[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 3.20 rather than 3.19 following the latest Bioconductor release on May 1. This may result in downtime to the build on demand functionality. We appreciate your

[Bioc-devel] Bioc2024 Nomination Deadline May 15

We are still accepting nominations for Bioc2024 Awards!! Please recognize an outstanding member of the Bioconductor community. We also dedicate one award to a junior developer or new package development. Award criteria can include but is not limited to: * Outstanding new package

[Bioc-devel] AMI Policy Change

In the past Bioconductor provided pre-configured AMI with certain Bioconductor releases, conferences, and workshops. We are moving these legacy AMI snapshots to a cold storage class. They will be available by request only; The time necessary for retrieval may range from 12 to 72 hours. These

Re: [Bioc-devel] Maintainer change

Thank you for reaching out. I will be in contact off list to help set up Camila Perico BiocCredentials account that will be needed to access. We will then grant push access to git.bioconductor.org. It will be up to Camila to adjust the package DESCRIPTION accordingly with a valid version

Re: [Bioc-devel] scaeData: not available for Bioconductor version '3.19'

It looks like it is clean on yesterday's report; normally it would be available shortly after propagation on a build day. We identified the issue and it should be made available shortly. We apologize for the delay. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive

[Bioc-devel] Bioconductor 3.19 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_19_release/ Cheers, Sent on behalf of the Bioconductor Core Team This email message may contain legally privileged and/or

[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] RELEASE_3_19 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_19 branch is now available on Bioconductor. Please sync your GitHub repositories with the latest updates to your package on Bioconductor for a RELEASE_3_19 branch as well as the devel branch.

Re: [Bioc-devel] Adding git write access for newly accepted package when a key already exists

There was a configuration issue on our end. This should now be corrected. Please also see this announcement from this morning. https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020416.html Commits are blocked for the release. We will announce when commits will resume (normally in a few

Re: [Bioc-devel] problem with git push to bioconductor ‘DENIED by fallthru’

Please see this announcement from this morning. https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020416.html Commits are blocked for the release. We will announce when commits will resume (normally in a few hours) Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park

Re: [Bioc-devel] Error on macOS (merida1)

The reviewers should be aware already but I can leave a message on the issue. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[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 (April 30 th 2024) 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: [Bioc-devel] cliqueMS request for undeprecation as all errors have been fixed

The package continues to fail. Please fix the package before we will un-deprecate. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Last day to make commits before Bioconductor RELEASE 3.19

Hello Bioconductor developers, We are still on track for Bioconductor Release 3.19 for this Wednesday May 1st. This means that tonight is the last day to commit changes to the devel branch before creation of the RELEASE_3_19 versions of your packages. And any changes you make to your

Re: [Bioc-devel] Fixed error on gemma.R

You're package will still be included in the release. We stress this deadline as packages that need bug corrections after the release would need to push to both branches. And any changes made last minute are not guaranteed to have a build report before we branch. Please keep an eye on the

Re: [Bioc-devel] cliqueMS request for undeprecation as all errors have been fixed

We will un-deprecate once the package is building and checking cleanly. We will look at today's build report when it is posted. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo,

Re: [Bioc-devel] Error on macOS (merida1)

Yes a package in submission should depend on R 4.4.0. Merida1 was accidently started for the package review process but should not have been included yet. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm &

Re: [Bioc-devel] MIRit fails to build on palomino3

We will look into it. If there is anything that needs to be done on your end we will reach out. 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] New annotation hub package?

I can assist you with this request. In the future there is the email h...@bioconductor.org for these types of requests instead of the developer mailing list as mentioned in the documentation. I'll contact you off mailing list for further details and instruction. Cheers, Lori Shepherd -

Re: [Bioc-devel] Package passing checks on Linux and macOS but failing on Windows

Yes your package will still be included in the release. Even if a package is failing, you would receive notifications and a deprecation cycle before the package would be officially removed. We like to see package fixed before a release so they can be made available to end users as soon as

Re: [Bioc-devel] Additional commit access for the BindingSiteFinder package

Could you please have the current maintainer Mirko Br�ggemann 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

Re: [Bioc-devel] singleCellTK

rk 14263 From: Bioc-devel on behalf of Kern, Lori via Bioc-devel Sent: Monday, April 22, 2024 9:08 AM To: bioc-devel@r-project.org ; Joshua Campbell Subject: Re: [Bioc-devel] singleCellTK Please try to push the change to fix the gvsa issue. We generally will only un-deprecate when we see

[Bioc-devel] Important Bioconductor Release 3.19 deadlines this week

The deadline for fixing packages in preparation for the release is this Friday April 26th. 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] git commit issues

I might suggest adding a new ssh key to your BiocCredentials account as it seems to be having issues with your key 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] git commit issues

Bioconductor does not have a main branch. Please refer to documentation http://contributions.bioconductor.org/git-version-control.html Bioconductor default branch is devel. If you have set up where your default branch is main do to another remote (like github), You can map main to devel

Re: [Bioc-devel] singleCellTK

Please try to push the change to fix the gvsa issue. We generally will only un-deprecate when we see a clean build/check report for at least the linux platform especially since the package has been failing for an extended period of time (since early December).

