[Bioc-devel] Bioconductor Board Nominations Open

Nominations are now open for the 2025 Bioconductor Community and Technical Advisory Boards! If you're interested in contributing to the Bioconductor project, or know someone who would be a great fit, please consider applying or nominating. Community Advisory Board (CAB): * Promote inclusive

Re: [Bioc-devel] Deprecate hiAnnotator

Thank you for reaching out. We can take care of the deprecation for you. Would you also like hiReadsProcessor deprecated as hiReadsProcessor depends on hiAnnotator and will not be able to build without it? I notice you are also the maintainer of that package. Cheers Lori Shepherd - Kern Bio

Re: [Bioc-devel] cyTOFpower

Thank you for letting us know. We will try to reach out to the newly listed contact information and decide how to proceed from there. We appreciate your correspondence and attention to this matter. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center

Re: [Bioc-devel] possible ExperimentHub cache problem in the BBS with gDNAx

I just redownloaded all listed ids. Let's see what happens on the next build Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From

Re: [Bioc-devel] possible ExperimentHub cache problem in the BBS with gDNAx

Can you provide the EH ids of the resources involved to reset? 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 o

Re: [Bioc-devel] hiReadsProcessor Bioconductor package

It looks like this is an empty message? Based on the title: It looks like your package has been failing in devel. https://bioconductor.org/checkResults/devel/bioc-LATEST/hiReadsProcessor/ The error message gives instructions on how to resolve the error. Let us know if you need further assistanc

Re: [Bioc-devel] hiReadsProcessor Bioconductor package

Thank you for your response. I can assist with deprecation. Thank you for letting us know. Cheers, 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] Help updating data in ExperimentHub

So a few follow up questions and comments It seems like you a referencing an ExperimentHub data package with the snapshot date; is that correct? And if so, you mentioned you updated the raw data; you have updated those files on the hosted server? And did you request an update to the metadata

Re: [Bioc-devel] Access to Git Credential for seqpac

Yes I will be in touch off list to assist with this. 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 behalf o

Re: [Bioc-devel] Adding maintainer to Macarron Bioconductor package

We can assist with this request as you are the current maintainer. We will have to create a BiocCredentials account for Amrisha Bhosle. I will be in contact off mailing list for the details on creating this account. Once created and activated, they will have push access to the package. Any em

Re: [Bioc-devel] Developer access to BayesSpace on BioConductor

It seems we have updated the configuration on our end to Ed Zhao last fall as requested, but they have not updated the DESCRIPTION accordingly. Please remember as we switch maintainer access, if the correspondence should also be updated that needs to be updated in the DESCRITPION of the packag

Re: [Bioc-devel] Not associated with a maintainer

Your package is still in the awaiting moderation stage which means it has not yet been added to our git.bioconductor.org location. You can ping on the issue that you are ready for another look at the package. Once the package is in a prereview or review stage, then it will be on git.bioconduc

Re: [Bioc-devel] Developer access to BayesSpace on BioConductor

Could we please have Matt Stone the currently listed maintainer verify this request. 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] Help Remote Installations

Hello Francesco, To expand on lluis reply: packages not on CRAN or Bioconductor are not allowed and strictly enforced on Bioconductor systems so please keep this in mind but agree that it is general practice to put these types of packages in Suggest. Lori Shepherd - Kern Bioconductor Core Tea

Re: [Bioc-devel] ssh key

I can assist with this and will be in touch off list for further communication Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 Fro

[Bioc-devel] Single Package Builder for new Bioconductor Submissions

Over the next few days, we will be transitioning the single package builder for new Bioconductor submissions to use Bioconductor 3.22 rather than 3.21 following the latest Bioconductor release on April 16. This may result in downtime to the build on demand functionality. We appreciate your un

[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 a few years ago, Bioconductor has moved archived versions of Bioconductor off the AWS cloudfront instance. Syncing t

[Bioc-devel] Bioconductor 3.21 is Released!

