[Rd] LCONS undefined for R_NO_REMAP

2018-01-30 Thread Jeroen Ooms
Rinternals.h has: #define CONS(a, b) cons((a), (b)) #define LCONS(a, b) lcons((a), (b)) However these are undefined when we compile with -DR_NO_REMAP. Maybe it's safer to define these using Rf_cons() and Rf_lcons() instead? __ R-devel@r-project.org mai

Re: [Rd] withTimeout bug, it does not work properly with nlme anymore

2018-01-30 Thread Martin Maechler
> Ramiro Barrantes > on Mon, 27 Nov 2017 21:02:52 + writes: > Hello, I was relying on withTimeout (from R.utils) to help > me stop nlme when it �hangs�. However, recently this > stopped working. I am pasting a reproducible example > below: withTimeout should stop

[Rd] Best practices in developing package: From a single file

2018-01-30 Thread Suzen, Mehmet
Dear R developers, I am wondering what are the best practices for developing an R package. I am aware of Hadley Wickham's best practice documentation/book (http://r-pkgs.had.co.nz/). I recall a couple of years ago there were some tools for generating a package out of a single file, such as using

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Brian G. Peterson
On Tue, 2018-01-30 at 17:00 +0100, Suzen, Mehmet wrote: > Dear R developers, > > I am wondering what are the best practices for developing an R > package. I am aware of Hadley Wickham's best practice > documentation/book (http://r-pkgs.had.co.nz/).  I recall a couple of > years ago there were some

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Michael Lawrence
I agree that it would make sense for the object to have c("by", "list") as its class attribute, since the object is known to behave as a list. However, it would may be too disruptive to make this change at this point. Hard to predict. Michael On Mon, Jan 29, 2018 at 5:00 PM, Dario Strbenac wrote

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Duncan Murdoch
On 30/01/2018 11:29 AM, Brian G. Peterson wrote: On Tue, 2018-01-30 at 17:00 +0100, Suzen, Mehmet wrote: Dear R developers, I am wondering what are the best practices for developing an R package. I am aware of Hadley Wickham's best practice documentation/book (http://r-pkgs.had.co.nz/).  I reca

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Cook, Malcolm
> >> I am wondering what are the best practices for developing an R > >> package. I am aware of Hadley Wickham's best practice > >> documentation/book (http://r-pkgs.had.co.nz/).  I recall a couple of > >> years ago there were some tools for generating a package out of a > >> single file, such

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Dirk Eddelbuettel
Mehmet, That is a loaded topic, not unlikely other topics preoccupying us these days. There is package.skeleton() in base R as you already mentioned. It drove me bonkers that it creates packages which then fail R CMD check, so I wrote a wrapper package (pkgKitten) with another helper function (k

[Rd] CRAN indices out of whack (for at least macOS)

2018-01-30 Thread Dirk Eddelbuettel
I have received three distinct (non-)bug reports where someone claimed a recent package of mine was broken ... simply because the macOS binary was not there. Is there something wrong with the cronjob providing the indices? Why is it pointing people to binaries that do not exist? Concretely, file

Re: [Rd] sum() returns NA on a long *logical* vector when nb of TRUE values exceeds 2^31

2018-01-30 Thread Hervé Pagès
Hi Martin, Henrik, Thanks for the follow up. @Martin: I vote for 2) without *any* hesitation :-) (and uniformity could be restored at some point in the future by having prod(), rowSums(), colSums(), and others align with the behavior of length() and sum()) Cheers, H. On 01/27/2018 03:06 AM,

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Kenny Bell
In response to Duncan regarding the use of roxygen2 from the point of view of a current user, I believe the issue he brings up is one of correlation rather than causation. Writing my first piece of R documentation was made much easier by using roxygen2, and it shallowed the learning curve substant

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Hervé Pagès
I agree that it makes sense to expect as.list() to perform a "strict coercion" i.e. to return an object of class "list", *even* on a list derivative. That's what as( , "list") does by default: # on a data.frame object as(data.frame(), "list") # object of class "list"

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Hervé Pagès
On 01/30/2018 02:24 PM, Hervé Pagès wrote: I agree that it makes sense to expect as.list() to perform a "strict coercion" i.e. to return an object of class "list", *even* on a list derivative. That's what as( , "list") does by default:   # on a data.frame object   as(data.frame(), "list")  # o

