package which primarily relies on C code that its

Re: [R-pkg-devel] access is denied

2019-06-20 Thread Jeff Newmiller
I have not had much luck doing package development on network drives. Try using a local drive. On June 20, 2019 11:26:42 AM CDT, Tomas Kalibera wrote: >If you have not already done so, I'd check the package directory (and >its parent) is not opened in any application, including Windows >Explo

Re: [R-pkg-devel] The correct way to put additional DLLs on windows?

2019-07-01 Thread Jeff Newmiller
A) You cannot assume the package code will have write access to the library directories. The user/admin who installs the package may never load the package. B) Downloading binary files for execution without the direct involvement of the user/admin is a security risk. C) Open-source package lice

Re: [R-pkg-devel] CRAN-compatible location for output of example code?

2019-07-04 Thread Jeff Newmiller
https://stat.ethz.ch/R-manual/R-devel/library/base/html/tempfile.html ?tempdir On July 4, 2019 3:25:25 PM PDT, Michael Gruenstaeudl wrote: >Assume an R package that generates a figure ('output.pdf') as the >result >of executing the example code specified in one of the manual files >(i.e. >an

[R-pkg-devel] Block quote in an Rd file?

2019-07-04 Thread Jeff Newmiller
Not seeing in "Writing R Extensions" a way to annotate a block quote in an Rd file. Any suggestions? -- Sent from my phone. Please excuse my brevity. __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Block quote in an Rd file?

2019-07-04 Thread Jeff Newmiller
Ehh... not that much. Will make do with a couple of quote marks. Thanks for the confirmation. On July 4, 2019 5:48:56 PM PDT, Duncan Murdoch wrote: >On 04/07/2019 7:43 p.m., Jeff Newmiller wrote: >> Not seeing in "Writing R Extensions" a way to annotate a block quote

Re: [R-pkg-devel] "Progress reports" for examples in packages --- SOLVED.

2019-07-06 Thread Jeff Newmiller
This is why I only put localization variables in .Rprofile and am always putting such options into my project-specific scripts. This may sound like I am a masochist, but I hate sharing my scripts with someone else contaminated with compatibility bombs like that. On July 6, 2019 8:19:27 PM PDT,

Re: [R-pkg-devel] Example fails in check

2019-07-26 Thread Jeff Newmiller
Pipes are very functional, unlike data.table. However, their extensive use of non-standard evaluation a la `subset` or `with` does complicate the package check process. As to the actual question, Imports announces that the magrittr package is a private dependency for your package. Users would h

Re: [R-pkg-devel] NAMESPACE issue and grDevices

2019-08-24 Thread Jeff Newmiller
I think yes. If a direct user of graphics opted not to call smoothScatter then they would have no need to even install KernSmooth. However, since generics automatically trigger loading of class-specific methods, one of which in your case includes that dependency, your package cannot avoid at lea

Re: [R-pkg-devel] URL of a frame (or a vignette)?

2019-09-01 Thread Jeff Newmiller
Wouldn't you just refer to [1] or one of the links mentioned there? [1] https://cran.r-project.org/package=bssm On September 1, 2019 7:22:43 AM PDT, Spencer Graves wrote: >Hello: > > >   How can I get a URL for a frame? > > >   Specifically, I want a URL that I can cite for the "bssm:

Re: [R-pkg-devel] URL of a frame (or a vignette)?

2019-09-01 Thread Jeff Newmiller
On >Behalf Of Georgi Boshnakov >Sent: 01 September 2019 15:57 >To: Spencer Graves; Jeff Newmiller; r-package-devel@r-project.org >Subject: Re: [R-pkg-devel] URL of a frame (or a vignette)? > >It may be better to use the canonical url, >https://cran.r-project.org/package=bssm, as in:

Re: [R-pkg-devel] URL of a frame (or a vignette)?

2019-09-01 Thread Jeff Newmiller
I don't know if [1] implies vignette persistence after archiving, but it might. I think it just has to fall back to a warning with an archive link to qualify. (Quite a slick trick if so because there can potentially be a parade of different package vignettes over time.) [1] https://stat.ethz.ch

Re: [R-pkg-devel] meta-question

2019-09-07 Thread Jeff Newmiller
I don't think this list is only for questions about submitting to CRAN, but it is specific to writing packages for R. If your question could just as easily apply to another language then you probably ought to ask elsewhere. Perhaps https://softwareengineering.stackexchange.com/help/on-topic ? On

Re: [R-pkg-devel] What counts as an API change?

