[Bioc-devel] List of Deprecated Packages for Bioc3.18

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 3.18: Software: User Requested * gaggle * LPEadj * macat

Re: [Bioc-devel] maintenance of software package YAPSA

Yes we can add a co maintainer. I will contact Zuguang Gu off mailing list to set up credentials for access. 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] Champ Analysis trouble

These questions are better asked on the support.bioconductor.org website. Please also include the code you are using that depicts the ERROR as well as your sessionInfo when posting. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatist

Re: [Bioc-devel] help with lack of permission on new package

The mailing list did not allow the attachment to come through. I have responded in a different email with some additional information. Cheers Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Stree

[Bioc-devel] Updates to Single Package Builder

Over the next day or two we will be running some updates on the Single Package Builder which may cause some intermittent downtime. We apologize for any inconvenience and appreciate your understanding. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Depar

Re: [Bioc-devel] help with lack of permission on new package

This might be helpful: http://contributions.bioconductor.org/git-version-control.html#faq specifically #14 / #15 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] Omada package failing due to removed dependency

The package code needs to be pushed to git.bioconductor.org not github. Just wanted to be sure you are trying to push to the right place. Could you please show the commands you are using with full output along with a git remote -v to make sure that is all set up correctly. There are useful gi

Re: [Bioc-devel] Omada package failing due to removed dependency

Also of note, When you push you will need to have a valid version bump but the build will not be triggered by a push instantly. The daily builder will pull, build, check all packages only once a day. The build report will show the version number and git commit id of what it last tried to use;

Re: [Bioc-devel] Omada package failing due to removed dependency

You'll need to find the merge conflicts and resolve them. Recommit those files and then it should go. 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 for bioconductor package name

As of right now that name does appear to be available. 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] Access to ROntoTools git

Is it possible to have Calin 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-devel on behalf of Stephe

Re: [Bioc-devel] Package submission deadline Bioconductor 3.18

We have not yet decided on a release date for 3.18. It should be announced, and the release schedule updated, in the next week or so. Generally the release is end of October or early November. The deadline to submit a package for review would roughly be the beginning of October. Lori Shep

Re: [Bioc-devel] Fwd: geneplast.data version number issue

Annotation packages are treated slightly different. We assume that annotation package version bumps indicate a change so they are the only set of packages that are not automatically bumped. However you are correct we probably should have in place to bump the newly submitted packages at release

Re: [Bioc-devel] Package submission deadline Bioconductor 3.18

We don't have a way to preemptively block use of those packages. It should happen naturally as when they are removed from CRAN the packages will start Erroring on the Bioconductor build system and they will receive warnings to fix or be at risk for deprecation. On my quick search over my local

Re: [Bioc-devel] bioconductor support email account reset issue

We are investigating the issue and will reach back out shortly. In the meantime please correct other ERROR/Warnings/Notes and you can let the reviewer know we are working on this issue. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostat

Re: [Bioc-devel] Including large files for the package

Hello, Regarding Hub use: What sort of information does the metadata contain? That would determine whether ExperimentHub or AnnotationHub is more appropriate. Is the file accessed directly from the http://ilincs.org/ portal with a url link or is there processing/filtering that occurs? The hubs

[Bioc-devel] Bioconductor 3.18 Release Schedule

The release date for Bioc 3.18 is tentatively schedule for Wednesday October 25th. The 3.18 release will use R-4.3. The following highlights important deadlines for the release. Important deadlines can be found on the website: https://bioconductor.org/developers/release-schedule/ As a Quick Su

[Bioc-devel] Deprecated Packages for Bioc 3.18

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. Please see the current list at https://support.bioconductor.org/p/9152979/ It should be noted, we did try to reach out to these

Re: [Bioc-devel] Submit additional data package to closed issue #2963

Hello I just commented on the issue. Since cfTools has already been accepted, added, and closed, please open the additional as a new issue. Thank you Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Car

Re: [Bioc-devel] Unable to push updated development package to Bioconductor

Have you checked http://contributions.bioconductor.org/git-version-control.html#faq specifically points: 13-16 Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 1426