Re: [Bioc-devel] Bioconductor will rename the default branch on `git.bioconductor.org` to `devel`

Hello maintainers, A little over a year ago, Bioconductor moved forward with a default branch renaming from 'master' to 'devel' on git.bioconductor.org. For an easier transition we have thus far left the deprecated 'master' branch and if you were pushing received a Warning message that this

Re: [Bioc-devel] Request to Retire COHCAP Bioconductor Package

We normally like to do a full round of a package in a deprecation state before removal completely (so deprecated in Bioc 3.19 and removed in Bioc 3.20) but since there are no reverse dependencies, I don't think this should be an issue to directly remove from 3.19 without deprecation. Please

[Bioc-devel] Release_3_18 branch is now frozen.

The RELEASE_3_18 branch is now frozen and no longer accepts push commits at git.bioconductor.org. See: https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020348.html And: https://bioconductor.org/developers/release-schedule/ Lori Shepherd - Kern Bioconductor Core Team Roswell Park

[Bioc-devel] RELEASE_3_18 branch frozen in a few hours

We are moving forward with the 3.19 release schedule. In roughly 4.5 hours the RELEASE_3_18 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 3.18 version of the package as we do not allow updates to

[Bioc-devel] Important Release 3.18 Freeze Announcment

The Code Freeze for the current Bioconductor 3.18 Release is scheduled for next Monday April 15, 2024. After this date there will be no changes to the code on this branch; this includes bug fixes or hot fixes. If your package is failing on the release build report, this weekend will be your

Re: [Bioc-devel] required force push to bioconductor

I will be in contact off list to discuss further options. 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: [Bioc-devel] List of Deprecated Packages for Bioc3.19

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 3.19. It should be noted, we did try to reach out to these package

Re: [Bioc-devel] Moderately large files in an Experiment Data package?

Yes we would recommend using ExperimentHub. Which is a database with pointers to the data files; so files are only downloaded when necessary to keep the package lightweight for end users. You have some options to where the data is stored. We encourage the use of zenodo or other well trusted

Re: [Bioc-devel] plyranges maintainer update

We have updated the configurations on our end. Michael should push changes to the description to update the maintainer on the landing pages and to receive any notifications from us. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

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

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: Friday, April 5, 2024 8:15 AM To: Robert Castelo <mailto:robert.cast...@upf.edu>; bioc-devel@r-project.org<mailto:bioc-devel@r-project.o

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

oc-devel on behalf of Kern, Lori via Bioc-devel Sent: Friday, April 5, 2024 8:15 AM To: Robert Castelo ; bioc-devel@r-project.org Subject: 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

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

tor package and I'm not comfortable installing the unreleased > > version of R on my machine and spending time debugging it in the case of > > possible problems. > > > > At the same time, I have an error, possibly caused by a new version of > > GO.db package, which BioNAR i

Re: [Bioc-devel] Updating Package Issue

What is the name of your package? Please keep in mind there are always two active branches of Bioconductor, currently RELEASE_3_18 and devel. Based on the information provided 1.28.0 would refer to a release version of a package while a verison number of 1.29.0 would indicate a devel

[Bioc-devel] Bioconductor 3.19 db0s, OrgDbs, and TxDbs now available

Hello Bioconductor community, The newest db0, OrgDb, and TxDb annotation packages for the upcoming Bioconductor 3.19 release are up and available for download in the devel version of Bioconductor. The deadline for submitting contributed annotation packages will be Wednesday April 17 th. The

Re: [Bioc-devel] CuvierLab -Request to add maintainers for HicAggR

I can assist with this and will be in touch with Dr. Tesfaye to set up a BiocCredentials account. 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] about deprecate package DNABarcode

e-0sY4TwWe9k6enUSTxs7T7NzRPMaF1o7X7Sudv_yBcA7MyqU4Rkr0JysgcZi4NDH-DGNG5NwCWYDuFYcwAZvo3PJxFsYoUs3DuuzjNCF6LTZUCwYx7HbDkI5egJHxtvLW3nLHHxCraI2tTk0Nr9bYwXfbDppHD_2urEZfSlOFri_PBHFt7_j8p0a5YHO-CyIfqLkIee405IJadEV36I3bVHk95UIDY9NfAda54OGyE2Fw8m_4ybIp_Djhw8BEGvmX2f6/https%3A%2F%2Fgithub.com%2Ffeldman4%2Fdna-barcodes>.

