Re: [R-pkg-devel] Usage of internet resources in examples

2020-10-21 Thread Martin Maechler
> Ben Bolker > on Tue, 20 Oct 2020 17:07:10 -0400 writes: > On 10/20/20 4:51 PM, Gábor Csárdi wrote: >> On Tue, Oct 20, 2020 at 9:45 PM Ben Bolker wrote: >> [...] >>> if (testthat::skip_on_cran()) >>> >>> all seem like reasonable solutions. >> >> I

Re: [R-pkg-devel] checking windows timing?

2020-10-14 Thread Martin Maechler
> Ben Bolker > on Tue, 13 Oct 2020 12:46:11 -0400 writes: >Following up on my questions from yesterday: >I've been advised to (drastically) reduce the checking > time of my package on CRAN's Windows platform (currently > at 23 min). I've gone through and

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

2020-10-08 Thread Martin Maechler
> Ben Bolker > on Wed, 7 Oct 2020 20:42:08 -0400 writes: > On 10/7/20 8:35 PM, Duncan Murdoch wrote: >> On 07/10/2020 8:32 p.m., Ben Bolker wrote: >>>     Thanks for the tip, I'll take a look. >>> >>>     Given that three relatively experienced package >>>

Re: [R-pkg-devel] How do you Rd reference parallel::mclapply() so it works also on Windows?

2020-07-08 Thread Martin Maechler
> Henrik Bengtsson > on Tue, 7 Jul 2020 18:11:00 -0700 writes: > Here's another "Non-file package-anchored link(s) ..." > issue. I'd like to reference parallel::mclapply() in my > help pages. With the new R-devel requirements, you have > to link to the file and not

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

2020-06-15 Thread Martin Maechler
> 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 think is new is that there are now tests for it. Previously

Re: [R-pkg-devel] Forward function call

2020-06-09 Thread Martin Maechler
> Göran Broström > on Mon, 8 Jun 2020 23:02:30 +0200 writes: > Thanks for the responses! > I found the suggestion > Call[[1]] <- quote(survival::coxph) > easiest to implement. And it works. and it is what we use in R's own R source code in several places (and

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

2020-06-02 Thread Martin Maechler
> Adelchi Azzalini > on Tue, 2 Jun 2020 08:32:37 +0200 writes: > Thanks for this information, Mark. Given the phrase > "small but important function my package uses", it seems > that you included in your package some code, reproducing > it verbatim. Do I understand

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

2020-05-05 Thread Martin Maechler
> Matthew Young > on Mon, 4 May 2020 09:09:55 + writes: > I progressively chopped bits out of the vignette till the > error stopped to identify the error. It was being caused > by inline latex, where I had two %% marks. I'm not really > sure why this broke

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

2020-04-18 Thread Martin Maechler
in setClassUnion("mMatrix", c("Matrix", "matrix")) : >>> unable to create union class: could not set members "Matrix" >>>> sessionInfo() >>> R Under development (unstable) (2020-04-07 r78175) >>> Platform: x86_

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

2020-04-08 Thread Martin Maechler
ere's nothing, anybody can reproduce from your posting. There have been changes in R's dealing with class unions etc, notably even *relating* to an earlier bug report on class unions exactly for such a case which was *triggered* when people built on such Matrix classes. But we would really

Re: [R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

2020-03-20 Thread Martin Maechler
> Erin Hodgesson Thu, 19 Mar 2020 22:44:39 -0600 writes: > Hi Tomas and others: > Here is the session Info. I also used the str example both without and > with changing the locale. > sI <- sessionInfo() >> str(sI) > List of 10 > $ R.version :List of 14

Re: [R-pkg-devel] Help on Windows CRAN Check

2020-03-05 Thread Martin Maechler
> John Lawson > on Thu, 5 Mar 2020 20:34:00 -0700 writes: > I see this error on windows CRAN Check > --- failure: the condition has length > 1 --- > --- srcref --- > : > --- package (from environment) --- > daewr > --- call from context --- > ihstep(y,

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

2020-01-20 Thread Martin Maechler
t" R package should use R's random number generators rather than (C library / Fortran library / ...). When using R's RNGs, your package behaves "R like" e.g., set.seed() has the desired effect, etc etc. What Avi Adler describes below is what I strongly believe you *

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

2019-12-05 Thread Martin Maechler
> Mat Fok via R-package-devel > on Wed, 4 Dec 2019 22:25:47 + writes: > Hi, > Thank you. I am wondering why the log would output .Rproj.user when it was already in the .Rignorefile. Hope the .Rignore file is correct anyways as I have mentioned below. If you really use