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Suzen, Mehmet
Dear All, Thank you for all valuable input and sorry for the off-topic for the list. I will try R-pkg-devel for further related questions. I was actually after "one-go" auto-documentation in-line or out of comments from a single file/environment in a similar spirit to 'package.skeleton or an ext

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Gabriel Becker
Dario, What version of R are you using. In my mildly old 3.4.0 installation and in the version of Revel I have lying around (also mildly old...) I don't see the behavior I think you are describing > b = by(1:2, 1:2, identity) > class(as.list(b)) [1] "list" > sessionInfo() R Under development

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Hervé Pagès
Hi Gabe, Interestingly the behavior of as.list() on by objects seem to depend on the object itself: > b1 <- by(1:2, 1:2, identity) > class(as.list(b1)) [1] "list" > b2 <- by(warpbreaks[, 1:2], warpbreaks[,"tension"], summary) > class(as.list(b2)) [1] "by" This is with R 3.4.3 and R devel (2017

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Michael Lawrence
by() does not always return a list. In Gabe's example, it returns an integer, thus it is coerced to a list. as.list() means that it should be a VECSXP, not necessarily with "list" in the class attribute. Michael On Tue, Jan 30, 2018 at 2:41 PM, Hervé Pagès wrote: > Hi Gabe, > > Interestingly th

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Suzen, Mehmet
On 30 January 2018 at 21:31, Cook, Malcolm wrote: > > I think you want to see the approach to generating a skeleton from a single > .R file presented in: > > Simple and sustainable R packaging using inlinedocs > http://inlinedocs.r-forge.r-project.org/ > > I have not used it in some time

Re: [Rd] Why R should never move to git

2018-01-30 Thread Suzen, Mehmet
This might be off topic, but if R-core development ever moves to git, I think it would make sense to have its own git service hosted by a university, rather than using github or gitlab. It is possible via https://gogs.io/ project. Just for the record. Best, -m ___

Re: [Rd] Why R should never move to git

2018-01-30 Thread Gábor Csárdi
While this is a very hypothetical argument, you could at least explain _why_ you would think so. If you were thinking about the unlikely event of GitHub / GitLab closing business, that is _not_ such a big to any active project that is hosted there. Gabor On Tue, Jan 30, 2018 at 11:07 PM, Suzen,

Re: [Rd] Why R should never move to git

2018-01-30 Thread Suzen, Mehmet
Gabor, I was just pointing out options. I think it is more of a policy decision than a technical one. For example, the very mailing list we are using is run by ETH Zurich with Martin Maechler. But it can well be run on google groups. Maybe this list should also move to google groups, it is unlikely

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Hervé Pagès
On 01/30/2018 02:50 PM, Michael Lawrence wrote: by() does not always return a list. In Gabe's example, it returns an integer, thus it is coerced to a list. as.list() means that it should be a VECSXP, not necessarily with "list" in the class attribute. The documentation is not particularly clea

Re: [Rd] as.list method for by Objects

2018-01-30 Thread Michael Lawrence
I just meant that the minimal contract for as.list() appears to be that it returns a VECSXP. To the user, we might say that is.list() will always return TRUE. I'm not sure we can expect consistency across methods beyond that, nor is it feasible at this point to match the semantics of the methods pa

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Duncan Murdoch
On 30/01/2018 4:30 PM, Kenny Bell wrote: In response to Duncan regarding the use of roxygen2 from the point of view of a current user, I believe the issue he brings up is one of correlation rather than causation. Could be. However, I think editing comments in a .R file is a bit harder than ed

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Duncan Murdoch
On 30/01/2018 4:12 PM, Dirk Eddelbuettel wrote: Mehmet, That is a loaded topic, not unlikely other topics preoccupying us these days. There is package.skeleton() in base R as you already mentioned. It drove me bonkers that it creates packages which then fail R CMD check, so I wrote a wrapper p

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Hadley Wickham
On Tue, Jan 30, 2018 at 4:55 PM, Duncan Murdoch wrote: > On 30/01/2018 4:30 PM, Kenny Bell wrote: >> >> In response to Duncan regarding the use of roxygen2 from the point of view >> of a current user, I believe the issue he brings up is one of correlation >> rather than causation. > > > Could be.

Re: [Rd] Best practices in developing package: From a single file

2018-01-30 Thread Hadley Wickham
>> There is package.skeleton() in base R as you already mentioned. It drove >> me >> bonkers that it creates packages which then fail R CMD check, so I wrote a >> wrapper package (pkgKitten) with another helper function (kitten()) which >> calls the base R helper and then cleans up it---but otherwi