Re: [Bioc-devel] Commit access for additional developer on missMethyl package

I'll be in touch with Calandra privately to set up a BiocCredentials account. Once that is established we can proceed with this request Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

[Bioc-devel] Important Bioconductor Release Deadlines

Import update: The Bioconductor Release will be May 1 following the release of R 4.4 on April 24. The Bioconductor 3.18 branch will be frozen Monday April 15th. After that date, no changes will be permitted ever on that branch. The deadline for devel Bioconductor 3.19 for packages to pass R

Re: [Bioc-devel] Request to add maintainers for diffHic

Do Hannah and Gordon already have BiocCredentials accounts? If so please let me know the email or userid. If not I can create them and Hannah and Gordon should let me know which email they would like for access and if they have a github id they would like associated with the account. Cheers,

Re: [Bioc-devel] Nominations for Bioconductor Awards 2024

We are still accepting nominations for Bioc2024 Awards!! Please recognize an outstanding member of the Bioconductor community. We also dedicate one award to a junior developer or new package development. Award criteria can include but is not limited to: * Outstanding new package

[Bioc-devel] New Package Submission Deadline today for Bioconductor 3.19

The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.19 release is today Friday March 22nd. Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and

Re: [Bioc-devel] Unable to update Bioconductor Git Credentials

I'm very sorry I did not see the email on March 13 regarding the BiocCredentials app. I will send you an email off list to work out the details. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton

Re: [Bioc-devel] Bioconductor Git Credentials

You could try looking at http://contributions.bioconductor.org/git-version-control.html#faq particularly #13, 14, and 15. If none of those help, I would suggest generating and adding a new key. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center

Re: [Bioc-devel] Bioconductor Git Credentials

It looks like the email got changed with the spillR submission. We assume the submitter is the maintainer of the package. So the username ChristofSeiler got associated with m.guazz...@student.maastrichtuniversity.nl. I have updated the account. Could you please try requesting a password reset

Re: [Bioc-devel] about deprecate package DNABarcode

The package is deprecated in devel. It will remain listed in the next Bioc 3.19 release, but deprecated, and removed from anticipated 3.20. The package will have up until the fall release (generally late Oct / early Nov) to reinstate before it will be removed. Cheers, Lori Shepherd - Kern

Re: [Bioc-devel] Unable to install "spoon" package due to R version 4.4 dependence

mac can get R-devel at this location https://mac.r-project.org/ Cheers 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] Deprecate pwOmics package

Thank you . We will begin the deprecation process. 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

Re: [Bioc-devel] AnnotationHub corrupted cache on nebbiolo1

I noticed that as well and just did the necessary steps to clean the cache. I expect this to clean up on the next build. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New

Re: [Bioc-devel] un-deprecation gscreend

Yes we will un-deprecate the package. If possible it would be great to also push the changes to RELEASE_3_18 branch as well if you have not done so already https://bioconductor.org/checkResults/release/bioc-LATEST/gscreend/ Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park

[Bioc-devel] Important Bioconductor Release Deadlines

Reminder: The final day to submit packages to the contribution tracker to attempt to be included in the Bioconductor 3.19 release is Friday March 22nd. Submission by this date does not guarantee inclusion, the package must still undergo an official review and be accepted by April 17th.

Re: [Bioc-devel] [EXTERN] Re: R package on Github uses Bioconductor depenencies and cant be installed.

It looks like a permission denied ERROR. Perhaps R was installed as root and you do not have access to write to the default R install directory. You should install to a directory you do have write permissions by setting a lib argument or by setting the .libPaths() Lori Shepherd - Kern

Re: [Bioc-devel] Access rights for simPIC repository, git fetch error

I would either add a new ssh key or check out the FAQ section at http://contributions.bioconductor.org/git-version-control.html#faq specifically, #13, 14, and 15 Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics

Re: [Bioc-devel] Having problems pushing changes to Bioconductor...

Sure these sections would probably be useful in your situation. pushing to github and bioconductor http://contributions.bioconductor.org/git-version-control.html#push-to-github-bioc And fixing bugs in release and devel

Re: [Bioc-devel] Having problems pushing changes to Bioconductor...