Re: [R-pkg-devel] R package which creates a directory in the user home dir

2019-10-17 Thread Martin Maechler
> Sigbert Klinke > on Thu, 17 Oct 2019 14:29:54 +0200 writes: > Hi, > I'am developing a package that circumvents the R package size limitation > for data sets. For this I store the data set in the internet (currently > GitHub) and download if it is requested. >

Re: [R-pkg-devel] R, BLAS, and FCLEN

2019-09-12 Thread Martin Maechler
> Göran Broström > on Wed, 11 Sep 2019 13:36:40 +0200 writes: > A followup question: Is it possible to call a BLAS/LAPACK subroutine, > where one parameter is character, from FORTRAN (77) code called by > .Fortran? (No problem "in the past".) [as there wasn't a reply

Re: [R-pkg-devel] set pkg_config for 3rd party software

2019-09-06 Thread Martin Maechler
>>>>> Ralf Stubner >>>>> on Fri, 6 Sep 2019 11:22:15 +0200 writes: > On Thu, Sep 5, 2019 at 6:36 PM Martin Maechler > wrote: >> For me (on Fedora 30) >> >> $ R CMD config LDFLAGS >> -L/usr/lib64

Re: [R-pkg-devel] set pkg_config for 3rd party software

2019-09-06 Thread Martin Maechler
>>>>> Martin Maechler >>>>> on Thu, 5 Sep 2019 18:36:03 +0200 writes: >>>>> Dirk Eddelbuettel >>>>> on Thu, 5 Sep 2019 10:14:21 -0500 writes: >> On 5 September 2019 at 16:53, Ralf Stubner wrote:

Re: [R-pkg-devel] set pkg_config for 3rd party software

2019-09-05 Thread Martin Maechler
> Sameh M Abdulah > on Fri, 30 Aug 2019 18:50:55 + writes: > Hi, > I recently asked some questions about my R package which were well responded by Dirk. > I have another question related to pkg_config path, > I am using this command to add the installation path

Re: [R-pkg-devel] Note on winbuilder-develop

2019-07-24 Thread Martin Maechler
>>>>> Duncan Murdoch >>>>> on Wed, 24 Jul 2019 06:12:35 -0400 writes: > On 24/07/2019 3:08 a.m., Martin Maechler wrote: >>>>>>> Roy Mendelssohn >>>>>>> on Tue, 23 Jul 2019 18:44:24 -0700 writes:

Re: [R-pkg-devel] Note on winbuilder-develop

2019-07-24 Thread Martin Maechler
nerated. -Roy just to rub the obvious into everybody's face ;-) :-D { apology for any offence ! } : If you'd use roxygen only initially and not anymore from then on, but rather then would keep hand-editing nicely humanly formatted man/*.Rd files, you would never see this (and quite a few "similar&qu

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

2019-07-02 Thread Martin Maechler
> Henrik Bengtsson > on Mon, 1 Jul 2019 20:36:26 -0700 writes: > FWIW, when running R CMD check mypkg_1.0.tar.gz > the example output is captured to the file > 'mypkg.Rcheck/mypkg-Ex.Rout', so you could monitor that > one for what's going on. > /Henrik Yes,

Re: [R-pkg-devel] .Rd, LaTeX and Unicode

2019-06-18 Thread Martin Maechler
engines (including "simple" pdflatex)... though really, I'm not the expert here, but I think it's a good point in time to reconsider how much UTF8 should be allowed/supported in *.Rd files. One problem: This is (slightly) the wrong mailing list; this would have been a perfect topic for 'R-devel'

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

2019-05-10 Thread Martin Maechler
> Ulrike Grömping > on Fri, 10 May 2019 06:39:39 +0200 writes: > Mark, > I used > if (getRversion()>="3.6.0") RNGkind(sample.kind="Rounding") > And that works. Actually, using rnorm afterwards also > yields the same random numbers. Yes, "of course",

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

2019-04-04 Thread Martin Maechler
> cartograflow@gmail com > on Wed, 3 Apr 2019 18:11:10 + writes: > Hi, > I come back to you  because I have always the problem with devtools::check of my package. But we've told you repeatedly now *NOT* to use it in this case, but rather use R CMD build ...

Re: [R-pkg-devel] Cran submission - warning with windows (cpp build library gmp)

2019-02-23 Thread Martin Maechler
> Kevin Ushey > on Fri, 22 Feb 2019 10:09:15 -0800 writes: > The 'long long' type does not exist in the C++98 > standard, so you need to explicitly request C++11 or > C++14 (the former which is now fairly broadly supported > across compilers on different systems).

