Re: [R-pkg-devel] C++11 requirements for package dependencies

2020-11-30 Thread Duncan Murdoch
On 30/11/2020 11:54 a.m., Duncan Murdoch wrote: On 30/11/2020 11:31 a.m., Dirk Eddelbuettel wrote: On 30 November 2020 at 11:27, Duncan Murdoch wrote: | I think that C++11 isn't a requirement of RcppArmadillo, it's an option It is as of the 10.* series of Armadillo and hence RcppArmadillo

Re: [R-pkg-devel] C++11 requirements for package dependencies

2020-11-30 Thread Duncan Murdoch
On 30/11/2020 11:31 a.m., Dirk Eddelbuettel wrote: On 30 November 2020 at 11:27, Duncan Murdoch wrote: | I think that C++11 isn't a requirement of RcppArmadillo, it's an option It is as of the 10.* series of Armadillo and hence RcppArmadillo 0.10.* I was going to complain that you should

Re: [R-pkg-devel] C++11 requirements for package dependencies

2020-11-30 Thread Duncan Murdoch
package did that, even though it isn't a system requirement for RcppArmadillo. But I could be wrong about this... Duncan Murdoch On 30/11/2020 11:06 a.m., Mark Clements wrote: [Apologies for cross-posting] A colleague uses a package I maintain (rstpm2) as a dependency in their package

Re: [R-pkg-devel] devtools::release() does not release

2020-11-26 Thread Duncan Murdoch
Why not use the CRAN submission web page, as documented here: https://cran.r-project.org/web/packages/policies.html#Submission? Duncan Murdoch On 26/11/2020 2:57 p.m., Gábor Csárdi wrote: Why not submit a bug report at the devtools repository? ❯ packageDescription("devtools")$Bug

Re: [R-pkg-devel] Failing vignette engine for package rasciidoc on solaris

2020-11-23 Thread Duncan Murdoch
d to build the vignette. This is described in Section 1.6, "Writing portable packages", of Writing R Extensions. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Having shiny as an optional dependency

2020-11-16 Thread Duncan Murdoch
ires those packages in the requireNamespace test. - Make sure your example code in help pages never calls that function unless shiny and shinyjqui are present, by a test similar to the above but a positive one: if (requireNamespace("shiny") && requireNamespace("shinyjqui&qu

Re: [R-pkg-devel] Error in loadNamespace(x) : there is no package called 'formatR'

2020-11-13 Thread Duncan Murdoch
On 13/11/2020 4:32 p.m., Gábor Csárdi wrote: On Fri, Nov 13, 2020 at 9:02 PM Duncan Murdoch wrote: [...] Things may have changed since Henrik and I wrote the code, but his description matches my understanding as well (and I think he's contributed more recently than I have). The way non-Sweave

Re: [R-pkg-devel] Error in loadNamespace(x) : there is no package called 'formatR'

2020-11-13 Thread Duncan Murdoch
clude rmarkdown and formatR, since they may not be explicitly used. Then putting them in the VignetteBuilder field will trigger an error if they are not also in Suggests. Duncan Murdoch My understanding is that R CMD build (and possibly other commands/functions as well) checks fo

Re: [R-pkg-devel] Import package countreg that is not on CRAN

2020-11-13 Thread Duncan Murdoch
ars, if at all. /Henrik On Fri, Nov 13, 2020 at 3:23 AM Duncan Murdoch wrote: On 13/11/2020 3:10 a.m., Jason Luo wrote: Hi, I'm submitting a new package (https://github.com/Penncil/pda/) to CRAN. It relies on some function (zerotrunc and hurdle in R/ODAP.R) from countreg ( https://rdrr.io/r

Re: [R-pkg-devel] Import package countreg that is not on CRAN

2020-11-13 Thread Duncan Murdoch
that dependency. - you could publicize that your package is on Github, and give up on publishing it on CRAN. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2020-11-12 Thread Duncan Murdoch
Actually I think it is a bug in the check code. I've just posted about this on the R-devel list. Duncan Murdoch On 12/11/2020 10:13 a.m., Martin Morgan wrote: This seems more like a problem with the CRAN test machine, with the movMF package installed with flexmix available but loaded

