Re: [R-pkg-devel] More on explosive dependencies

2018-07-16 Thread David Hugh-Jones
Hi Russell, That's v helpful and I am going to try it myself. Can I just ask what goes in your namespace file (and what roxygen tags you use) for the relevant methods? David On Tue, 17 Jul 2018 at 02:29, Lenth, Russell V wrote: > Thanks to all who responded. I am pleased to say that with

Re: [R-pkg-devel] More on explosive dependencies

2018-07-16 Thread Lenth, Russell V
Thanks to all who responded. I am pleased to say that with your help, I have managed to work around this problem by dynamically registering the methods. My file zzz.R contains code to register various methods having generics in coda and multcomp. Those packages are in Suggests (not Imports) and

Re: [Rd] Top level \Sexpr and R CMD check

2018-07-16 Thread Gábor Csárdi
The patch indeed solves the issue. Thanks much, G. On Thu, Jul 12, 2018 at 5:29 PM Duncan Murdoch wrote: > > On 12/07/2018 9:46 AM, Gábor Csárdi wrote: > > On Thu, Jul 12, 2018 at 2:30 PM Gábor Csárdi wrote: > >> > >> On Thu, Jul 12, 2018 at 2:21 PM Duncan Murdoch > >> wrote: > >>> I think I

Re: [R-pkg-devel] Package builds, installs, and runs but does not pass devtools::check()

2018-07-16 Thread Zhian Kamvar
Using dplyr like that is for exploratory data analysis. You'll want to refer to dplyr's "Programming with dplyr" vignette for using dplyr in a package: https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html

Re: [R-pkg-devel] Package builds, installs, and runs but does not pass devtools::check()

2018-07-16 Thread Fox, John
Dear Michael, You could add a call to globalVariables() in the package sources for cases like this. I hope this helps, John - John Fox Professor Emeritus McMaster University Hamilton, Ontario, Canada Web:

Re: [R-pkg-devel] Package builds, installs, and runs but does not pass devtools::check()

2018-07-16 Thread Michael Hannon
Thanks, Georgi. I've changed my approach and now do what I gather is recommended practice: put all external package names into the "Imports" section of the DESCRIPTION file and then use the fully-qualified names for functions from those packages, as: dplyr::select() The "check" operation is

[Rd] Output mis-encoded on Windows w/ RGui 3.5.1 in strange case

2018-07-16 Thread Kevin Ushey
Given the following R script: x <- 1 print(list()) save(x, file = tempfile()) output <- encodeString("apple") print(output) If I source this script from RGui on Windows, I see the output: > source("encoding.R") list() [1] "\002ÿþapple\003ÿþ" That is, it's as though R

[Rd] Memory leakage from large lists

2018-07-16 Thread Daniel Raduta
Hello, I am experiencing a very noticeable memory leak when using large lists of large data. The code below creates a list of matrices, yet the memory does not free up after removing that item and performing a garbage collection. Is there a something I can do to prevent this memory leak? Any help

Re: [Rd] persp command

2018-07-16 Thread Christian Rau
Dear Robert, Thank you for pointing out the existence of the two different conventions in mathematics and physics --- sorry that I hadn't investigated this in advance. As far as I am aware, the mathematicians use the "physics" convention quite often, but can certainly accept the different

Re: [Rd] persp command

2018-07-16 Thread Robert Baer
On 7/16/2018 7:28 AM, Christian Rau wrote: Dear R-devel mailing list, I am wondering whether the "theta" and "phi" parameters of the "persp" function in the graphics commands are named in error (the names seem to have been swapped). Not that it is authoritative, but one gleans from wikipedia,

Re: [Bioc-devel] BiocManager now on CRAN

2018-07-16 Thread Gabe Becker
Ah, of course. I should have realized that. Makes sense. I'll get that fixed in devel soon. Thanks and sorry for the noise. ~G On Mon, Jul 16, 2018 at 9:37 AM, Marcel Ramos wrote: > Hi Gabe, > > Please note that we are only making changes to packages in *bioc-devel*. > > BiocManager wouldn't

Re: [Bioc-devel] BiocManager now on CRAN

2018-07-16 Thread Gabe Becker
Marcel et al, My genbankr package is one of the ones that mentions biocLite (in README.md, actually, not the vignette proper, but still...). Historically this was just because I had missed your email and hadn't updated it, but when I sat down to do it I ran into an issue: BiocManager, while a

[Rd] persp command

2018-07-16 Thread Christian Rau
Dear R-devel mailing list, I am wondering whether the "theta" and "phi" parameters of the "persp" function in the graphics commands are named in error (the names seem to have been swapped). Also, in the documentation to "persp", reference is made to "colatitude" when the effect in the image is

Re: [R-pkg-devel] Reverse dependencies - again

2018-07-16 Thread Dirk Eddelbuettel
On 11 July 2018 at 10:00, J C Nash wrote: | 2) Is it time to consider an effort to provide online revdep checking | that would avoid pressure on CRAN team directly and would provide | clearer indicators of the issues raised by a particular package? That is very close to my R Foundation Summit

Re: [R-pkg-devel] More on explosive dependencies

2018-07-16 Thread Iñaki Úcar
El lun., 16 jul. 2018 a las 3:24, Lenth, Russell V () escribió: > > Package developers, > > I posted a question a couple of months ago dealing with how to reduce the > number of dependencies in a package. Part of the specific issue I face is > that I have a `cld` S3 method for which the generic

Re: [R-pkg-devel] More on explosive dependencies

2018-07-16 Thread David Hugh-Jones
Hi Russ, Possibly relevant: the modelgenerics package (on GitHub) does exactly what you're suggesting for standard model functions like `nobs` etc. I think at some point it is going to become part of the tidyverse. D On Mon, 16 Jul 2018 at 02:24, Lenth, Russell V wrote: > Package