Re: [R-pkg-devel] New CRAN internet policy

2018-12-07 Thread Martin Maechler
> Hadley Wickham > on Thu, 6 Dec 2018 10:22:47 -0600 writes: > Hi all, > I'd love to get some clarification on what the new internet policy > means for packages like httr: >> Packages which use Internet resources should fail gracefully with an informative >>

Re: [R-pkg-devel] Get an empty note for "checking DESCRIPTION meta-information" when I run devtools::build_win()

2018-07-26 Thread Martin Maechler
: Invalid role specification: ‘Foobar’. > So the bug is really in the Windows version of R that was running for you when you've used devtools::build_win() or in build_win() itself. "rth" is a correct role and you should *NOT* replace it by something less appropriate ...

Re: [R-pkg-devel] Conditional use of suggested package in example code

2018-05-30 Thread Martin Maechler
> Christian Sigg > on Wed, 30 May 2018 11:08:38 +0200 writes: > I am updating the ’nsprcomp’ package to follow the recommendations of Section of the Writing R Extensions manual. > Before the update, the example code for the `nsprcomp` function looked like this:

Re: [R-pkg-devel] Creating S3 methods for S4 classes

2018-05-25 Thread Martin Maechler
delayed archiving the official archives considerably for now; to still see the current thread on R-devel, you can use one of the *other* archives: ==> )) Best, Martin Maechler __ R-package-devel@r-project

Re: [R-pkg-devel] Courtesy methods and explosive dependencies

2018-05-25 Thread Martin Maechler
ckage I think should not be in the strict dependencies of 'multcomp' but rather in its "Suggests" something I'd say must be true for all data packages: The whole idea of data packages is that they should be needed for interesting help page examples, vignettes, maybe even tests, but

Re: [R-pkg-devel] Creating S3 methods for S4 classes

2018-05-24 Thread Martin Maechler
Dear Joris, in my eyes, this is clearly a Q that should be asked on R-devel, not R-package-devel ... > Joris Meys > on Thu, 24 May 2018 14:17:07 +0200 writes: > Dear all, per the manual, one should create and register > both the S3 and a S4 method if one needs a method for

Re: [R-pkg-devel] File link does not exist : how to get the correct one?

2018-05-18 Thread Martin Maechler
> Duncan Murdoch > on Fri, 18 May 2018 11:42:53 -0400 writes: > On 18/05/2018 11:37 AM, Duncan Murdoch wrote: >> On 18/05/2018 11:29 AM, Duncan Murdoch wrote: >>> On 18/05/2018 11:06 AM, Joris Meys wrote: Hi all, The latest changes in R cause a

Re: [R-pkg-devel] mvrnorm, eigen, tests, and R CMD check

2018-05-18 Thread Martin Maechler
> William Dunlap > on Thu, 17 May 2018 11:28:50 -0700 writes: > Your explanation needs to be a bit more general in the > case of identical eigenvalues - each distinct eigenvalue > has an associated subspace, whose dimension is the number > repeats of that eigenvalue

Re: [R-pkg-devel] mvrnorm, eigen, tests, and R CMD check

2018-05-17 Thread Martin Maechler
>>>>> Duncan Murdoch >>>>> on Thu, 17 May 2018 12:13:01 -0400 writes: > On 17/05/2018 11:53 AM, Martin Maechler wrote: >>>>>>> Kevin Coombes ... on Thu, 17 >>>>>>> May 2018 11:21:23 -0400 writes:

Re: [R-pkg-devel] mvrnorm, eigen, tests, and R CMD check

2018-05-17 Thread Martin Maechler
even when the length is specified they are still > only defined up to a scalar of modulus one (the sign for real > matrices). It's not a warning but a "recall that" .. maybe because the author already assumed that only thorough users would read that and for them it would be a recall of something they'd have learned *and* not entirely forgotten since ;-) Martin Maechler ETH Zurich __ mailing list

Re: [R-pkg-devel] vignette via devtools: sometimes found, sometimes not (same package)

2018-04-20 Thread Martin Maechler
the vignettes) into > a website. Then you make that available to your students, > e.g. through github pages. Hmm, sounds nice .. at first: In teaching (and research!) I particularly emphasize people use CRAN (or Bioconductor) packages. Why on earth is pkgdown not on CRAN ? Martin

Re: [R-pkg-devel] Rd files: using \link[pkg]{foo} when file names differ between OSs

2018-04-16 Thread Martin Maechler
is to have two copies of the help file, one in man/unix, one > in man/windows, but that doesn't seem appropriate from your description. > Duncan Murdoch and mid-term, I really think R and (CRAN, Bioc, ...) packages should not do what we (R core) did here. Rather, \alias{mclapply} sh

Re: [R-pkg-devel] Warning: rBind is deprecated

2018-03-22 Thread Martin Maechler
your packages: a) replace cBind() by cbind() and rBind() by rbind() b) Ensure that your package depends on at least R 3.2.0, i.e. possibly add a 'Depends: R (>= 3.2.0)' to your DESCRIPTION file. Of course feel free to comment / ask privately or here {R-devel only} if necessary. Wit

Re: [R-pkg-devel] R-devel warning: You used a knitr feature that depends on the digest package.