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

2020-11-11 Thread Duncan Murdoch
of them sets a method that you're using. Duncan Murdoch On 11/11/2020 3:31 p.m., Kevin R. Coombes wrote: Oh, I forgot to mention explicitly that checking (with --as-cran) on the development version of R on Windows also produces no errors or warnings. On 11/11/2020 1:39 PM, Kevin R. Coombes

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

2020-11-11 Thread Duncan Murdoch
. But that function runs a new R instance, and I didn't get to debugging that. I'll try again later today if nobody else figures it out. Duncan Murdoch On 11/11/2020 12:03 p.m., Kevin R. Coombes wrote: Hi Duncan, Oops; I didn't realize I had forgotten to push updates to the OOMPA web site

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

2020-11-11 Thread Duncan Murdoch
Uwe suggested you suggest flexmix, but I see below you already tried that. I'd like to take a look, but I can't find your package. The existing version on CRAN gives the URL as http://oompa.r-forge.r-project.org/, but I can't see it mentioned there. Duncan Murdoch On 11/11/2020 8:44 a.m

Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

2020-11-05 Thread Duncan Murdoch
s). I am not sure about this one; I'd need to look at the package to check. Is it on Github? Duncan Murdoch Have ever someone faced a similar issue? However, it seems ineffective. Is there any possibility to be a false negative? I am sending bellow the links for the check logs. package GALLO_

Re: [R-pkg-devel] import with except(ion)

2020-10-31 Thread Duncan Murdoch
ate an error, because you don't support frailty in this context? Could you clarify that? Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] checking PDF version of manual without hyperrefs or index ... ERROR

2020-10-29 Thread Duncan Murdoch
I don't know the best solution, but one workaround would be to replace "fl" in your Rd files with "fl". Duncan Murdoch On 29/10/2020 10:34 a.m., Anthony Hammond wrote: Hello, I'm attempting to upload a package to CRAN and although it passes the R CMD checks that I run, it d

Re: [R-pkg-devel] Warning on r-oldrel-macos-x86_64

2020-10-25 Thread Duncan Murdoch
, or - test for it in the vignette, or - remove the dependency by being explicit about stringsAsFactors = FALSE. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Licenses

2020-10-22 Thread Duncan Murdoch
On 22/10/2020 12:56 p.m., Marc Schwartz wrote: On Oct 22, 2020, at 12:12 PM, Duncan Murdoch wrote: On 22/10/2020 11:55 a.m., Marc Schwartz wrote: On Oct 22, 2020, at 11:19 AM, Marc Schwartz wrote: On Oct 22, 2020, at 10:21 AM, Kevin R. Coombes wrote: Hi, I am developing a package

Re: [R-pkg-devel] Licenses

2020-10-22 Thread Duncan Murdoch
ut R could still do computations on them, as described in ?library in the "Licenses" section. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Licenses

2020-10-22 Thread Duncan Murdoch
apparently does and ignore the NOTE? flowCore is a Bioconductor package, not on CRAN. Are you intending to send yours there, or to CRAN? I suspect Bioconductor is happy with the Hutch's license. Duncan Murdoch __ R-package-devel@r-project.org

Re: [R-pkg-devel] CRAN pending status , left up in the air

2020-10-19 Thread Duncan Murdoch
onable people, but they have their own priorities. If you can make it easier for them to achieve their priorities, they'll appreciate it. If you ask them to change their priorities, they might not. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] puzzling CRAN rejection

2020-10-13 Thread Duncan Murdoch
On 13/10/2020 5:33 a.m., Iñaki Ucar wrote: On Tue, 13 Oct 2020 at 01:47, Ben Bolker wrote: On 10/12/20 7:37 PM, Duncan Murdoch wrote: On 12/10/2020 6:51 p.m., Ben Bolker wrote: On 10/12/20 6:36 PM, Duncan Murdoch wrote: On 12/10/2020 6:14 p.m., Ben Bolker wrote: I'd say a mismatch

Re: [R-pkg-devel] puzzling CRAN rejection

2020-10-12 Thread Duncan Murdoch
On 12/10/2020 6:51 p.m., Ben Bolker wrote: On 10/12/20 6:36 PM, Duncan Murdoch wrote: On 12/10/2020 6:14 p.m., Ben Bolker wrote: I'd say a mismatch in saved output isn't a small problem, it's either a too-sensitive test or something serious. Duncan Murdoch     That's fair enough