Thanks to all developers and community members for contributing to the project! Please see the full release announcement: https://bioconductor.org/news/bioc_3_21_release/ If you have local checkouts of Bioconductor repositories, please remember to sync/git pull for updated versions of the packa

Re: [Bioc-devel] Unexpected Build Failure for BulkSignalR

Thank you for your quick attention to this matter. I can look into the palamino error if it persists post Bioconductor release (later this week or early next). The error did not prevent the package from being included in this April 16 release. I am also looking into making the BiocFileCache

[Bioc-devel] RELEASE_3_21 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_21 branch is now available on Bioconductor. Please sync your GitHub repositories with the latest updates to your package on Bioconductor for a RELEASE_3_21 branch as well as the devel branch. Th

[Bioc-devel] All commits to Bioconductor stopped from 7:30 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/ As of 7:30 am ET today, (April 15th 2025) , all branches of all packages in Bioconductor are frozen. We will notify here once we are done with the

[Bioc-devel] Last day to make commits before Bioconductor RELEASE 3.21

We are still on track for Bioconductor Release 3.21 for this Wednesday April 16th. This means that tonight is the last day to commit changes to the devel branch before creation of the RELEASE_3_21 versions of your packages. And any changes you make to your packages at this point will not be re

[Bioc-devel] Important Bioconductor Release 3.21

The deadline for fixing packages in preparation for the release is today Friday April 11th. All packages should be installing, building, and checking without ERROR in the Bioconductor build report. While you can continue to push changes past this date, this ensures all changes are reflected in

Re: [Bioc-devel] Final Reminder: Submit Your Abstract for GBCC2025 by April 8th!

The R 4.5 release is this Friday April 11. More over, it will not be available via BiocManager in devel because it needs to build on our builders. It is failing across all https://bioconductor.org/checkResults/devel/bioc-LATEST/RbowtieCuda/ but that is expected because of the Nvidia GPU/cuda

Re: [Bioc-devel] KEGGREST error in build reports

There was a fix pushed to github but not yet included into git.bioconductor.org. We will merge the changes over shortly. We apologize for the inconvenience Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm

[Bioc-devel] Important Bioconductor Release 3.21

The deadline for fixing packages in preparation for the release is this Friday April 11th. All packages should be installing, building, and checking without ERROR in the Bioconductor devel build report. While you can continue to push changes past this date, this ensures all changes are reflecte

Re: [Bioc-devel] List of Deprecated Packages for Bioc3.21

issue tracker). However, I don't see these packages on this list. Are these cases handled differently? Best, Llu�s On Thu, 27 Mar 2025 at 15:56, Kern, Lori via Bioc-devel mailto:bioc-devel@r-project.org>> wrote: The Bioconductor Team is continuing to identify packages that will be

Re: [Bioc-devel] List of Deprecated Packages for Bioc3.21

a package. These packages do not have the dependency removed on the devel branch as far as I can tell or the maintainers are aware of the situation ( no activity on their issue tracker). However, I don't see these packages on this list. Are these cases handled differently? Best,

Re: [Bioc-devel] Build error for cfTools

Likely it is a compatibility issue with python version and available modules. You might look at updating the package to be compatible with a more recent version of tensorflow The core team is preparing for the release and might not be able to help debug this until post release. Maybe someone

Re: [Bioc-devel] Build error for cfTools

Yes it does as it has not built at all for the given cycle, it would not be available via BiocManager to the end user. You can verify that it has not yet built by looking at the bottom of the package landing page at Package Archive section and having nothing available for the windows section:

[Bioc-devel] Release_3_20 branch is now frozen

The RELEASE_3_19 branch is now frozen and no longer accepts push commits at git.bioconductor.org. See https://stat.ethz.ch/pipermail/bioc-devel/2025-March/020947.html Full Release Schedule available here: https://bioconductor.org/developers/release-schedule/ Lori Shepherd - Kern Biocond

[Bioc-devel] RELEASE_3_20 frozen in a few hours

We are moving forward with the 3.21 release schedule. In roughly 4.5 hours the RELEASE_3_20 will be frozen and no longer accept commits. Any changes or bug corrections that are not pushed up by this time will not be in the Bioconductor 3.20 version of the package as we do not allow updates to

Re: [Bioc-devel] Add second maintainer for strandCheckR

Is it possible to have the current maintainer Thu-Hien confirm this? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-

Re: [Bioc-devel] Author ORCID IDs on package landing pages

I've created an issue to follow up on this https://github.com/Bioconductor/bioconductor.org/issues/311 [https://opengraph.githubassets.com/1e22887806ba5da8bbc927bdeec52318167678d7194156054ad31954399e9b1f/Bioconductor/bioconductor.org/issues/311]

Re: [Bioc-devel] segmentSeq problems reported for BioC 3.20 but not BioC 3.21: is there a need to change the code?

