Re: [R-pkg-devel] RFC: an interface to manage use of parallelism in packages

On Wed, 25 Oct 2023, Ivan Krylov wrote: Summary: at the end of this message is a link to an R package implementing an interface for managing the use of execution units in R packages. As a package maintainer, would you agree to use something like this? Does it look sufficiently reasonable to

[R-pkg-devel] PkgA imports PkgB, and PkgB suggests PkgA?

Hi All, I vaguely recall that, on CRAN, if PkgA imports PkgB, then PkgB cannot import PkgA. (Please correct me if I am wrong.) How about this? PkgA imports PkgB (because PkgA has some helper functions for using PkgB) PkgB suggests PkgA (because some vignettes or examples in PkgB use those

Re: [Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0

Forgot to mention that the package actually got installed, but is unloadable (not surprisingly):     > "CoreGx" %in% rownames(installed.packages())     [1] TRUE     > suppressWarnings(suppressMessages(library(CoreGx)))     Error : in method for ‘updateObject’ with signature

[Rd] 'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0

Hi list, Here is an example:     hpages@XPS15:~$ R CMD INSTALL CoreGx     * installing to library ‘/home/hpages/R/R-4.4.r85388/site-library’     * installing *source* package ‘CoreGx’ ...     ** using staged installation     ** R     ** data     *** moving datasets to lazyload DB     **

[Bioc-devel] ReactomeGSA missing in Bioconductor 3.18?

Hi everyone, For a while the build system reported an error that our ReactomeGSA package cannot be build due to the missing dependency of the "ReactomeGSA.data" package which is required to build the vignettes and is listed in the "Suggests" section. ReactomeGSA.data seems to building fine

Re: [R-pkg-devel] [r-package-devel] Win.Metafile and package check - "Found the platform-specific device:"

On Fri, 3 Nov 2023, wayne.w.jo...@shell.com wrote: Dear R-Package-Devel, As part of GWSDAT package (https://github.com/waynegitshell/GWSDAT) we support the option to output plots to a WMF (https://r-graphics.org/recipe-output-vector-wmf) format if, and only if, the user is on Windows.

Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

Yes. An initial space does the trick. Thanks. J On 2023-11-03 11:48, Serguei Sokol wrote: Le 03/11/2023 à 15:54, J C Nash a écrit : I've spent a couple of hours with an Rmarkdown document where I was describing some spherical coordinates made up of a radius r and some angles. I wanted to fix

Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

Le 03/11/2023 à 15:54, J C Nash a écrit : I've spent a couple of hours with an Rmarkdown document where I was describing some spherical coordinates made up of a radius r and some angles. I wanted to fix the radius at 1. In my Rmarkdown text I wrote    Thus we have `r = 1` ... To avoid a

Re: [R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

A code chunk does always begin with a triple backtick at the beginning of a line. The term for what you encountered is "inline code" used to embed computed results into the markdown text as though you had typed them directly. Check out

Re: [Bioc-devel] EpiCompare: transferring maintainership

We will need to create a BiocCredentials account for Tom Roberts if he does not have one yet. We would need to know what email Tom would like for access there as well as if they have a github id? I can create the account and allow access. After access to the package, it will be up to the new

[Bioc-devel] EpiCompare: transferring maintainership

Hi Bioconductor team, I'm currently the maintainer of Bioconductor package, EpiCompare. I'm writing to request transfer of maintainership to Tom Roberts ( tomroberts.wor...@gmail.com). Please could you let me know what is required? Thanks so much! Best wishes, Sera [[alternative HTML

[R-pkg-devel] Rmarkdown fails if (quote) r (space) is used

I've spent a couple of hours with an Rmarkdown document where I was describing some spherical coordinates made up of a radius r and some angles. I wanted to fix the radius at 1. In my Rmarkdown text I wrote Thus we have `r = 1` ... This caused failure to render with "unexpected =". I was

[Rd] svd() of a 30000 by 30000 matrix segfaults: 32-bit length overflow in LAPACK?

Dear Dr. Robert M Flight, dear R-developers, By an accident, I've noticed this problem reported on Mastodon [1]. On a computer with ≥32G of RAM, running the following code (which may take 5 CPU-hours and allocate 27G of RAM!) results in a segfault: n_val <- 3 tmp_matrix <-

Re: [Bioc-devel] gwasurvivr is looking for a new owner/maintainer

Ali - I'll email you separately! If any other folks are interested, please still inquire as we figure out the ownership handoff. Thank you! Abbas On Fri, Nov 3, 2023 at 9:01 AM Ali Sajid Imami wrote: > I am definitely interested, as I am working heavily with GWAS data now. > > > On Nov 3,

[R-pkg-devel] [r-package-devel] Win.Metafile and package check - "Found the platform-specific device:"

Dear R-Package-Devel, As part of GWSDAT package (https://github.com/waynegitshell/GWSDAT) we support the option to output plots to a WMF (https://r-graphics.org/recipe-output-vector-wmf) format if, and only if, the user is on Windows. However, when I run the package checks on here it

[Bioc-devel] gwasurvivr is looking for a new owner/maintainer

Dear Bioconductor Developers, We are looking for a new primary owner for gwasurvivr . This package allows users to build multivariate Cox models on typed/imputed GWAS data. It seems to have quite a few regular users and has

Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

On Wed, 1 Nov 2023, David Hugh-Jones wrote: Aside from the package question, surely the other issue here is that Prof Ripley’s email is extraordinarily rude. Any paid employee would be sacked for that. I appreciate R and CRAN are volunteer-run organisations, but I don’t think that should be

Re: [Bioc-devel] Add a package to BiocCredentials

Hi Lori, Thanks for that. Yes, I can confirm that Mengbo Li is one of the scider authors and maintainers. Could you please grant Mengbo access to scider on Bioc git? Best, Yunshun From: Kern, Lori Sent: Friday, November 3, 2023 22:15 To:

Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

Guys, Martin, I am very sorry you spent all that time. I am sceptical that this is a correct interpretation of the law, given what I see on Twitter daily, and I would not take a university as an authority on this. But that is neither here nor there – if I made you waste your time, that's my bad

Re: [R-pkg-devel] Package bioOED has been removed from CRAN just for personal reasons

Dear R-package-devel readers *and* notably writers, In Europe there are (diverse) laws about privacy etc, and those, (and/or some politeness) do not allow free citing of private e-mail communications in public nor ad hominem remarks in such public communication. For this reason, I (as mailing

Re: [Bioc-devel] Add a package to BiocCredentials

Yunchun Chen as the current maintainer can you please confirm this request? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From:

[Bioc-devel] Add a package to BiocCredentials

Dear core team, Hope this email finds you well. Could I please have scider (https://bioconductor.org/packages/release/bioc/html/scider.html) added to my Bioc git credentials? The email address is li...@wehi.edu.au. I have also cc-ed the current maintainer of the

[Bioc-devel] problems when updating MOSim package

Dear Lori, We have made some changes in the MOSim package and we are now trying to update the package in Bioconductor. However, we cannot make it. This is the error message we get: PS W:\MOSim> git push upstream devel g...@git.bioconductor.org: Permission denied (publickey). fatal: Could not