Re: [R-pkg-devel] puzzling CRAN rejection

2020-10-12 Thread Duncan Murdoch
On 12/10/2020 6:14 p.m., Ben Bolker wrote: I'd say a mismatch in saved output isn't a small problem, it's either a too-sensitive test or something serious. Duncan Murdoch That's fair enough, but it would be nice if (1) this were a NOTE and I don't think so. As I said, I think

Re: [R-pkg-devel] puzzling CRAN rejection

2020-10-12 Thread Duncan Murdoch
On 12/10/2020 5:17 p.m., Ben Bolker wrote: On 10/12/20 4:40 PM, Duncan Murdoch wrote: There's this one in https://win-builder.r-project.org/incoming_pretest/lme4_1.1-24_20201012_210730/Windows/00check.log:   Comparing 'lmer-1.Rout' to 'lmer-1.Rout.save' ...428d427 < boundary (singu

Re: [R-pkg-devel] puzzling CRAN rejection

2020-10-12 Thread Duncan Murdoch
lmer-1.Rout.save The difference also doesn't show up in the x64 versions of the files. Duncan Murdoch On 12/10/2020 4:03 p.m., Ben Bolker wrote: Before I risk wasting the CRAN maintainers' time with a query, can anyone see what I'm missing here? Everything I can see looks OK, with the po

Re: [R-pkg-devel] Procedure for the transfer or an R package maintainership

2020-10-11 Thread Duncan Murdoch
I've added enough info for you. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Static vignettes / bibtex warning in Debian

2020-10-10 Thread Duncan Murdoch
need to worry about: that other package has probably been updated to drop the bibtex dependence, but Debian hasn't got the update yet. I don't know how you determine which is the "guilty" package. Maybe there are more hints in the check log? Duncan Murdoch On 10/10/2020 12:53 p.

Re: [R-pkg-devel] rlang not available on Windows builder machine with R-devel

2020-10-09 Thread Duncan Murdoch
, mention the failure in your submission message and say that you're assuming it's a problem on their end. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?

2020-10-08 Thread Duncan Murdoch
When I tried that on MacOS, it did the gs compression with gs_quality set to "none", which does nothing. I don't know what quality CRAN uses, but for me setting the environment variable GS_QUALITY=screen made a big difference. Duncan Murdoch On 08/10/2020 11:10 a.m., John Fox wr

Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?

2020-10-07 Thread Duncan Murdoch
to clarify: I've never noticed the problem you mention. I just know how to debug R CMD build. Duncan cheers Ben On 10/7/20 8:31 PM, Duncan Murdoch wrote: I don't know the answer to your question, but you can debug the --compact-vignettes option as follows. debug(tools::compactPDF

Re: [R-pkg-devel] is R CMD build --compact-vignettes working as expected?

2020-10-07 Thread Duncan Murdoch
those criteria. When I trick it into accepting the compaction, it does put the compacted PDF into the tarball. Duncan Murdoch On 07/10/2020 6:03 p.m., John Fox wrote: Dear Ben, On 2020-10-07 5:26 p.m., Ben Bolker wrote:   I hope so too. The (annoying) workaround is to compact the vignette yourself

Re: [R-pkg-devel] A note from CRAN package check

2020-09-28 Thread Duncan Murdoch
to distribute your package in some other way besides CRAN. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] CRAN Windows failure due to old pandoc ?

2020-09-26 Thread Duncan Murdoch
On 26/09/2020 12:54 p.m., Dirk Eddelbuettel wrote: On 26 September 2020 at 11:50, Duncan Murdoch wrote: | On 26/09/2020 9:14 a.m., Dirk Eddelbuettel wrote: | > | > I had a submission fail and bomb with this error on Windows: | > | >Flavor: r-devel-windows-ix86+x86_64 | &g

Re: [R-pkg-devel] CRAN Windows failure due to old pandoc ?