2018-02-07 Thread Martin Maechler
> Gábor Csárdi > on Tue, 6 Feb 2018 19:26:55 -0800 writes: > codetools is a recommended package, and it is part of most R > installations. is a bit more strict, it does have the > recommended packages, on some builders at least, so

Re: [R-pkg-devel] Working with R-devel

2018-01-24 Thread Martin Maechler
> Uwe Ligges > on Wed, 24 Jan 2018 11:23:50 +0100 writes: > On 24.01.2018 03:20, Dirk Eddelbuettel wrote: >> >> I am going in circles here and have lost my way. I used to have means to >> build R-devel (still do) and use it for local

Re: [R-pkg-devel] Exited with status -1073741819.

2017-11-29 Thread Martin Maechler
ause then, using 'Rcmd build ' would almost surely give you more clues than just "does not build". > On 29-11-2017 11:16, Martin Maechler wrote: >>>>>>> Rampal S Etienne <> >>>>>>> on Wed, 29 Nov 201

Re: [R-pkg-devel] Exited with status -1073741819.

2017-11-29 Thread Martin Maechler
checks of your package run without any problem with all 5 versions of R-devel there : so it may rather be something specific to your setup ?? Martin Maechler > On 29-11-2017 0:36, Dason Kurkiewicz wrote: >> Do y

Re: [R-pkg-devel] [Rd] package check fail on Windows-release only?

2017-11-21 Thread Martin Maechler
> Paul Johnson > on Mon, 20 Nov 2017 14:59:26 -0600 writes: > I mistakenly left a write in "/tmp" in the rockchalk package (version > 1.8.109) that I uploaded last Friday. Kurt H wrote and asked me to fix > today. > While uploading a new one, I

Re: [R-pkg-devel] Package required and available but unsuitable version: 'stats'

2017-07-20 Thread Martin Maechler
> Maxime Turgeon > on Thu, 20 Jul 2017 15:51:18 + writes: > Hi Jernej, > The check errors you get are for older releases of R (3.3.2 and 3.3.3). The issue arises from your requirement in DESCRIPTION that the version of stats should be

Re: [R-pkg-devel] problem with package_native_routine_registration_skeleton

2017-06-22 Thread Martin Maechler
>>>>> Martin Maechler <> >>>>> on Thu, 22 Jun 2017 09:57:41 +0200 writes: >>>>> Mark van der Loo <> >>>>> on Thu, 22 Jun 2017 07:33:49 + writes: >>

Re: [R-pkg-devel] multiple bibentry()s in CITATION

2017-03-27 Thread Martin Maechler
time for 3.4.0. Martin > Best, > John >> -Original Message- >> From: Martin Maechler [] >> Sent: Monday, January 16, 2017 10:02 AM >> To: Fox, John <> >> Cc: r-packag

Re: [R-pkg-devel] Extending an S3 method, but putting the package in Suggests?

2017-03-14 Thread Martin Maechler
ror prone and can be resolved by correct imports as those mentioned. Martin > David > On Tue, 14 Mar 2017 at 09:06, Martin Maechler <> > wrote: >> >>>>> David Hugh-Jones <> &g

Re: [R-pkg-devel] Extending an S3 method, but putting the package in Suggests?

2017-03-14 Thread Martin Maechler
> David Hugh-Jones > on Tue, 14 Mar 2017 02:46:35 + writes: > David Hugh-Jones > on Tue, 14 Mar 2017 02:46:35 + writes: > Hi, > Cross-posted from SO: >

Re: [R-pkg-devel] tryCatch defensive programming guidance

2017-03-01 Thread Martin Maechler
> Berry Boessenkool > on Wed, 1 Mar 2017 14:52:10 + writes: > Hi Glenn, > Better late than never: > couldn't you simply use try? > result <- try( log("a") ) > The printing is horrible: people will think an error > occured

Re: [R-pkg-devel] no visible global function definition for ‘par’

