Re: [Rd] Experimental CI tool for R

2020-07-23 Thread Simon Urbanek
Jeroen, This is great! It is definitely a good basis to build on. However, I wonder why your macOS setup is so extremely stripped down (not even Cairo, tcltk nor X11 - and not TeX, either) and as far from what we actually use as possible (using gcc instead of clang, openblas etc.). How do

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

2020-07-23 Thread Helmut Schütz
Dear Duncan, Duncan Murdoch wrote on 2020-07-22 23:48: On 22/07/2020 5:40 p.m., Helmut Schütz wrote: Duncan Murdoch wrote on 2020-07-22 21:42: 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

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

2020-07-23 Thread Helmut Schütz
Hi David, David Cortes wrote on 2020-07-23 13:16: It is explained here: https://cran.r-project.org/web/packages/policies.html Section about source packages: "Packages should not write in the user’s home filespace (including clipboards), nor anywhere else on the file system apart from the R

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

2020-07-23 Thread Dirk Eddelbuettel
Helmut, For previous uploads you affirmed that you read the CRAN Repository Policy which states * The code and examples provided in a package should never do anything which might be regarded as malicious or anti-social. The following are illustrative examples from past

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

2020-07-23 Thread David Cortes
It is explained here: https://cran.r-project.org/web/packages/policies.html Section about source packages: "Packages should not write in the user’s home filespace (including clipboards), nor anywhere else on the file system apart from the R session’s temporary directory (or during installation in

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

2020-07-23 Thread Duncan Murdoch
On 23/07/2020 8:18 a.m., Helmut Schütz wrote: Hi David, David Cortes wrote on 2020-07-23 13:16: It is explained here: https://cran.r-project.org/web/packages/policies.html Section about source packages: "Packages should not write in the user’s home filespace (including clipboards), nor

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

2020-07-23 Thread William Dunlap
R-4.0 introduced a new function, tools::R_user_dir(package, which), where which is one of "data", "config", and "cache". It gives standard directory names in which to place package-and-user-specific files which you want to last longer than one R session. I suppose you will still have to ask the

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

2020-07-23 Thread Sebastian Meyer
Back to the original topic: graphics.off() is probably not what you want. It shuts down *all* open graphics devices, not just the current one. Example code or your plotting functions should not do that. Calling graphics.off() in example code will also disturb standard R CMD check. Before running

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

2020-07-23 Thread bill
Thanks for the quick response both Duncan and Gábor. I've reported it here in case others want to follow-up there: https://github.com/r-lib/roxygen2/issues/1121 -Original Message- From: Gábor Csárdi Sent: Thursday, July 23, 2020 5:25 PM To: Duncan Murdoch Cc: b...@denney.ws; R

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

2020-07-23 Thread Duncan Murdoch
On 23/07/2020 5:11 p.m., Helmut Schütz wrote: Hi Dirk, Dirk Eddelbuettel wrote on 2020-07-23 15:16: Helmut, For previous uploads you affirmed that you read the CRAN Repository Policy which states [...] Your package appears to violate that requirement. As I wrote previously the

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

2020-07-23 Thread Helmut Schütz
Hi Sebastian, Sebastian Meyer wrote on 2020-07-23 16:52: Back to the original topic: THX! Calling graphics.off() in example code will also disturb standard R CMD check. Before running the examples, R CMD check opens a pdf device to store any graphics output [1]. You will find the resulting

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

2020-07-23 Thread Gábor Csárdi
On Thu, Jul 23, 2020 at 9:58 PM Duncan Murdoch wrote: > > On 23/07/2020 4:14 p.m., b...@denney.ws wrote: [...] > > If you change the source to include the explicit characters (i.e. use > pattern = c("μ", "µ") instead of pattern=c("\u03bc", "\u00b5")), does > that help? > > It may cause other

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

2020-07-23 Thread Gábor Csárdi
On Thu, Jul 23, 2020 at 10:25 PM Gábor Csárdi wrote: > > On Thu, Jul 23, 2020 at 9:58 PM Duncan Murdoch > wrote: > > > > On 23/07/2020 4:14 p.m., b...@denney.ws wrote: [...] > Bill, please report a roxygen2 issue at > https://github.com/r-lib/roxygen2/issues and we can probably fix this. [...]

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

2020-07-23 Thread Duncan Murdoch
On 23/07/2020 4:14 p.m., b...@denney.ws wrote: Hello, I have a personal package that I�d eventually like to clean up and either find other packages to be homes for the functions or perhaps eventually release it on CRAN. To that end, I try to keep package checks working. One of the

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

2020-07-23 Thread bill
Hello, I have a personal package that I�d eventually like to clean up and either find other packages to be homes for the functions or perhaps eventually release it on CRAN. To that end, I try to keep package checks working. One of the functions that I use is to try to simplify Unicode

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

2020-07-23 Thread Helmut Schütz
Hi Dirk, Dirk Eddelbuettel wrote on 2020-07-23 15:16: Helmut, For previous uploads you affirmed that you read the CRAN Repository Policy which states [...] Your package appears to violate that requirement. As I wrote previously the statement continues with "Limited exceptions may be

[Bioc-devel] build error on EnMCB package

2020-07-23 Thread xin wwa
Hello BioConductor team, We have a build error problem. We tested our package locally and find that the function cph in cms packages has changed recently which caused the error. We changed the function and tested in our environment and submitted it to git.bioconductor.org, however the error

[Bioc-devel] BiocCheck space indentation in Rmakrdown vignette documents

2020-07-23 Thread Carlos A. Catania (AKA Harpo)
Hello BioConductor Team, We are in the final steps prior to submitting a new package to Bioconductor. As recommended, we want our package to pass BiocCheck with no Errors, Warnings, or Notes. However, we have a problem regarding the indentation of a vignette written rmarkdown. -- BEGIN