2020-09-26 Thread Duncan Murdoch
on't meet the stated requirements. Since SystemRequirements is free-form, I can see why CRAN doesn't do automatic interpretation of it, but it would be nice if they did. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Dependency needs to be loaded manually even its specified in the package

2020-09-18 Thread Duncan Murdoch
. Rather, you declare dependency relationsships via DESCRIPTION (and likely NAMESPACE). See "Writing R Extensions" for all the details. I think you misread the post: this was an example of code a user would run, not code from the package. Dunc

Re: [R-pkg-devel] Dependency needs to be loaded manually even its specified in the package

2020-09-18 Thread Duncan Murdoch
this by adding the envir argument to exists() in that call, e.g. test <- sapply(ffun, exists, mode = "function", envir = parent.env(environment())) but it would be better to not try to invent a new object system. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2020-09-14 Thread Duncan Murdoch
and explain why you would like them to export foo, or (if the license permits it) just copy the source of foo into your own package, giving appropriate credit to the original author. Duncan Murdoch Thanks to Duncan for a practical solution. Best, Zhu -Original Message- From: Duncan

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

2020-09-14 Thread Duncan Murdoch
, if you maintain both packages, then you should be ready to modify mypkg as soon as you modify pkg:::foo. Duncan Murdoch Thanks, Zhu You don't need either pkg:: or pkg::: if you are calling the function from within the package. You may need one of those if the call is coming from a user

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

2020-09-14 Thread Duncan Murdoch
to declare that mypkg Imports pkg. (This is a line in its DESCRIPTION file.) I think that's what the WARNING is telling you. Duncan Murdoch Thanks, Zhu -Original Message- From: R-package-devel On Behalf Of Duncan Murdoch Sent: Sunday, September 13, 2020 3:20 PM To: David Kepplinger ;

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

2020-09-13 Thread Duncan Murdoch
On 13/09/2020 3:51 p.m., David Kepplinger wrote: Dear list members, I submitted an update for my package and got automatically rejected by the incoming checks (as expected from my own checks) for using `:::` calls to access the package's namespace. "There are ::: calls to the package's

Re: [R-pkg-devel] fixing problems in submitted R package

2020-09-04 Thread Duncan Murdoch
"Is it a real problem to drop some empty sections in some MAN files. These functions will not be direct used by users" If they aren't functions that the users will see, then they don't need to be exported and documented. Duncan Murdoch Thank you a lot and sorry for so basic questi

Re: [R-pkg-devel] visible binding for '<<-' assignment

2020-09-03 Thread Duncan Murdoch
when they load the package and then they won't need to deal with all the Unicode escape sequences after that. You shouldn't be doing that. Write a function that returns those results, and tell the user that if they store them in a global variable named "string_fixes" (or whateve

Re: [R-pkg-devel] Modeltime 0.1.0 Submission Failing - Not Sure What To Do

2020-09-01 Thread Duncan Murdoch
re fairly certain the rejection is a false positive, please reply-all to this message and explain." Having OK results rejected sure seems like a false positive! Duncan Murdoch Best, Max Turgeon Assistant Professor Department of Statistics Department of Computer Science University of Manit

Re: [R-pkg-devel] R CMD check "unable to verify current time"

2020-08-27 Thread Duncan Murdoch
R tries to get the time from http://worldtimeapi.org/api/timezone/UTC or http://worldclockapi.com/api/json/utc/now The first one doesn't accept UTC as a timezone; it appears to want etc/UTC instead. The second one is offline. Duncan Murdoch If both of those fail, you'll get the message you

Re: [R-pkg-devel] Etiquette for package submissions that do not automatically pass checks?

2020-08-14 Thread Duncan Murdoch
r::.something, you shouldn't need clusterExport(). Then you will meet the technical requirement and not need any explanation. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Package Anchored Links with R-Dev

2020-08-09 Thread Duncan Murdoch
On 09/08/2020 3:15 p.m., Ben Bolker wrote: On 8/9/20 3:08 PM, Duncan Murdoch wrote: On 09/08/2020 2:59 p.m., John Mount wrote: Firstly: thanks to Ben for the help/fix. I know nobody asked, but. Having to guess where the documentation is just to refer to it is just going to be really brittle