Could you please show the commands you are trying along with a git remote -v I've check the configuration on our end and everything looks correct. You'll need to make sure you are pointing to one of the uploaded ssh keys on the BiocCredentials account (or create a new one if you are on a

[Bioc-devel] Bioconductor 3.19 Release Schedule

The release date for Bioc 3.19 is tentatively scheduled for Wednesday April 24th. The 3.19 release will use R-4.4. With R dependency 4.4, these deadlines are subject to change once CRAN announces their official 4.4 release date. We are releasing this tentative schedule to allow for adequate

[Bioc-devel] List of Deprecated Packages for Bioc3.19

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 3.19. It should be noted, we did try to reach out to these package

Re: [Bioc-devel] R package on Github uses Bioconductor depenencies and cant be installed.

Bioconductor packages need to be installed with BiocManager. If you do BiocManager::install("klausjung-hannover/bootGSEA") That should also find Bioconductor package dependencies. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

Re: [Bioc-devel] TADCompare, permissions denied

Everything looks correct on our configuration. You might need to add a new ssh key to your BiocCredentials account. Or since there are multiple keys on your account already, explicitly state the correct ssh key you would like to use . Lori Shepherd - Kern Bioconductor Core Team Roswell

Re: [Bioc-devel] Build errors from recent breaking ggplot2 changes

We often don't like having to do a manual uninstall / reinstall of a package because that will not fix the issue for any typical user on their local system. It would be best to have complexupset bump there version so that everyone (universally) would get a fresh install. Hopefully they would

[Bioc-devel] Nominations for Bioconductor Awards 2024

Bioconductor is excited to announce an opportunity to recognize those making significant outstanding contributions to the Bioconductor community. The Bioconductor project is announcing the call for Bioconductor Awards, honoring various forms of contributions to the project. Four awardees will

Re: [Bioc-devel] Package submission- external dependancy

Could you please provide a link to the tool for evaluation? We will take a look to see if it is feasible. Also note it would be helpful to have an INSTALL file and list the system dependency in your DESCRIPTION as well. http://contributions.bioconductor.org/sysdep.html#sysdep Cheers, Lori

Re: [Bioc-devel] Project Application Reactivation request.

I will reopen the issue for you to continue. 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 of Ali

[Bioc-devel] Note about packages submitted for Bioconductor 3.19

Developers should be aware that Bioconductor 3.19 will likely be released in April 2024 following the CRAN release of version 4.4 of R. Because the group of active reviewers is small, submissions after March 15 have a high likelihood of not being reviewed for inclusion in Bioc 3.19. We

Re: [Bioc-devel] Failed to activate account for Bioconductor git credentials

We have located the source of the ERROR with push access. As this involves some other information I will email you off list for resolution. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm &

Re: [Bioc-devel] BiocCheck error

The mailing list check will only occur accurately on our system. I believe this bug with BiocCheck is fixed in the current devel version 1.39.21 but will let the contributor that worked on the bug comment for sure. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park

Re: [Bioc-devel] build reports for apple silicon

They are linked off the check result main page: https://bioconductor.org/checkResults/ Because we can not run them daily they are not in the main report. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm &

Re: [Bioc-devel] autonomics devel : how to reproduce bioc build errors best ?

I just tried locally with R-devel and making sure all the package dependencies were updated and can reproduce this. I suggest making sure you have an updated installation or maybe try using the BIoconductor docker if you don't have access to R-devel.

Re: [Bioc-devel] mail not associated with a mantainer of bioconductor package

We have not currently added your package to git.bioconductor.org as there were changes requested before we would clone to our system as indicated by the "awaiting moderation" and "pending pre-review changes". Admins normally look at package once or twice a week and should moderator your

Re: [Bioc-devel] Deprecation Request for openPrimeRui

Yes I will take care of the deprecation. Thank you for letting us know. If you change your mind, please remember to request un-deprecation here. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm &

Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

mailing list again, even though I already signed up previously, resolved that error. I am not sure if this practice should be advised, and I did receive an auto email with subject line "Mailman privacy alert", telling me that I've already signed up. Thanks. Best, Boyi On M

Re: [Bioc-devel] Single Package Builder failing to detect subscription to the Bioc-devel mailing list

I can confirm that this email is subscribed. We can open an issue on BiocCheck to investigate this more. In the meantime I will comment on your submission issue to ignore the error for now. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

Re: [Bioc-devel] Build Report Response

Depending on when you pushed Wednesday night you might have missed the cutoff for the pull for the builders for Thursday report. We only pull, build, and check once a day. Since the Thursday report shows version 1.2.3 as shown on the report