Ideally the RELEASE_3_20 branch should build and check without TIMEOUT/ERROR as well as devel. This is to ensure users on that branch have working code for their version of R since Bioconductor releases are closely associated with a version of R. If there were changes pushed to the devel bra

[Bioc-devel] List of Deprecated Packages for Bioc3.21

The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. This is the current list of deprecated packages for Bioc 3.21. It should be noted, we did try to reach out to these package mainta

[Bioc-devel] Important Release Deadline RELEASE_3_20 Freeze and API Feature Freeze of devel

We are moving forward with the 3.21 release reschedule. The RELEASE_3_20 branch will be frozen and no longer accept commits as of this coming Monday March 31. Any changes or bug corrections that are not pushed up by Monday (noon EST) will not be in the Bioconductor 3.20 branch of the package a

Re: [Bioc-devel] Add second maintainer for limpa package

We have updated the configuration on our end to allow Mengbo to push to the repo. Cheers, 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] autonomics current release: to fix or not ?

We would appreciate the fix being pushed to release as that branch is specific to the version of R (4.4) and those users rather than R 4.5 that devel is associated with. We don't allow pushes to frozen branches so past Monday March 31 the package would remain in that state forever more on the B

Re: [Bioc-devel] Important Bioconductor Release Deadlines

My apologies for any confusion 2 weeks until the 3.20 Freeze. The current release 3.20 freeze is NOT next Monday March 24 it is Monday March 31st. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm

[Bioc-devel] Important Bioconductor Release Deadlines

Please remember, The Bioconductor 3.20 branch will be frozen Monday March 24th. After that date, no changes will be permitted ever on that branch. The deadline for devel Bioconductor 3.21 packages to pass R CMD build and R CMD check is Friday April 11th. While you will still be able to make co

Re: [Bioc-devel] Adding new maintainer to package TFEA.ChIP

Excellent. we will adjust the configuration on our end and reach out off list to Yosra with instructions. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 1426

Re: [Bioc-devel] Bioconductor archive?

It looks like the Date/Publication field is only present when there was a change on the branch post release. (ie. any package that has a version x.y.(z+n) instead of x.y.0. After a release is frozen and a new release occurs, Bioconductor does not allow any changes or fixes even to bugs. A rel

Re: [Bioc-devel] PRONE Release Branch RELEASE_3_20 Not Updating

Please see related answer to a similar question https://stat.ethz.ch/pipermail/bioc-devel/2025-March/020862.html Release is not built everyday and takes longer to build. The pull for Thur report was Monday which was before your commit to git.bioconductor.org. It will likely appear in today's

Re: [Bioc-devel] Adding new maintainer to package TFEA.ChIP

Thank you for reaching out. As the current maintainer of the package we can proceed with this request. We would need the name, email and github id (if available) for the new maintainer to create the BiocCredentials account needed for Bioconductor maintenance. After which we can change the co

Re: [Bioc-devel] New version of rmspc - error

After a package is submitted to Bioconductor it runs on the daily build and not on demand builds that occurred during the submission process. I'm not sure which build report you are looking but the devel is still ERRORing across all platforms with the latest version that is pushed to git.biocond

[Bioc-devel] Bioconductor 3.21 db0s, OrgDbs, and TxDbs now available

Hello Bioconductor community, The newest db0, OrgDb, and TxDb annotation packages for the upcoming Bioconductor 3.21 release are up and available for download in the devel version of Bioconductor. The deadline for submitting contributed annotation packages will be Wednesday April 9th The new

[Bioc-devel] Important Bioconductor Release Deadlines

Packages submitted to the new package submission queue at this time are a first come first serve basis. Reviewers are volunteer and review packages as time permits. Submitting now will not guarantee inclusion into 3.21. It must pass the submission process including an official review and be ac

Re: [Bioc-devel] How to provide hotfix for current release

Just to add some additional info/debugging: At the top of the build report page, it indicates when the snapshot date occurred (git pull of packages). For the 3/3 report the actual snapshot was "Approx. Package Snapshot Date/Time (git pull): 2025-02-27 13:00 -0500 (Thu, 27 Feb 2025)" . https:/