Re: [R-pkg-devel] Package Anchored Links with R-Dev

2020-08-09 Thread Duncan Murdoch
were fine. That's not correct. The system could often work around the error, but not always. Duncan Murdoch Future: if don't correctly specify where the help is you are wrong. Going forward: reorganizing a package's help can break referring packages. This sort of brittleness is going

Re: [R-pkg-devel] Package Anchored Links with R-Dev

2020-08-09 Thread Duncan Murdoch
are finally warning about the unreliability. Duncan Murdoch On Sun, Aug 9, 2020 at 2:01 PM John Mount wrote: With "R Under development (unstable) (2020-07-05 r78784)" (Windows) documentation references such as "\link[utils]{dump.frames}" trigger "Non-file package-anchored

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

2020-08-07 Thread Duncan Murdoch
On 07/08/2020 6:53 p.m., Helmut Schütz wrote: Hi Duncan, Duncan Murdoch wrote on 2020-08-07 21:55: On 07/08/2020 3:22 p.m., Helmut Schütz wrote: I see. However, the HTML-source states This manual is for R, version 4.1.0 Under development (2020-08-06). I was relying on the PDF-version (4.0.2

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

2020-08-07 Thread Duncan Murdoch
On 07/08/2020 3:22 p.m., Helmut Schütz wrote: Hi Duncan, Duncan Murdoch wrote on 2020-08-07 18:39: You're reading the wrong version of the manual.  This is in the R-devel manual: "Packages referred to by these ‘other forms’ should be declared in the DESCRIPTION file, in the ‘De

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

2020-08-07 Thread Duncan Murdoch
/r-devel/R-exts.html. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2020-07-23 Thread Duncan Murdoch
s to "E:/Users/{Username}/Documents/"... It can resolve anywhere you like (as long as its writable), by specifying the TMPDIR environment variable. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] Check Error Due to Unicode in Documentation

2020-07-23 Thread Duncan Murdoch
As a workaround, is there a way to say that this one particular .Rd file should be edited by hand, instead of auto-generated? Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2020-07-23 Thread Duncan Murdoch
opy the result files to another location and closes the console, everything would be lost and the user would have to start again from scratch. I think that this is not very user-friendly. I would issue an error instead of a warning, and in the error message, suggest some code that should wo

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

2020-07-22 Thread Duncan Murdoch
On 22/07/2020 5:40 p.m., Helmut Schütz wrote: Duncan Murdoch wrote on 2020-07-22 21:42: On 22/07/2020 1:25 p.m., Helmut Schütz wrote: [...] The problem is that I cannot reproduce it as well. Only CHECK laments about dev.off() which I changed to graphics.off() in the meantime. library

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

2020-07-22 Thread Duncan Murdoch
You don't test whether the call to png() succeeded. During a check, it probably wouldn't, because you aren't allowed to write to "~/". Your package should be writing to tempdir(), or a location entered by the user. Duncan Murdoch __ R-

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

2020-07-22 Thread Duncan Murdoch
ar are each length one variables, this test is logically equivalent to if (foo) { Is that really what you intended? Duncan Murdoch   dev <- dev.list()   if (!is.null(dev)) {     if (dev == 2) invisible(dev.off())   } } without success (same error). Even the more general if (fo

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

2020-07-11 Thread Duncan Murdoch
-pick methods. Best Regards, Pavel On Sat, 2020-07-11 at 07:29 -0400, Duncan Murdoch wrote: If the semantics of the two generics must remain identical in the future, then there is an implicit dependency between the code in the packages. You sho

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

2020-07-11 Thread Duncan Murdoch
If the semantics of the two generics must remain identical in the future, then there is an implicit dependency between the code in the packages. You should formalize this by using one of the dependency mechanisms that the language provides, i.e. the clean solution. Duncan Murdoch On 10/07

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Duncan Murdoch
your update, then ask to update bit. Since it doesn't depend on ff, it won't trigger an ff update. You can't expect R to know they were never meant to be installed together unless you record that fact in the dependencies in the DESCRIPTION file. Duncan Murdoch If there is a problem when

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Duncan Murdoch
t it's not so obvious how to make the new bit depend on the new ff. There's no way to say that the dependency is only to a help page, and circular strong dependencies are messy, so I'd suggest you use one of the other options I offered: a dynamic link in the Rd file, or no link at all. Duncan M

