Re: [Rd] Halfway through writing an "IDE" with support for R; Proof of concept, and request for suggestions.

On Sat, Jun 15, 2019 at 01:13:07PM +1200, Abby Spurdle wrote: What about Atom, VS Code and the like? Or what about taking a project that meets most of the constraints and pushing to cover all of them, or even forking it and modifying the part you don't like? I'm not prepared to endorse GitHub

Re: [R-pkg-devel] R CMD check Rcpp_1.0.1.tar.gz error

Howdy, There is a dedicated list for Rcpp we recommend users use... On 17 June 2019 at 20:56, Wang, Zhu wrote: | installing *source* package 'Rcpp' ... | ** package 'Rcpp' successfully unpacked and MD5 sums checked | ** using non-staged installation | ** libs | g++ -std=gnu++11

Re: [R-pkg-devel] R CMD check Rcpp_1.0.1.tar.gz error

Indeed it is from .R/Makevars. Thanks! From: Ben Bolker Sent: Monday, June 17, 2019 4:03 PM To: Wang, Zhu Cc: R-package-devel@r-project.org Subject: Re: [R-pkg-devel] R CMD check Rcpp_1.0.1.tar.gz error This looks like it's caused by the quotation marks around the compiler flags ("-g ... "),

Re: [R-pkg-devel] R CMD check Rcpp_1.0.1.tar.gz error

This looks like it's caused by the quotation marks around the compiler flags ("-g ... "), but I couldn't tell you how they got there or how to get rid of them ... On Tue, Jun 18, 2019, 6:57 AM Wang, Zhu wrote: > Dear all, > > For some reason, I couldn't install Rcpp >

[R-pkg-devel] R CMD check Rcpp_1.0.1.tar.gz error

Dear all, For some reason, I couldn't install Rcpp https://cran.r-project.org/web/packages/Rcpp/index.html, and R CMD check generated the error message below. I also attached Makeconf file referred below. Thanks for your attention. Zhu Wang installing *source* package 'Rcpp' ... ** package

Re: [Bioc-devel] failing package TimeSeriesExperiment

Dear Lori, I sorry for a late response. I have finally found time to look into the package error. I fixed the current error while check is performed for TimeSeriesExperiment, however, there is another that I cannot address due to dependencies. My package uses a voom() function from limma

Re: [Bioc-devel] Linking packages in man pages

Huh, that would make a lot of sense. But what's strange is that the dplyr package uses the same syntax ( https://github.com/tidyverse/dplyr/blob/master/man/reexports.Rd, line 39): \item{magrittr}{\code{\link[magrittr]{\%>\%}}} And the documentation for `%>%` is actually pipe.html. I'll probably

Re: [Bioc-devel] Linking packages in man pages

The problem is that the use of \link[]{} syntax requires that the help page is _named_ "%<>%.html" -- extremely unlikely! Actually the help page is named "compound.html". Again, avoid the problem of providing the name of the help page by letting R do the work for you `\code{\link{"\%<>\%"}}

Re: [Bioc-devel] Linking packages in man pages

Makes sense for mclapply, I'll remove the links in the documentation. What about `%<>%` from magrittr? From my recollection, it should also be available on Windows machines. Thanks, Sid On Mon, Jun 17, 2019 at 4:05 PM Martin Morgan wrote: > mclapply is not available or documented on Windows.