Re: [Bioc-devel] Error during download data by GDCquery_clinic

It looks like a bug in the code that was fix in devel but not pushed to release (assuming you are using Bioc 3.20 / R 4.4? as you did not provide your sessionInfo?) We will ask the maintainers to fix the release version. While its not recommended to install from outside BiocManager::install to

[Bioc-devel] Bioconductor 3.21 Release Schedule

The release date for Bioc 3.21 is tentatively scheduled for Wednesday April 16th. The 3.21 release will use R-4.5. With the R dependency for 3.21 being R-4.5, these deadlines are subject to change based on CRAN official R-4.5 release date. The following highlights important deadlines for the re

Re: [Bioc-devel] Issue with devel package

Package accepted remain in devel until the next full Bioconductor release. It will move to a release at the next Bioconductor release which will be in April. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics E

Re: [Bioc-devel] crupR submission re-activation (again)

Yes we will reopen the issue. Can you please send me the link to the closed issue. 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] experimenthub package timeout and resubmission

chevreulShiny needs chevreulPlot. chevreulPlot needs chevreulData however on the closed submission issue and according to your reviewer you were no longer submitting chevreulData to Bioconductor. It is not available because it has not been processed. Please continue conversation on the gi

Re: [Bioc-devel] Add a maintainer for MuData

Yes we can assist with this request. I will be in touch off list for more information 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] Bioconductor checking error: example failed due to a suggest package of a dependecy package of my package

If the microbiome package is needed for functionality in your package, it should be listed as a dependency of your package DESCRIPTION. It currently is not listed as a Depend, Import, or Suggest. Linux will check that all needed dependencies are declared in the DESCRIPTION so that packages ca

Re: [Bioc-devel] Add maintainer to package TreeAndLeaf

Thank you for reaching out. We have updated the credentials on our end to allow access. Remember to update the DESCRIPTION of the package accordingly for automatic messages and communication if needed. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer

Re: [Bioc-devel] Additional maintainer for package AssessORFData

We can assist with this request. We will be in touch off mailing list if additional information is required 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] ExperimentHub ft resource with password

I know Martin and a collogue worked on trying to get a version of the hubs updated to have a licensing acceptance portion which required substantial efforts/rewrites as the base database of hubs had to migrate/change as well. I can look around to see where that left off. I think its similar but

Re: [Bioc-devel] spoon problems reported Multiple platform build/check BioC 3.21

It might be possible that it stems from changes in R itself or a dependent package you utilize. Bioc 3.21/Devel is using R-devel (R 4.5) it might be worth testing on that version of R with all updated devel Bioconductor packages. It looks like perhaps with using BRISC package. I was able to

Re: [Bioc-devel] rmspc problems reported in the Multiple platform build/check report for BioC 3.20

__ From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> on behalf of Kern, Lori via Bioc-devel mailto:bioc-devel@r-project.org>> Sent: Tuesday, December 17, 2024 7:07 AM To: Meriem Bahda mailto:meriemba...@gmail.com>>; bioc-devel@r-project

Re: [Bioc-devel] Segfault in viewMeans from IRanges on R-devel with Bioc-devel

I do not see any information besides the title. Please provide the code you tried and the relevant sessionInfo if we are to help or investigate further. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & C

Re: [Bioc-devel] Deprecation request for CBEA

Thank you for letting us know. We will begin the deprecation process for the package. We appreciate your contribution to Bioconductor. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Bu

Re: [Bioc-devel] Cleaned large datafiles in "batchCorr" package under review

I can assist with this request. I'll be in touch off the mailing list to finalize details. 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] Issue Installing hugene10stv1cdf on R 4.4.2

Could you please share your sessionInfo() so we know what OS you are using. Also can you please show the full output including the ERROR when running BiocManager::install("hugene10stv1cdf") I just tried locally and was able to install without issues. Lori Shepherd - Kern Bioconductor Core T

Re: [Bioc-devel] Fix dependency issues in devel and release

You should update the package yourself by pushing to the RELEASE_3_20 and devel branches on git.bioconductor.org 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] Inquiry Regarding Landing Page

Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Ali Mostafa Sent: Wednesday, December 18, 2024 10:06 PM To: Jacques Serizay Cc: Kern, Lori via Bioc-devel Subject: Re: [Bioc-devel]

