[Bioc-devel] Macarron Next BiocRelease

Hi Bioc Team, We have fixed the windows build error for the Macarron package for the next BioC release https://bioconductor.org/checkResults/release/bioc-LATEST/Macarron/. Are the next steps to push the Macarron github changes into the new BioC release branch following the tutorial below?

Re: [Rd] as.character.Date() strips names in R 4.3.2 beta, bug?

On Tue, Oct 24, 2023 at 10:53:10AM +0200, Martin Maechler wrote: > Yes, this change has been *very* intentional: as.character() for > these objects since 4.3.0 (April 2023) finally behaves as other > as.character() methods and *does* drop attributes. [...] Thank you for the detailed explanation

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

oops, sorry, indeed, the question was about the gDNAx package and now it's all green, including kunpeng2, thank you!! robert. On 10/24/23 15:52, Hervé Pagès wrote: > > That was actually about the gDNAx package (based on the URL you > provided in your original post), which will hopefully turn

[Bioc-devel] RELEASE_3_18 branch is now available and push access is re-enabled

Dear Maintainers, You are now able to push your commits to the Bioconductor git server. The RELEASE_3_18 branch is now available on Bioconductor. Please sync your GitHub repositories with the latest updates to your package on Bioconductor for a RELEASE_3_18 branch as well as the devel branch.

Re: [Bioc-devel] Is my package suitable for Bioconductor?

I am happy to talk on Zoom about this, since I have some interest in this work. Best, Kasper On Tue, Oct 24, 2023 at 9:21 AM Vincent Carey wrote: > agreedthis discussion is best discussed in the open > > On Tue, Oct 24, 2023 at 8:57 AM Lluís Revilla > wrote: > > > Hi Tim, > > > > I think

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

You are not the only one; I did the same with some of my examples. Would it be an option to ask for a default R-option, 'max.ncores', that specifies the maximum number of cores a process is allowed to use? CRAN could then require that that examples, tests and vignettes respect this option.

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

That was actually about the gDNAx package (based on the URL you provided in your original post), which will hopefully turn green on kunpeng2 today: https://bioconductor.org/checkResults/3.18/bioc-LATEST/gDNAx Best, H. On 10/23/23 23:29, Robert Castelo wrote: > > Hervé, Martin, > > Thank you

Re: [Bioc-devel] Is my package suitable for Bioconductor?

agreedthis discussion is best discussed in the open On Tue, Oct 24, 2023 at 8:57 AM Lluís Revilla wrote: > Hi Tim, > > I think there is a mentorship program for cases like this (I am not sure if > it still accepts mentees): > https://www.bioconductor.org/developers/new-developer-program/ >

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

On 24 October 2023 at 15:55, Ivan Krylov wrote: | В Tue, 24 Oct 2023 10:37:48 + | "Helske, Jouni" пишет: | | > Examples with CPU time > 2.5 times elapsed time | > user system elapsed ratio | > exchange 1.196 0.04 0.159 7.774 | | I've downloaded the archived copy of the

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

Chapter 15 in Wickham and Bryan, R Packages, discuss "Advanced Testing Techniques". Their current section "15.4.1 Skip a test" includes the following: test_that("some long-running thing works", { skip_on_cran() # test code that can potentially take "a while" to run }) Have you

Re: [Bioc-devel] Is my package suitable for Bioconductor?

Hi Tim, I think there is a mentorship program for cases like this (I am not sure if it still accepts mentees): https://www.bioconductor.org/developers/new-developer-program/ I also recommend the book the Bioconductor community wrote to help with submissions:

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

В Tue, 24 Oct 2023 10:37:48 + "Helske, Jouni" пишет: > Examples with CPU time > 2.5 times elapsed time > user system elapsed ratio > exchange 1.196 0.04 0.159 7.774 I've downloaded the archived copy of the package from the CRAN FTP server, installed it and tried:

[Bioc-devel] Bioconductor Mirrors - Important Updates During Release Time

For anyone that is maintaining a Bioconductor mirror/rsync please make any necessary updates within the next two weeks regarding location / legacy Bioconductor releases. Starting last year, Bioconductor has moved archived versions of Bioconductor off the AWS cloudfront instance. Syncing to

[Bioc-devel] All commits to Bioconductor stopped from 8:00 am ET for release

Dear Maintainers, Please keep in mind that we are on schedule for our release as given in https://bioconductor.org/developers/release-schedule/ Today (October 24 th 2023) at 8:00 am ET, We will freeze the commits to all the branches and all packages in Bioconductor. We will notify here once we

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

In my case recently, after an hour or so’s messing about I disabled some tests and example executions to get rid of the offending times. I doubt that i am the only one to do that. On Tue, 24 Oct 2023 at 9:38 pm, Helske, Jouni wrote: > Thanks for the help, I now tried resubmitting with >

Re: [Rd] About FlexiBLAS in the R-admin docs

On 10/11/23 23:12, George Ostrouchov wrote: I agree that the "R Installation and Administration" guide statement about FlexiBLAS needs an update. Standard R in CentOS Stream 9, which is now downstream from Fedora, gives the following result for Matrix products in sessionInfo():

[Bioc-devel] Is my package suitable for Bioconductor?

Hello, My collaborators and I are considering submitting our R package for single-cell CRISPR screen data analysis to Bioconductor (package website and e-book ). We have several questions about the

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

Hi, > quickBamFlagSummary(eh[["EH8081"]]) see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation loading from cache [E::hts_hopen] Failed to open file /home/biocbuild/.cache/R/ExperimentHub/1d1f2d2a8e1eab_8133 [E::hts_open_format] Failed to open file

Re: [R-pkg-devel] Too many cores used in examples (not caused by data.table)

Thanks for the help, I now tried resubmitting with Sys.setenv("OMP_THREAD_LIMIT" = 2) at the top of the exchange example, but I still get the same note: Examples with CPU time > 2.5 times elapsed time user system elapsed ratio exchange 1.196 0.04 0.159 7.774 Not sure what to try

Re: [Rd] as.character.Date() strips names in R 4.3.2 beta, bug?

> Andrew Piskorski > on Tue, 24 Oct 2023 00:01:58 -0400 writes: > In previous versions of R, Not in R 4.3.0 or 4.3.1 {you are a bit late with updating ..}. > as.character.Date() retained any names on > its input vector. In R 4.3.2 beta, it removes names. Is

Re: [Bioc-devel] atena build error on kunpeng2 Linux openEuler 22.03 LTS-SP1 / aarch64

Hervé, Martin, Thank you so much, atena builds and checks cleanly now on kunpeng2 too!! https://bioconductor.org/checkResults/3.18/bioc-LATEST/atena cheers, robert. On 10/23/23 20:46, Hervé Pagès wrote: > > On 10/23/23 11:45, Martin Grigorov wrote: > >> Hi, >> >> >