[Bioc-devel] Single Package Builder Maintenance

We will be performing maintenance on the single package builder for new submissions today. There may be short intervals where the on-demand/build on version bump capabilities will not be accessible. We appreciate your understanding. Cheers, Lori Shepherd - Kern Bioconductor Core Team Rosw

Re: [Bioc-devel] Deprecated Packages for Bioc 3.18

2023 at 10:50 AM Kern, Lori via Bioc-devel < bioc-devel@r-project.org> wrote: > 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. > > Please see the cur

[Bioc-devel] Important Bioconductor Release Deadlines

The final day to submit packages to the contribution tracker to attempt to be included in the Bioconductor 3.18 release is Friday September 29th. Submission by this date does not guarantee inclusion, the package must still undergo an official review and be accepted by October 18th. Please rem

Re: [Bioc-devel] magpie package failing unit test

For What it's worth, I can also reproduce this locally. Please make sure you are using the correct version of R (4.3.1 Patched) and that all your packages are up-to-date with BiocManager::install and BiocManager::valid. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive

Re: [Bioc-devel] Lost access to my email

Just to confirm you no longer have access to shg...@uams.edu? 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] Lost access to my email

I will be in touch off list about resetting your BiocCredentials account so you can manage your ssh keys for access to the packages. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffal

Re: [Bioc-devel] Not receiving original posts for watched tags at bioconductor support

There was some issue posted here: https://github.com/Bioconductor/support.bioconductor.org/issues/78 We are aware of the issue of not being emailed on the first post and are actively looking into a fix for it. Thank you for letting us know. Lori Shepherd - Kern Bioconductor Core Team Roswel

[Bioc-devel] New Package Submission Deadline today for Bioconductor 3.18

The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.18 release is today Friday September 29th. Please note: submission by this date does not guarantee it will be included - the package must undergo an official review

Re: [Bioc-devel] Use of master vs devel branch on g...@git.bioconductor.org

You should not be pushing to master. We have left it there temporarily on packages as we make this transition to using devel permanently. Pushing to devel should work and we can help investigate further why this isn't working for you. Please provide output for git remote -v git fetch --all gi

[Bioc-devel] Important Release 3.17 Freeze Announcment

The Code Freeze for the current Bioconductor 3.17 Release was scheduled for next Monday October 9, 2023. Due to the United States and Canada Holiday, the freeze will occur on Tuesday October 10, 2023. After this date there will be no changes to the code on this branch; this includes bug fixes

Re: [Bioc-devel] Vignette files causing package to exceed 5 MB size limit

The data is now available in the hub > query(eh, "TumourMethData") ExperimentHub with 4 records # snapshotDate(): 2023-10-06 # $dataprovider: University of California San Francisco, Washington Universi... # $species: Homo sapiens # $rdataclass: RangedSummarizedExperiment # additional mcols(): taxo

Re: [Bioc-devel] Vignette files causing package to exceed 5 MB size limit

Sorry about that. I had two emails back to back and responded to the wrong one. Is there a way to create and save and compress the images? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Street

[Bioc-devel] RELEASE_3_17 branch frozen in a few hours

We are moving forward with the 3.18 release schedule. In roughly 5 hours the RELEASE_3_17 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 3.17 version of the package as we do not allow updates to pa

[Bioc-devel] Release_3_17 branch is now frozen.