Re: [Bioc-devel] Question regarding new ssh key

You can log on directly to the BiocCredentials account to see if it is pulled automatically (as well as add any keys manually). There is no need to delete the old one unless you want to. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Bios

Re: [Bioc-devel] betaHMM problems reported in the Multiple platform build/check report for BioC 3.21

Thank you for your questions. Your package is currently failing on both release and devel, therefore the changes should be pushed to both. You would need to push to a RELEASE_30 branch to fix release, and devel branch to fix devel Lori Shepherd - Kern Bioconductor Core Team Roswell Park

Re: [Bioc-devel] rmspc problems reported in the Multiple platform build/check report for BioC 3.20

Our system administrator is currently out of office. When they return we will look into this. 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] Not able to make changes to repository push to g...@git.bioconductor.org

Bioconductor will initially only give the maintainer of the package push access. It is best practice for only one person to have access to push changes; while the other should submit changes to the maintainers repository for merges and review. If multiple people really need push access, You w

Re: [Bioc-devel] groHMM package error

I don't see a valid version bump? If there is no version bump, then it will not propagate on our system 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] groHMM package error

So the command that fails: git push origin master If we break down the command, it loosely is saying push to the remote listed as origin to the branch designation master and I'm on a branch called master (implied) Looking at your origin remote: origin g...@github.com:Kraus-Lab/groHMM.git That

Re: [Bioc-devel] Which remote branch to push changes to

It depends on if these are bug fixes/vital to package usage or not. If they are then you should push to both RELEASE_3_20 and devel. If they are not and are enhancements/new features, then we would highly recommend to only push to the devel branch. There is no master branch on Bioconductor any

Re: [Bioc-devel] [EXTERNAL] SRAdb problems reported in the Multiple platform build/check report for BioC 3.21

gunzip function was removed from GEOquery. See https://code.bioconductor.org/browse/GEOquery/commit/b3f81349f937870ae030757b454a02fa759b4da7 So you will either have to find a replacement function or implement your own. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Can

Re: [Bioc-devel] Okay to push a hotfix for an existing release?

Yes if it is a bug fix and required for the package to function properly, It is okay to push to the RELEASE_3_20 branch. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York

Re: [Bioc-devel] change of maintainer

As Anna already had a BiocCredentials account, we have made the switch on our configurations. Anna should be all set Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 142

Re: [Bioc-devel] Request to Add an Additional Developer to CRISPRseek on Bioconductor

We can assist with this request. We will need to set up a BiocCredentials account for Dr. Kai Hu. I will be in touch off mailing list to continue this process. It will be recommended that the additional maintainer also sign up for the bioc-devel mailing list and support site with appropriate w

Re: [Bioc-devel] Build error: missing downloadthis dependency

It looks like from the downloadthis CRAN page https://cran.r-project.org/web/packages/downloadthis/index.html, that the macOS binary for devel (using R 4.5.0) is not yet available. I think it is safe to ignore this ERROR in devel until the binary is produced by CRAN and this ERROR should res

Re: [Bioc-devel] Unable to push changes to g...@git.bioconductor.org:packages

The 'master' branch on Bioconductor has been deprecated for over a year and recently removed from access. The default branch in Bioconductor is now 'devel'. See https://support.bioconductor.org/p/9149923/ You can also check out the instructions at https://contributions.bioconductor.org/git-

[Bioc-devel] Single Package Builder for New Bioconductor Submissions

Over the next few days we will be moving the builder for new Bioconductor submissions to use Bioc 3.21. During that time the on-demand build feature may be intermittently unavailable. We appreciate your understanding. Also of note: for those of you with packages with "awaiting moderation" . W

Re: [Bioc-devel] SurfR Enrichment_barplot git<->builder sync issues

We do not sync github repositories automatically. You will need to push your changes to git.bioconductor.org. The repository on our git server is the only version Bioconductor knows/propagates. A new version will not propagate without a valid version bump as well. Please see https://contribut

Re: [Bioc-devel] SurfR Enrichment_barplot git<->builder sync issues

You mentioned it was the examples; I see you are using roxygen; did you run document and check in the new man files officially? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo,

Re: [Bioc-devel] Is it possible to reopen a closed issue on to push reviewed code for the next release ?

