Re: [Rd] R-devel internal errors during check produce?

2020-06-26 Thread Jan Gorecki
So the unique.default is from the R tools package during checks. I don't see those issues on CRAN checks. Exact environment where I am reproducing this issue is a fresh ubuntu, no R packages pre-installed docker pull registry.gitlab.com/jangorecki/dockerfiles/r-devel

[Rd] R-devel internal errors during check produce?

2020-06-26 Thread Jan Gorecki
Hi R developers, On R-devel (2020-06-24 r78746) I am getting those two new exceptions during R check. I found a change which eventually may be related https://github.com/wch/r-source/commit/69de92b9fb1b7f2a7c8d1394b8d56050881a5465 I think this may be a regression. I grep'ed package manuals and R

[Rd] Error in substring: invalid multibyte string

2020-06-26 Thread Toby Hocking
Hi all, I'm getting the following error from substring: > substr("Jens Oehlschl\xe4gel-Akiyoshi", 1, 100) Error in substr("Jens Oehlschl\xe4gel-Akiyoshi", 1, 100) : invalid multibyte string at 'gel-A<6b>iyoshi' Is that normal / intended? I've tried setting the Encoding/locale to Latin-1/UTF-8

[Rd] Change in lapply's missing argument passing

2020-06-26 Thread William Dunlap via R-devel
Consider the following expression, in which we pass 'i=', with no value given for the 'i' argument, to lapply. lapply("x", function(i, j) c(i=missing(i),j=missing(j), i=) >From R-2.14.0 (2011-10-31) through R-3.4.4 (2018-03-15) this evaluated to c(i=TRUE, j=FALSE). From R-3.5.0 (2018-04-23)

Re: [R-pkg-devel] error when submit a package

2020-06-26 Thread Guo, Wei (NIH/NIMH) [C] via R-package-devel
Thank you all for the help. I do ask a question about a package _outside of CRAN yesterday. But I have new questions today about the global variable undefined, which was read from an Rdata object. Thank you for your kind help again. Best, Wei -Original Message- From: Dirk Eddelbuettel

Re: [R-pkg-devel] error when submit a package

2020-06-26 Thread Dirk Eddelbuettel
On 26 June 2020 at 19:16, Zehao Xu wrote: | Package suggested but not available for checking: 'actigraphy' | | ``` | | This stackoverflow https://stackoverflow.com/questions/51453717/issue-with-r-package-check-on-windows-package-suggested-but-not-available-str can solve you problem No,

Re: [R-pkg-devel] error when submit a package

2020-06-26 Thread Paul Hibbing
* The fourth can likely be addressed by if(getRversion() >= "2.15.1") utils::globalVariables(c("IV", "M", "filename2id", "wear_flag")) See https://github.com/tidyverse/magrittr/issues/29 * The fifth suggests you need to replace the default vignette title with something specific to your package.

Re: [R-pkg-devel] error when submit a package

2020-06-26 Thread Zehao Xu
Well, The first note can be ignored (Note that you are the maintainer), the second one ``` Maintainer: 'Wei Guoi ' Authors@R: 'Wei Guo ' ``` clearly, you miss spelled your name... the third one, ``` checking package dependencies ... NOTE Package suggested but not available for

Re: [Bioc-devel] Unable to reproduce OS/X build error for "netDx" package

2020-06-26 Thread Mike Smith
Hi Shraddha, I don't know what Java the build system uses, but I can reproduce the error with Java 13. It's fine with Java 8 as you say. I wont copy the whole error message as it's the same as I see on the build system, but I do notice that in the middle I see: Java 8 detected This seems

Re: [R-pkg-devel] error when submit a package

2020-06-26 Thread Bert Gunter
Did you not post this before and receive answers? Please explain why the previous answers were insufficient. "Some notes are not fixable" is not a satisfactory response. Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka

[R-pkg-devel] error when submit a package

2020-06-26 Thread Guo, Wei (NIH/NIMH) [C] via R-package-devel
Good afternoon, I am trying to submit my package to CRAN, and it failed to pass the checks due to 5 notes. I am wondering how to fix it. Within the 5 notes, some are not fixable. Thanks. Best, Wei Dear maintainer, package postGGIR_2.0.0.tar.gz does not pass the incoming checks

Re: [Bioc-devel] Deprecated a contained class

2020-06-26 Thread Hervé Pagès
Hi Martin, Don't know how/where to implement a deprecation message that wouldn't be confusing for the end users. FWIW if the replacement of class Original with class New is just a renaming (everything else remains the same), a situation I've dealt with a lot in the

Re: [Rd] R 4.0.1-4.0.2 built with Intel Composer 19.0-19.1.1, error in "make check" on CentOS 7.7

2020-06-26 Thread Ryan Novosielski
> On Jun 25, 2020, at 8:06 AM, Ivan Krylov wrote: > > On Wed, 24 Jun 2020 18:56:06 + > Ryan Novosielski wrote: > > On my machine, getOption('expressions') is 5000 and the example from > the test correctly stops with length(traceback()) == 2500. (And the > simpler example of f <- function()

Re: [Rd] R 4.0.1-4.0.2 built with Intel Composer 19.0-19.1.1, error in "make check" on CentOS 7.7

2020-06-26 Thread Ryan Novosielski
> On Jun 25, 2020, at 10:31 AM, Bjørn-Helge Mevik wrote: > > Signed PGP part > Ryan Novosielski writes: > >> Hi there, >> >> I initially asked about this on r-help and was told this might be a better >> venue. I’m not really convinced from reading the posting guide, but I’ll >> give it a

[Bioc-devel] Deprecated a contained class

2020-06-26 Thread Martin Morgan
Pkg A provides a (virtual) class "Original". Pkg B creates a derived class setClass("Derived", contains = "Original") Pkg A would like to deprecate "Original" and replace with "New". Any ideas on how to implement a deprecation message so that the Pkg B maintainer knows that their use of class