The RELEASE_3_17 branch is now frozen and no longer accepts push commits at git.bioconductor.org. See: https://stat.ethz.ch/pipermail/bioc-devel/2023-October/019926.html and https://bioconductor.org/developers/release-schedule/ Thank you. Lori Shepherd - Kern Bioconductor Core Team Roswell

Re: [Bioc-devel] AnnotationHub Integration

Yes it seems appropriate. Depending on the type of data maybe ExperimentHub would be preferred over AnnotationHub. It depends on what information you are providing. We do have multiple types of data provided in the hubs. Many data are in database type objects like sqlite and such. This is ab

Re: [Bioc-devel] Updating the maintainer (or adding a new one) for the Mergeomics package

Yes I can assist with the switch. I will contact off list for information to create a BiocCredentials account. This account mapping handles access to packages and allows the maintainer to add ssh keys for access. Once the replacement maintainer has access, it will be up to them to change the DE

[Bioc-devel] Important Bioconductor Release 3.18 deadlines this week

The deadline for fixing packages in preparation for the release is this Friday October 20th. 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] Final list of deprecated package Release 3.18

The Bioconductor Team is continuing to identify packages that will be deprecated. The final list of deprecated package for 3.18 may be found at https://support.bioconductor.org/p/9152979/ It should be noted, we did try to reach out to the package maintainers as listed in the DESCRIPTION of the

Re: [Bioc-devel] Final list of deprecated package Release 3.18

very popular and frequently used package. Anyone has a way to check in with some of the authors - seems that both Gabe Becker and Michael Lawrence are authors. I will also take a look what's going wrong. From: Bioc-devel on behalf of Kern, Lori via Bioc-de

[Bioc-devel] Hub access temporarily unavailable

Hello Bioconductor, We are experiencing temporary downtime of the experimenthub and annotationhub. We are working on a resolution as soon as possible. We appreciate your understanding. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biost

Re: [Bioc-devel] Push update to an existing remote branch

Bioconductor does not have a main branch. The default branch on BIoconductor is devel. If your local or github branch is called main, you need to map the main branch to the devel branch of Bioconductor. git push upstream main:devel Lori Shepherd - Kern Bioconductor Core Team Roswell Park

Re: [Bioc-devel] groHMM package error

There is no RELEASE_3_18 branch until the release next week (created automatically by the core team on release day) . All updates should be pushed to the devel branch. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinf

Re: [Bioc-devel] Hub access temporarily unavailable

___ From: Bioc-devel on behalf of Kern, Lori via Bioc-devel Sent: Wednesday, October 18, 2023 9:29 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Hub access temporarily unavailable Hello Bioconductor, We are experiencing temporary downtime of the experimenthub and annotationhub. We are

[Bioc-devel] Last day to make commits before Bioconductor RELEASE 3.18

Hello Bioconductor developers, We are still on track for Bioconductor Release 3.18 for this Wednesday October 25th. This means that tonight is the last day to commit changes to the devel branch before creation of the RELEASE_3_18 versions of your packages. And any changes you make to your pac

[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

[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 le

[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. Th

Re: [Bioc-devel] Macarron Next BiocRelease

yes. Please push to both devel and RELEASE_3_18 with your changes. remember to pull first as there will be version bumps from the core team from yesterdays Bioc 3.18 creation. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics &

Re: [Bioc-devel] groHMM package error

You should make sure you are using the latest version of R and have updated Bioconductor/CRAN packages by running BiocManager::valid and/or BiocManager:install . I can reproduce this locally. Running your vignette it has to do with this line: > upGenes <- kgChr7[de==1,] Error: invalid subscrip

[Bioc-devel] Bioconductor 3.18 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_18_release/ Cheers, Sent on behalf of the Bioconductor Core Team Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensiv

[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 wer

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 on

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 Bio

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] 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 Biocond

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] 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] 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 Biocondu

[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 and

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 cleanl

[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 t

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

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] 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: Bioc

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 Ca

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 Departm

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 R

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 Depa

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 v

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

[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 new

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 https://bioconductor.org/checkResults/3.18/bioc-LATE

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

p the 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,

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 & C

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 package

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. lorikern@jbcj433:~/BioconductorPackages/Sof

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 & C

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 Comprehensiv

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 & Carlton

[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 encoura

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 Sa

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 S

[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 be

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

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 Par

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 Biostatist

[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 maint

[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 plan

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 differ

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 http://contributions.bioconductor.org/git-version-control.html#bug-fix-in-rele

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] [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 Bioco

[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. Please

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 Com

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 Yor

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 of

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: Bio

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] 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

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