Re: [R-pkg-devel] Unable to get past CRAN submission checks for package cubature

On 10 May 2021 at 13:01, Balasubramanian Narasimhan wrote: | It appears that I am unable to get beyond the auto-check service. Any | suggestions? I have tried for several weeks, and four emails, to get an answer concerning an auto-archived submission. Ironically, it aimed to address the very

[R-pkg-devel] Unable to get past CRAN submission checks for package cubature

I submitted a minor update of cubature (suggesting rmarkdown for vignettes) and received a message that the package generated warnings. However, the warnings were noted to be untrustworthy (see email below). I noted this in the submission comments as well as the reply to the auto-check email.

Re: [Bioc-devel] CTCF AnnotationHub package

The issue was immediately closed because of the issue with the version number as indicated directly on the message in the issue. https://github.com/Bioconductor/Contributions/issues/2108#issuecomment-836766063 As far as uploading data to S3, As indicated in the documentation

[Bioc-devel] CTCF AnnotationHub package

I'm submitting the CTCF AnnotationHub package, https://github.com/mdozmorov/CTCF, with the coordinates of predicted CTCF binding sites as GRanges. The package builds on all OSs, passes AnnotationHubData:::makeAnnotationHubMetadata(). It has been submitted to the tracker, but was immediately closed

Re: [Bioc-devel] Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check

Please also remember to update package NEWS files for any information about changes to your packages during this last development cycle. Bioconductor collates all package news files as part of the release announcement. See the example from the 3.12 release announcement here:

[Bioc-devel] Bioc 3.13 Feature Freeze and Deadline for passing R CMD build/check

Developers, The release of Bioconductor 3.13 is scheduled for next week. Please respect the 'feature freeze' of 3.13 where we ask that all commits are limited to bug fixes and documentation (no more API changes). The deadline to pass R CMD build and check on the daily builders is this coming

[Bioc-devel] BFG clean-up and reset for compartmap

Hi all, We had a couple manifest files that were needing to be cleaned out to pass BiocCheck and were removed using the BFG. I�d like to request a reset/force pull upstream into the BioC devel git server repo

Re: [Rd] R-devel new warning: no longer be an S4 object

> Jan Gorecki > on Mon, 10 May 2021 12:42:09 +0200 writes: > Hi R-devs, > R 4.0.5 gives no warning. Is it expected? Searching the news for "I(" > doesn't give any info. Thanks > z = I(getClass("MethodDefinition")) Now what exactly did you intend with the above line

Re: [Bioc-devel] Maintainer change Bioconductor packages

Dear Nitesh, I think that in the rush of Suhaib leaving, we didn’t finalise this process. Is it acceptable to have a group email/account as maintainer? We would have gene-express...@ebi.ac.uk, which email gets to all the Expression Atlas team members. Then we wouldn’t need to repeat the

Re: [Bioc-devel] Transfer Maintainership of the Package NetSAM

Sorry, I used the wrong email address for the new maintainer. Here is the correct information: First Name: Zhiao Last Name: Shi Email: zhiao@gmail.com Bing From: "Zhang, Bing" Date: Sunday, May 9, 2021 at 10:04 PM To: "maintai...@bioconductor.org" ,

[Bioc-devel] Transfer Maintainership of the Package NetSAM

Dear Sir or Madam, I am the maintainer of the Bioconductor package NetSAM (https://bioconductor.org/packages/release/bioc/html/NetSAM.html ). My lab moved from the Vanderbilt University to the Baylor College of Medicine a few years ago, and my email address used for NetSAM was my Vanderbilt

[Rd] R-devel new warning: no longer be an S4 object

Hi R-devs, R 4.0.5 gives no warning. Is it expected? Searching the news for "I(" doesn't give any info. Thanks z = I(getClass("MethodDefinition")) Warning message: In `class<-`(x, unique.default(c("AsIs", oldClass(x : Setting class(x) to multiple strings ("AsIs", "classRepresentation",

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

The data/experiment and many data/annotation packages are not hosted in our git (!) so it would be necessary to take another approach (rsync + untar?) to obtaining their source. Martin On 5/10/21, 6:03 AM, "Bioc-devel on behalf of Mike Smith" wrote: Hi Steffen, Thanks for the

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

Hi Steffen, Thanks for the feedback. I've been referencing this email thread when presenting about developing the code website, so it might be old but it wasn't forgotten! Right now I think we still don't quite meet your use case, as https://code.bioconductor.org/ currently only lists the

Re: [Bioc-devel] Do we have an unpacked archive for BioC, so that we can URL link to individual files ?

Hi, this is a follow-up to a rather old thread, but with Mike Smith's (twitter: @grimbough) https://code.bioconductor.org/ We now have exactly what I had been looking for. Thanks Mike and BioC team ! Yours, Steffen On Mon, 2017-11-20 at 17:07 -0500, Martin Morgan wrote: > On