[Bioc-devel] bioconductor.org has a new look!

https://bioconductor.org/ has a new look. Bioconductor worked with nearform to help redesign and enhance the bioconductor.org website. We have many more improvements that we hope to roll out over time but we hope you enjoy the

Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout

rk 14263 From: Bioc-devel on behalf of Kern, Lori via Bioc-devel Sent: Friday, December 15, 2023 9:36 AM To: Jacopo Ronchi ; Hervé Pagès Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout I ca

Re: [Bioc-devel] maintainer access for projectR

We have granted access. 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 of Genevieve Stein-O'Brien

Re: [Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout

I can update the SPB to have that environment variable set. I will also cross check it with the current variables set on the daily builder. It may not be until next week that it is implemented. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center

Re: [Bioc-devel] Use of dontest in function documentation

Not if its justified but I'd be sure to mark the man pages as internal (if using roxygen you can do @keywords internal) . Normally that is referring to any exported function. I assume adequate testing, or examples in exported functions are run? Lori Shepherd - Kern Bioconductor Core Team

Re: [Bioc-devel] Request for undeprecation for exomePeak2

exomePeak2 was never deprecated. You can push to the devel branch to also fix the package in devel and then it will be available https://bioconductor.org/checkResults/devel/bioc-LATEST/exomePeak2/ Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center

Re: [Bioc-devel] FATAL: W any packages/*** *** DENIED by fallthru

We have updated the access credentials. Please remember to update the DESCRIPTION of the package accordingly. Should the BiocCredentials account associated withwuk...@bi.a.u-tokyo.ac.jp be deleted completely? Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive

Re: [Bioc-devel] Not getting emails from watched tags

Thank you for reporting. This has been a known issue we are working on. 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] FATAL: W any packages/*** *** DENIED by fallthru

It would help to also show the output of the commands. Likely you need to add or create a new ssh key to the BiocCredentials app as I checked the configuration on our end and everything looks correct. See https://contributions.bioconductor.org/git-version-control.html#faq particularly maybe #1,

Re: [Bioc-devel] un-deprecation Request biomvRCNS

Thank you. I will undeprecate and add back into devel (3.19) manifest/report. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Single Package Builder for new submission

We will be updating the single package builder for new package submissions to run on the devel version of Bioconductor (3.19) and R (4.4). During the update period there may be periods of intermittent downtime where build on demand is unavailable. We appreciate your understanding during this

Re: [Bioc-devel] Request to reverse package deprecation (and support pushing changes)

Responded to the slack message as well but so it is documented on the mailing list. If the package was deprecated, yes you must request undeprecation here. The package was failing for over 6 months without updates or efforts to fix. We will only undeprecate once the package is building

[Bioc-devel] CRAN downtime may effect package installation

There is an announcement at https://cran.r-project.org/ Dear users, The CRAN Admin Team will perform system upgrades during the period Wednesday November 15 until Thursday November 16, 2023. There will be intermittent outages in service during this time. We thank you for your understanding

Re: [Bioc-devel] Package check error despite commit

Experiment Data packages are built twice a week on Tuesday and Thursday. The schedule is found on the check home page https://bioconductor.org/checkResults/ The changes were only pushed up on November 10 so they should be reflected in tomorrow's report. Cheers, Lori Shepherd - Kern

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

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:

Re: [Bioc-devel] problems when updating MOSim package

You will likely have to add a new ssh key to your BiocCredentials account. I checked the config file your username does have access. Just a reminder your sign in for https://git.bioconductor.org/BiocCredentials/ uses the other email sota...@eio.upv.es Cheers, Lori Shepherd - Kern

Re: [Bioc-devel] [ext] Re: RCAS build error on Nebbiolo2 - Missing BiocManager

Yes adding BiocManager to the suggest field of your DESCRIPTION will likely correct the ERROR 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] Change package name

This is not an easy process and will involve manual intervention from the team. What is the package name? Is it already accepted into Bioconductor or is in still in the submission process? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

Re: [Bioc-devel] Maximum allowed cores on Bioconductor Build System?

I believe the recommendation is not to use more than 2 cores. 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

[Bioc-devel] BiocFileCache/ExperimentHub/AnnotationHub

There was a bug reported relating to BiocFileCache compatibility with the new version dbplyr. This affected BiocFileCache, ExperimentHub, and AnnotationHub. This has already been corrected in BiocFileCache versions 2.10.1 (Release_3_18) and 2.11.1 (devel/3.19) respectively. These versions

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