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-02 Thread Duncan Murdoch
he next update when the new ff is available. Duncan Murdoch On 02/07/2020 6:47 a.m., Dr. Jens Oehlschlägel wrote: Thanks Gabor and Duncan, It's actually in ff/man/clone.rd, not clone.ff.rd. There is no ff/man/clone.ff.rd file. but there *is* clone.ff.rd in the >= 4.0.0 versions of the package

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-07-01 Thread Duncan Murdoch
f" I asked the maintainers to explain what is wrong and what to do and got no answer. Does someone here can help? It's actually in ff/man/clone.rd, not clone.ff.rd. There is no ff/man/clone.ff.rd file. Duncan Murdoch Best regards Jens On 16.06.20 22:31, Gábor Csárdi wrote: Th

Re: [R-pkg-devel] package CatDataAnalysis

2020-06-28 Thread Duncan Murdoch
on the Github site, so when people follow your link they'll find the description.) Duncan Murdoch On 28/06/2020 12:07 p.m., Charles Geyer wrote: I have a package that has the datasets for Categorical Data Analysis by Agresti that do not appear in the book. The whole package is a github repo

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

2020-06-23 Thread Duncan Murdoch
::filter was a generic and someone wrote a method for dplyr::filter, clearly a call to stats::filter should not use that method. It's even possible that some package doing time series analysis in the tidyverse framework would want to have methods for both generics. Duncan Murdoch Best, W

Re: [R-pkg-devel] Proper CRAN way - How to handle dependency of java jar file?

2020-06-23 Thread Duncan Murdoch
nt version of a package. Duncan Murdoch On 23/06/2020 8:18 a.m., Rainer M Krug wrote: Hi I have a package called `plantuml` (https://github.com/rkrug/plantuml) which converts plantuml code to UML graphs. It uses for this the java program https://plantuml.com which is Open Source. As it is n

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

2020-06-23 Thread Duncan Murdoch
o see their documentation." One of the links is to the ?tidy page in the generics package. You are allowed to say ?broom::tidy, and then you don't go to the list of possibilities, you go directly to the one you asked for. Duncan Murdoch __ R-pac

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

2020-06-23 Thread Duncan Murdoch
le, but I can't see how it would change what generics are available. Can you give an example of what you're worried about? Duncan Murdoch Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breath

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

2020-06-22 Thread Duncan Murdoch
l, union Users don't get warned about overriding names in packages they've loaded, because that would just be irritating. Duncan Murdoch So, we might try protecting the generic definitions of "foo" in both packages by enclosing them in something like: tryCatch(invisible(metho

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

2020-06-22 Thread Duncan Murdoch
rtFrom(pkgA, fooA = foo) though this doesn't appear to be documented in the usual places. Duncan Murdoch Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comi

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

2020-06-22 Thread Duncan Murdoch
o reason to believe that pkgA::foo has anything whatsoever to do with pkgB::foo without this. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] how to prevent a small package from yielding a large installed size?

2020-06-15 Thread Duncan Murdoch
On 15/06/2020 1:24 p.m., Ivan Krylov wrote: On Mon, 15 Jun 2020 12:52:20 -0400 Duncan Murdoch wrote: maybe someone else can suggest how to read an object from the .rdb file using R code. Internally R uses C code for this. This function seems to work for me: # filename: the .rdb file

Re: [R-pkg-devel] how to prevent a small package from yielding a large installed size?

2020-06-15 Thread Duncan Murdoch
R uses C code for this. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-06-15 Thread Duncan Murdoch
On 15/06/2020 12:05 p.m., Martin Maechler wrote: Duncan Murdoch on Sun, 14 Jun 2020 07:28:03 -0400 writes: > I agree with almost everything you wrote, except one thing: this isn't > newly enforced, it has been enforced since the help system began. What > I thi

Re: [R-pkg-devel] how to prevent a small package from yielding a large installed size?

2020-06-15 Thread Duncan Murdoch
n rdx$references. Duncan Murdoch On 15/06/2020 7:13 a.m., Daniel Kelley wrote: I am working on a package (https://github.com/ArgoCanada/argoFloats) that has a 412K source tarball (most of which is data; the R code is 176K), but that creates a library .rdb file of MUCH larger size, namely 7.2M.

Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3

2020-06-14 Thread Duncan Murdoch
On 14/06/2020 10:59 a.m., Joshua N Pritikin wrote: On Sun, Jun 14, 2020 at 09:17:32AM -0400, Duncan Murdoch wrote: Since you're using Rmarkdown, you can use a variable for the eval chunk option, e.g. put this in your setup chunk: knitr::opts_chunk$set(eval = !is_CRAN) This works except

Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3

2020-06-14 Thread Duncan Murdoch
export NOT_CRAN=true when I build locally. But CRAN check still complains, You shouldn't call q() from a vignette. Since you're using Rmarkdown, you can use a variable for the eval chunk option, e.g. put this in your setup chunk: knitr::opts_chunk$set(eval = !is_CRAN) Duncan Murdoch On

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

2020-06-14 Thread Duncan Murdoch
der. Or if you want stuff installed in data after the package is installed, just put it there in the source, not in inst/data: and follow the rules for that folder from Writing R Extensions. Duncan Murdoch __ R-package-devel@r-project.org mailing list

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-06-14 Thread Duncan Murdoch
I agree with almost everything you wrote, except one thing: this isn't newly enforced, it has been enforced since the help system began. What I think is new is that there are now tests for it. Previously those links just wouldn't work. Duncan Murdoch On 14/06/2020 6:26 a.m., Gábor Csárdi

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-06-14 Thread Duncan Murdoch
On 13/06/2020 9:00 p.m., Gábor Csárdi wrote: On Sat, Jun 13, 2020 at 8:10 PM Duncan Murdoch wrote: On 13/06/2020 1:17 p.m., Zhian Kamvar wrote: [...] Is this a new policy? Zhian, it seems that some of the problematic links are created by roxygen2. You can fix these using this PR: https

Re: [R-pkg-devel] check cross-references error: Non-file package-anchored link(s)

2020-06-13 Thread Duncan Murdoch
ce other R core members that it would have been a good change. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [R-pkg-devel] email misleading: checking CRAN incoming feasibility ... NOTE Maintainer

2020-06-08 Thread Duncan Murdoch
The built-in way is to put those tests in a separate directory, and specify that directory when you run R CMD check. For example, rgl has directory "inst/slowTests", and I use these options to R CMD check: --test-dir=inst/slowTests Duncan Murdoch On 08/06/2020 10:52 a.m., Spen

Re: [R-pkg-devel] Vignette depends on BH

2020-06-02 Thread Duncan Murdoch
r chunk option "exec" to FALSE in all code chunks. } Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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

2020-06-02 Thread Duncan Murdoch
be R shouldn't have tried to use MARC roles, or should have invented an additional one. It's a bit late for that now, though. Duncan Murdoch So, I think the safe way is to include the original authors in the author list (and check their license carefully). In general, "check

Re: [R-pkg-devel] Workflow for Javascript in package?

2020-06-01 Thread Duncan Murdoch
kage = "rgl"), "rglClass.js")) rm(text) I'm not completely sure this is supported/allowed, though I don't see a CRAN rule to disallow it. Now I can work on splitting up the big file, and doing a somewhat more complicated install of rglClass.js. Duncan Murdoch https://cra

[R-pkg-devel] Workflow for Javascript in package?

2020-06-01 Thread Duncan Murdoch
containing htmlwidgets that do this "properly", or point to instructions for the standard workflow for Javascript library development outside of R that I could adapt? Duncan Murdoch __ R-package-devel@r-project.org mailing list https://

Re: [R-pkg-devel] Error creating union class: object ‘.__C__compMatrix’ not found

2020-05-18 Thread Duncan Murdoch
independently of R. The current version on CRAN is 1.2-18, but the R-forge version is 1.3-0. Neither one exports mMatrix. Duncan Murdoch In this case I'd rather use a conditional import and definition. I'll try that route. Bests, Renaud Sent with ProtonMail Secure Email

Re: [R-pkg-devel] Package submission failed with two warnings

2020-05-15 Thread Duncan Murdoch
say what's happening. Is your package online somewhere so we could try it on different machines? Duncan Murdoch On 15/05/2020 12:46 a.m., FARSHAD TABASINEJAD wrote: Dear R-package-devel experts, This is the first time I’m writing to this platform about a package I recently submitted to CRAN