Re: [Bioc-devel] Linking packages in man pages

mclapply is not available or documented on Windows. I think the solution is actually to be vague, and replace \code{\link[parallel]{mclapply}}) with \code{\link{mclapply}} at https://github.com/sellerslab/gemini/blob/b1408bdce22df08d6950fee578eaac7665f54960/R/gemini_parallelization.R#L9 Martin

[Bioc-devel] Linking packages in man pages

Hello, I have been getting the following warnings upon package building on tokay1: Found the following significant warnings: Rd warning: C:/Users/pkgbuild/AppData/Local/Temp/RtmpwTSgiX/R.INSTALLe1c5c6b6ce1/gemini/man/gemini_parallelization.Rd:14: file link 'mclapply' in package 'parallel'

Re: [Rd] [External] Re: R C API resize matrix

On Mon, 17 Jun 2019, Simon Urbanek wrote: > Matrix is just a vector with the dim attribute. Assuming it is not referenced > by anyone, you can set any values to the dim attribute. As for the vector, > you can use SET_LENGTH() to shorten it - but I'm not sure how official it is > - it was

Re: [Rd] R C API resize matrix

Matrix is just a vector with the dim attribute. Assuming it is not referenced by anyone, you can set any values to the dim attribute. As for the vector, you can use SET_LENGTH() to shorten it - but I'm not sure how official it is - it was originally designed to work, but there were abuses of

Re: [R-pkg-devel] Unsure how to fix 'Package required but not available: 'dvmisc'' (which is CRAN pkg) error

On Mon, 17 Jun 2019 at 12:18, Marta Karaś wrote: > > Hi Iñaki, > > Thank you a lot for answering! Just to clarify, you basically suggest > resubmitting without any change (except from adding relevant note in > cran-comments.md)? Yes, that's correct. Iñaki

Re: [R-pkg-devel] Unsure how to fix 'Package required but not available: 'dvmisc'' (which is CRAN pkg) error

Hi Iñaki, Thank you a lot for answering! Just to clarify, you basically suggest resubmitting without any change (except from adding relevant note in cran-comments.md)? Marta On Mon, Jun 17, 2019 at 12:13 PM Iñaki Ucar wrote: > On Mon, 17 Jun 2019 at 11:13, Marta Karaś wrote: > > > > Dear

Re: [R-pkg-devel] Unsure how to fix 'Package required but not available: 'dvmisc'' (which is CRAN pkg) error

On Mon, 17 Jun 2019 at 11:13, Marta Karaś wrote: > > Dear all, > > I am trying to submit update to my R package `adept` (GitHub code link > ) and I got pre-test error on Windows > (error check log link >

Re: [R-pkg-devel] package submission errors gsl

Thanks a lot. - Mail original - De: "Iñaki Ucar" À: "halaleh kamari" Cc: "r-package-devel" Envoyé: Dimanche 16 Juin 2019 17:41:17 Objet: Re: [R-pkg-devel] package submission errors gsl On Sun, 16 Jun 2019 at 17:25, halaleh kamari wrote: > > Hi, > I'm trying to submit my first package

[R-pkg-devel] Unsure how to fix 'Package required but not available: 'dvmisc'' (which is CRAN pkg) error

Dear all, I am trying to submit update to my R package `adept` (GitHub code link ) and I got pre-test error on Windows (error check log link ) - Error

Re: [Rd] Bug report: 'formula("x")' loops infinitely ('formula("y")' does not)

> P Poncet via R-devel > on Fri, 14 Jun 2019 19:56:14 + writes: > Dear,   > The script'formula("x")' loops infinitely. well ... if it would really, your computer would still be running and heating ... ;-) > More specifically, it throws the following error:  >

[Rd] Bug report: 'formula("x")' loops infinitely ('formula("y")' does not)

Dear,   The script'formula("x")' loops infinitely. More specifically, it throws thefollowing error:    Error: evaluationnested too deeply: infinite recursion / options(expressions=)?    As a side effect,this makes an IDE like RStudio to crash. On the other hand,the script 'formula("y")' 

[Rd] R C API resize matrix

Hi, Is there a way to resize a matrix defined as follows: SEXP a = PROTECT(allocMatrix(INTSXP, 10, 2)); int *pa = INTEGER(a) To row = 5 and col = 1 or do I have to allocate a second matrix "b" with pointer *pb and do a "for" loop to transfer the value of a to b? Thank you Best regards Morgan