2017-01-31 Thread Martin Maechler
t;median", "model.tables", > | "na.action", "na.omit", "pf", "ts", "var") > | importFrom("utils", "read.table", "str", "tail", "write.table") > |

Re: [R-pkg-devel] multiple bibentry()s in CITATION

2017-01-16 Thread Martin Maechler
, e.g., > options(citation.bibtex.max = 1); citation(package = "copula") To cite the R package copula in publications use: Marius Hofert, Ivan Kojadinovic, Martin Maechler and Jun Yan (2017). copula: Multivariate Dependence with Copulas. R package version 0.999-16 URL https://CRAN.R-pro

Re: [R-pkg-devel] Question about configure file and system requirements

2016-11-21 Thread Martin Maechler
me logic that you should not list 'Depends', 'Imports', 'Suggests', etc of those packages. Martin Maechler ETH Zurich > Asking this because the "configure" and system > requirements are already present in the imported packages, > so my configuration check

Re: [R-pkg-devel] fastICA on not installed?

2016-10-12 Thread Martin Maechler mentions different formats, including Epub. Martin Maechler ETH Zurich __ mailing list

Re: [R-pkg-devel] relation between vignettes and help files

2016-07-18 Thread Martin Maechler
of info between help files and > vignettes? > Ross > > From: Martin Maechler [] > Sent: Friday, July 15, 2016 5:32 AM > To: Duncan Murdoch > Cc: Enrico Schumann; Boylan, Ross; r-package-devel@r-proje

Re: [R-pkg-devel] using printf() in C code (package 'powell')

2016-05-04 Thread Martin Maechler
Warnings(.) etc. This will definitely not go away with R 3.3.0 or any later version of R. But then maintainer("powell") is still active, and his e-mail address at your fingertips,..., right ? --> I've BCC'ed Sundar, so he is informed. With best regards, Martin M

Re: [R-pkg-devel] Is it possible to protect a word from the spell checker?

2016-03-02 Thread Martin Maechler
> Hana Sevcikova > on Tue, 1 Mar 2016 11:45:34 -0800 writes: > If it's in the DESCRIPTION file put the word into quotes. > Hana Indeed, thank you Hana! To add - embarrassingly I've only learned this about a week ago - they need to be *single* quotes (as used

Re: [R-pkg-devel] Development Testers?

2016-02-09 Thread Martin Maechler
indeed quite focused (with a somewhat different focus). And yes, for the specific, I'd strongly recommend R-SIG-HPC (in addition, i.e., with the very rare case of sensible cross posting). Best regards, Martin -- Martin Maechler ETH Zurich and R Core Team > Regards, Charles > On F

Re: [R-pkg-devel] S3 length method behavior

2016-02-02 Thread Martin Maechler
> Barry Rowlingson > on Tue, 2 Feb 2016 17:23:46 + writes: > On Tue, Feb 2, 2016 at 3:28 PM, Hadley Wickham wrote: >> I've found that it's a very bad idea to provide length or names >> methods for just this reason.

Re: [R-pkg-devel] Problems with :::

2016-02-01 Thread Martin Maechler
> Kirill Müller > on Thu, 28 Jan 2016 17:42:12 +0100 writes: > On 28.01.2016 14:20, Duncan Murdoch wrote: >> If the class is just "mytable", then you'll have to >> change it to "ftable" before calling stats::format(). > Side note: The

Re: [R-pkg-devel] Return Value of By Function

2015-09-15 Thread Martin Maechler
ling list for such questions ! Please ask on different list (or forum), e.g., on R-help. Martin Maechler __ mailing list

Re: [R-pkg-devel] Visible bindings and reference classes

2015-08-11 Thread Martin Maechler
with that. So there must be something peculiar in your package leading to the - warnings. Maybe you should look into the source code of such other CRAN packages to see how they do it differently than you. Best regards, Martin Martin Maechler, ETH Zurich After some googling, I came across the page

Re: [R-pkg-devel] apparent S3 methods note in R CMD check

2015-06-13 Thread Martin Maechler
wrote: Dear Martin, Thank you for addressing this issue. Introducing a nonS3method() directive in NAMESPACE seems a reasonable solution. It could replace export() for functions with .s in their names. Best, John On Fri, 12 Jun 2015 09:55:18 +0200 Martin Maechler

Re: [R-pkg-devel] use of `` across platforms in RStudio

2015-06-13 Thread Martin Maechler
Alex Chubaty on Fri, 12 Jun 2015 14:41:56 -0700 writes: Dear list members, Use of platform-specific code to open new plot devices (e.g., `quartz`, `x11`) is discouraged in favour of using ``; however, this does not work in RStudio. A