2019-09-25 Thread Jeff Newmiller
Both of your examples are incompatible. foo <- function (a, b, c, d, e = NA ) (add with default value) would be compatible. Your second example cannot be made compatible even with default values because the positional behaviour has changed. On September 25, 2019 6:51:58 AM PDT, David Hugh-Jone

Re: [R-pkg-devel] What counts as an API change?

2019-09-25 Thread Jeff Newmiller
ate the force of the idea that an API >change >is an API change, and should be defined precisely. > >Best, >David > > >On Wed, 25 Sep 2019 at 15:01, Jeff Newmiller >wrote: > >> Both of your examples are incompatible. >> >> foo <- function (a, b, c,

Re: [R-pkg-devel] What counts as an API change?

2019-09-25 Thread Jeff Newmiller
ts, given the position of ... . So maybe this is my get >out of >jail free card. If I add "fill", existing function calls won't break, >and I >can call this "adding functionality in a backwards-compatible manner". > >David > > >On Wed, 25 Sep 2

Re: [R-pkg-devel] Fwd: Passing CRAN check when an examples must save a file

2019-09-27 Thread Jeff Newmiller
Read the Posting Guide... sending html formatted email corrupts your message. Reading between the garbage... a) Pasting an extension is not necessary. b) using tempfile() in your example as an argument to sink( file=) is a straightforward way to illustrate that a file can be created. On Septemb

Re: [R-pkg-devel] Seeking for best way to manage package transitive dependencies

2019-10-10 Thread Jeff Newmiller
Seems quite clear to me. If dplyr chooses to re-implement pipes (e.g. based on [1]) then you should not be importing from magrittr unless you had a specific reason to, and if you do then you should not make assumptions about where the dplyr pipe came from. [1] https://github.com/moodymudskipper

Re: [R-pkg-devel] winbuilder fails for package depending on rJava

2019-10-29 Thread Jeff Newmiller
I suspect David did not read the subject line. This is about winbuilder [1]. I don't know who runs that service (Uwe?), but this sounds like they need to investigate. [1] https://win-builder.r-project.org/ On October 29, 2019 9:28:23 AM PDT, David Winsemius wrote: > >On 10/29/19 4:48 AM, Kevi

Re: [R-pkg-devel] winbuilder fails for package depending on rJava

2019-10-29 Thread Jeff Newmiller
Once again, you can color me mystified. Are you reading logs not referred to in this email thread? On October 29, 2019 12:28:59 PM PDT, David Winsemius wrote: > >On 10/29/19 12:22 PM, Jeff Newmiller wrote: >> I suspect David did not read the subject line. This is about >winbuild

Re: [R-pkg-devel] winbuilder fails for package depending on rJava

2019-10-29 Thread Jeff Newmiller
wrote: > >On 10/29/19 2:12 PM, Jeff Newmiller wrote: >> Once again, you can color me mystified. Are you reading logs not >referred to in this email thread? > >Hi Jeff; > >I suppose am reading else. I ran: > >maintainer("rJava") > > >... a

Re: [R-pkg-devel] How to Document and S3 Method for the Parenthesis Class?

2019-11-07 Thread Jeff Newmiller
There are three types of quoting in R... " and ' are for strings, and ` (backtick) is for symbols. On November 7, 2019 6:35:49 AM PST, b...@denney.ws wrote: >Hi, > > > >Short version of the question: How does one document a method for the >"(" >class in a .Rd file? > > > >Details: > >I recentl

Re: [R-pkg-devel] How to Document and S3 Method for the Parenthesis Class?

2019-11-07 Thread Jeff Newmiller
\\@" <- 1 > >(This is selected to show how bad things can be done-- not as an >example to advocate.) > >-Original Message- >From: Jeff Newmiller >Sent: Thursday, November 7, 2019 10:43 AM >To: r-package-devel@r-project.org; b...@denney.ws >Subject: Re:

Re: [R-pkg-devel] Including in my vignette a figure drawn outside R

2019-12-03 Thread Jeff Newmiller
You could use DiagrammeR. On December 3, 2019 7:36:19 AM PST, Michael Dewey wrote: >I am planning to include a flow-chart in the vignette of one of my >packages (metap). I am planning to draw it using dot from Graphviz. I >know that there is Rgraphviz which would do the whole thing in R but I

