[Bioc-devel] plyranges maintainer update

Hi bioc-devel, I would like to request for me to removed as maintainer of the plyranges package and for > to be added as maintainer. Thank you for your help. Kind regards, Stuart Stuart Lee stuart.andrew@gmail.com

Re: [Rd] [External] Bug in out-of-bounds assignment of list object to expression() vector

Thanks for the report. Fixed in R-devel and R-patched (both R-4-4-branch and R-4-3-branch). On Fri, 5 Apr 2024, June Choe wrote: [You don't often get email from jchoe...@gmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] There seems to be a bug in

Re: [Rd] [External] Re: Bug in out-of-bounds assignment of list object to expression() vector

Thanks all for looking into this. Unfortunately I don't know my way around Bugzilla and I'm a bit occupied for the next few days - it would be great if a bug report could be opened on my behalf. Best, June On Fri, Apr 5, 2024 at 10:12 AM wrote: > On Fri, 5 Apr 2024, Ivan Krylov via R-devel

Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

Nice example of a reproducible bug report and rapid bug-fix! [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Rd] [External] Re: Bug in out-of-bounds assignment of list object to expression() vector

On Fri, 5 Apr 2024, Ivan Krylov via R-devel wrote: On Fri, 5 Apr 2024 08:15:20 -0400 June Choe wrote: When assigning a list to an out of bounds index (ex: the next, n+1 index), it errors the same but now changes the values of the vector to NULL: ``` x <- expression(a,b,c) x[[4]] <- list() #

Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

Of Note: The fix actually occurs in the AnnotationHub code base. It has been pushed to both release and devel. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

that's great, thank you so much Lori! robert. On 4/5/24 15:02, Kern, Lori wrote: > I found the bug.  Testing and pushing up a fix. > > Cheers, > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > >

Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

I found the bug. Testing and pushing up a fix. Cheers, 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 on

Re: [Rd] Bug in out-of-bounds assignment of list object to expression() vector

Yes, definitely looks like a bug. Are you able to submit it to bugs.r-project.org? Duncan Murdoch On 05/04/2024 8:15 a.m., June Choe wrote: There seems to be a bug in out-of-bounds assignment of list objects to an expression() vector. Tested on release and devel. (Many thanks to folks over at

Re: [Rd] Bug in out-of-bounds assignment of list object to expression() vector

On Fri, 5 Apr 2024 08:15:20 -0400 June Choe wrote: > When assigning a list to an out of bounds index (ex: the next, n+1 > index), it errors the same but now changes the values of the vector > to NULL: > > ``` > x <- expression(a,b,c) > x[[4]] <- list() # Error > x > #> expression(NULL, NULL,

[Rd] Bug in out-of-bounds assignment of list object to expression() vector

There seems to be a bug in out-of-bounds assignment of list objects to an expression() vector. Tested on release and devel. (Many thanks to folks over at Mastodon for the help narrowing down this bug) When assigning a list into an existing index, it correctly errors on incompatible type, and the

Re: [Bioc-devel] duplicated entries with 'ExperimentHub(localHub=TRUE)'

I will have to look at how offline changes the loading of the files. That is an odd and unexpected behavior. They aren't actually duplicate files, what is happening is it is displaying the entry for the bam file (.bam) and the index file (.bai) as separate entries when offline instead of

Re: [Bioc-devel] Important Bioconductor Release Deadlines

It is also important to note that R-devel is available throughout this last 6 months since the previous 3.18 release. Out devel branch has been building against it all along. It is available via direct download, dockers, github actions, etc. That is why we have the two branches of

Re: [Bioc-devel] Important Bioconductor Release Deadlines

On Fri, Apr 5, 2024 at 12:56 AM Anatoly Sorokin wrote: > > Dear Levi, > > minor correction: not requiring but working with. Testing against r-devel > and requiring it for development are two different things. If the > development and maintenance of the Bioconductor package would be my only >