Re: [R-pkg-devel] MathJax for Rd files

2020-05-14 Thread Duncan Murdoch
On 14/05/2020 5:46 a.m., Gábor Csárdi wrote: On Thu, May 14, 2020 at 10:27 AM Duncan Murdoch wrote: On 14/05/2020 3:30 a.m., Georgi Boshnakov wrote: The issue is not with Rstudio per se but that in devtools' development mode help() is modified to show the Rd files in the source directory

Re: [R-pkg-devel] MathJax for Rd files

2020-05-14 Thread Duncan Murdoch
On 14/05/2020 5:46 a.m., Gábor Csárdi wrote: On Thu, May 14, 2020 at 10:27 AM Duncan Murdoch wrote: On 14/05/2020 3:30 a.m., Georgi Boshnakov wrote: The issue is not with Rstudio per se but that in devtools' development mode help() is modified to show the Rd files in the source directory

Re: [R-pkg-devel] MathJax for Rd files

2020-05-14 Thread Duncan Murdoch
. Yes, the error appears to be in the pkgload::load_rd_macros() function here: https://github.com/r-lib/pkgload/blob/1b1adc39628671f2ea4256f0bebcdb76e1f89f45/R/dev-help.r#L47. It doesn't look at the DESCRIPTION file to see if there's an RdMacros entry. Duncan Murdoch Rdpack::viewRd() can

Re: [R-pkg-devel] RES: RES: MathJax for Rd files

2020-05-13 Thread Duncan Murdoch
(Rd, outfile, macros = system.file("help/macros/mathjax.Rd", package = "mathjaxr"))) so that it works if you use it on a different system that puts the library somewhere else. Duncan Murdoch I added the macros \loadmathjax and \mjsdeqn in the mgidi.R file, ran devtools::docu

Re: [R-pkg-devel] RES: MathJax for Rd files

2020-05-13 Thread Duncan Murdoch
useful package. Congratulations on the efforts for developing it. Sounds like it's a devtools issue. I don't know how they are simulating the install, but it needs to say to use the mathjaxr macros when converting the Rd pages. Duncan Murdoch Best Olivoto -Mensagem original--

Re: [R-pkg-devel] how to specify to let a package only build 64bit on CRAN

2020-05-11 Thread Duncan Murdoch
would probably get it accepted. Duncan Murdoch best, Jan Jan Wijffels Statistician www.bnosac.be  | +32 486 611708 ‐‐‐ Original Message ‐‐‐ On Monday 11 May 2020 14:39, Duncan Murdoch wrote: On 11/05/2020 7:54 a.m., Jan Wijffels wrote: Hello everyone, I have a package which I

Re: [R-pkg-devel] how to specify to let a package only build 64bit on CRAN

2020-05-11 Thread Duncan Murdoch
On 11/05/2020 7:54 a.m., Jan Wijffels wrote: Hello everyone, I have a package which I would like to host on CRAN. The package is at https://github.com/bnosac/golgotha The package only builds on 64bit however because the package uses R package reticulate which requires a python library called

Re: [R-pkg-devel] Rmarkdown vignette yields r inline warning on windows build [EXT]

2020-05-05 Thread Duncan Murdoch
a minimal reproducible example, and it'll probably be easy to work out whether it's R, R Markdown, knitr, Pandoc, or LaTeX that has the bug. (Naturally I suspect it's not R, and past experience makes me think it's not LaTeX, but there are still three other possibilities in the list.)

Re: [R-pkg-devel] CRAN-Policies

2020-04-23 Thread Duncan Murdoch
, but I am not sure if these are actually common requirements now or not.) I'd guess the requests will vary depending on who the reviewer is and what their mood is, but if you ignore their requests, you're not going to put them in a better mood. Duncan Murdoch Copy of the chang

Re: [R-pkg-devel] WARNING Files in the 'vignettes' directory but no files in 'inst/doc':

2020-04-23 Thread Duncan Murdoch
the source file to one of those, or choose a different vignette engine. knitr::rmarkdown is the usual engine to use with R Markdown files. Duncan Murdoch __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

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