Re: [R-pkg-devel] New Package olr 4 NOTES

2019-12-05 Thread Jeff Newmiller
I have not had good luck building packages for final delivery using devtools... use the command line, Luke! On December 5, 2019 7:40:46 AM PST, Mat Fok via R-package-devel wrote: >Hi Max, >Following your comment about, ".Rbuildignore is used by R CMD build to >exclude some files from the bundle

Re: [R-pkg-devel] pandoc lua filter error with win devel check

2020-01-06 Thread Jeff Newmiller
Pandoc is not part of the standard R documentation tooling... you must be doing something special, and doing something special makes getting a package accepted more challenging. Perhaps if you were more specific you might get a more specific response. On January 6, 2020 1:38:44 PM PST, Fernando

Re: [R-pkg-devel] For reproducibility issue

2020-01-17 Thread Jeff Newmiller
As an existing package I suspect that it already calls the R RNG, but the default RNG changed [1] so you need to call RNGkind(sample.kind = "Rounding") before calling set.seed in your test code to compare with old results. [1] https://stackoverflow.com/questions/47199415/is-set-seed-consistent-

Re: [R-pkg-devel] Optional library dependencies for compiled code

2020-01-29 Thread Jeff Newmiller
Complex system dependencies are not cleanly handled by the R packaging system, but Suggesting other packages is. You could create or re-use an existing package for each external dependency and possibly even let the user specify which one they want to your dependent package the way DBI handles da

Re: [R-pkg-devel] Warning: parse error in file 'Rraven-Ex.R'

2020-02-04 Thread Jeff Newmiller
In your examples. On February 4, 2020 5:53:08 PM PST, Marcelo Araya Salas wrote: >Hi all > >I got this error from CRAN tests: > >Warning: parse error in file 'Rraven-Ex.R': >'\.' is an unrecognized escape in character string starting ""\." > >However, I can't find the original file where the err

Re: [R-pkg-devel] Private S3 Method not Found

2020-02-17 Thread Jeff Newmiller
I don't think it is possible to avoid exporting S3 methods from a package and still have the class behave as intended. Use a regular function if name encapsulation is important to you. On February 17, 2020 8:33:30 AM PST, b...@denney.ws wrote: >Thanks for the pointer! Adding >"S3method(knit_pri

Re: [R-pkg-devel] First R package, want to release to CRAN, have some questions about R CMD check and README.md

2020-03-07 Thread Jeff Newmiller
README.md is a github convention... do not try to treat it like part of the R package documentation. Instead, list it in your .Rbuildignore file and use it to inform developers how to change the package and to direct (potential) users browsing the GitHub repo to read the more conventional R docu

Re: [R-pkg-devel] First R package, want to release to CRAN, have some questions about R CMD check and README.md

2020-03-07 Thread Jeff Newmiller
> >Appreciate the help! > >On Sat, Mar 7, 2020 at 1:55 PM Jeff Newmiller > >wrote: > >> README.md is a github convention... do not try to treat it like part >of >> the R package documentation. Instead, list it in your .Rbuildignore >file >> and use it to i

Re: [R-pkg-devel] First R package, want to release to CRAN, have some questions about R CMD check and README.md

2020-03-07 Thread Jeff Newmiller
very nice to >have. > >I'm not sure what the error you are seeing is, but having README on >CRAN is >nice. > >Have you .Rbuildignore 'd README.Rmd?? That should be ignored if I >remember >correctly. > >-Robert > >On Sat, Mar 7, 2020, 5:55 PM Jeff Newmille

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

2020-03-08 Thread Jeff Newmiller
You seem to think this is a bad thing. R does encourage lenient argument checking... what rock have you been under for the last 20 years? On March 8, 2020 5:41:51 AM PDT, David Hugh-Jones wrote: >You're quite right :-) But I think the polemic still holds, because I >have >to add manual argument

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

2020-03-08 Thread Jeff Newmiller
the form: > >@param ... Not used. > >Cheers, >David > > >On Sun, 8 Mar 2020 at 16:24, Jeff Newmiller >wrote: > >> You seem to think this is a bad thing. R does encourage lenient >argument >> checking... what rock have you been under for the last 20 ye

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-depend

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

2020-03-09 Thread Jeff Newmiller
case should inherit 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 New

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 or

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 propos

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 “dat

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

2020-04-07 Thread Jeff Newmiller
n simply prints the 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-fr

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 t

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 pack

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