You should not created a new issue and just request the issue be reopened. You will not receive build reports until the issue is ready to be re-opened Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Car

Re: [Bioc-devel] Cannot trace "Warning"

This seems to be an error on our system. We will investigate why a Warning label is produced when there is none in the report. You may ignore for now. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carl

Re: [Bioc-devel] Policies regarding forked packages

FWIW: Bioconductor does follow CRAN policy except we do not change or have a tag for "orphaned" packages. We consider an unmaintained package that is failing in this category so anything that is up for deprecation/removal and if someone is trying to reach the maintainer and they remain unrespo

[Bioc-devel] Bioconductor 3.20 is Released!

Thanks to all developers and community members for contributing to the project! Please see the full release announcement: https://bioconductor.org/news/bioc_3_20_release/ Cheers, Sent on behalf of the Bioconductor Core Team This email message may contain legally privileged and/or confidential

Re: [Bioc-devel] Last day to make commits before Bioconductor RELEASE 3.20

Yes we would consider a TIMEOUT as broken as it would prevent the package from propagating and being available to end users. If we know maintainers are actively trying to fix the issues and actively pushing to the git.biocondutor.org repo to try to remedy the situation, we would be more lenien

[Bioc-devel] RELEASE_3_20 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_20 branch is now available on Bioconductor. Please sync your GitHub repositories with the latest updates to your package on Bioconductor for a RELEASE_3_20 branch as well as the devel branch. Th

[Bioc-devel] All commits to Bioconductor stopped from 7:00 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/ As of 7 am ET today, (October 29 th 2024) , all branches of all packages in Bioconductor are frozen. We will notify here once we are done with the

[Bioc-devel] Last day to make commits before Bioconductor RELEASE 3.20

Hello Bioconductor developers, We are still on track for Bioconductor Release 3.20 for this Wednesday October 30th. This means that tonight is the last day to commit changes to the devel branch before creation of the RELEASE_3_20 versions of your packages. And any changes you make to your pac

[Bioc-devel] Important Bioconductor Release 3.20

The deadline for fixing packages in preparation for the release is today Friday October 25th. All packages should be installing, building, and checking without ERROR in the Bioconductor build report. While you can continue to push changes past this date, this ensures all changes are reflected i

Re: [Bioc-devel] ANCOMBC Package Error on Kunpeng2 Platform

Thank you for reaching out. The ERROR will not affect your package being released in 3.20. We will investigate why CVXR is not available on that platform. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinforma

[Bioc-devel] Important Bioconductor Release 3.20 deadlines this week

The deadline for fixing packages in preparation for the release is this Friday October 25th. All packages should be installing, building, and checking without ERROR in the Bioconductor build report. While you can continue to push changes past this date, this ensures all changes are reflected in

[Bioc-devel] List of Deprecated Packages for Bioc3.20

The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. This is the current list of deprecated packages for Bioc 3.20. It should be noted, we did try to reach out to these package maint

Re: [Bioc-devel] Review status of BulkSignalR

Package Reviewers are volunteer and often have other responsibilities and duties. We recommend packages are submitted early to ensure adequate review time. Every release the reviewers get overwhelmed with packages submitted within 4-6 weeks of the deadline. They do the best they can. I will

[Bioc-devel] Release_3_19 branch is now frozen

The RELEASE_3_19 branch is now frozen and no longer accepts push commits at git.bioconductor.org. See https://stat.ethz.ch/pipermail/bioc-devel/2024-October/020639.html and https://bioconductor.org/developers/release-schedule/ Lori Shepherd - Kern Bioconductor Core Team Roswell Park Compreh

Re: [Bioc-devel] EpiCompare - Transfer maintainer

We have adjusted the configurations on our end and they should now have access. Please remember to have them push the changes to the DESCRIPTION file (which will also update the landing page) Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

[Bioc-devel] RELEASE_3_19 branch frozen in a few hours

We are moving forward with the 3.20 release schedule. In roughly 4.5 hours the RELEASE_3_19 will be frozen and no longer accept commits. Any changes or bug corrections that are not pushed up by this time will not be in the Bioconductor 3.19 version of the package as we do not allow updates to

Re: [Bioc-devel] OrgDB entry for Homo sapiens and Mus musculus missing in AnnotationHub

We apologize for the disruption. They have been reinstated and should now be available. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 _

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