[Bioc-devel] New Package Submission Deadline for Bioc Release 3.12

The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.12 release is Friday October 2nd. Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be

Re: [Bioc-devel] [EXTERNAL]Re: Update R package I developed which has been released by bioconductor

Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Xiaowen Chen Sent: Thursday, September 24, 2020 10:04 PM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: [EXTERNAL]Re:

Re: [Bioc-devel] Extensive updates to DiffBind: help reviewing docs and/or beta testing?

Hello, Others may chime in with their opinions as well but my own thoughts... I see no reason not to post on the support.bioconductor.org site to request some beta testing users. I suggest using the "NEWS Event" for post type also explaining / informing of some of the big /extensive changes

Re: [Bioc-devel] BiocCheckGitClone error

Carlton Streets Buffalo, New York 14263 From: Emilie Secherre Sent: Wednesday, September 23, 2020 3:35 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocCheckGitClone error I still couldn't fix the issue, therefore is that

Re: [Bioc-devel] BiocCheckGitClone error

Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Emilie Secherre Sent: Tuesday, September 22, 2020 9:04 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org

Re: [Bioc-devel] Bioconductor package DegNorm

Tuesday, September 22, 2020 8:48 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bioconductor package DegNorm Hi Lori, I have made changes to some of the R functions a few months ago, also I have changed version etc (recently fixed a few bugs). But I noticed in the

Re: [Bioc-devel] BiocCheckGitClone error

We run BiocCheckGitClone on a raw clone of the github directory. If you are running it locally and had .gitignored those files before pushing to github then you should be okay. A way to test this would be to do a git clone​ of your github repository, in a different, temporary location to

Re: [Bioc-devel] Update R package I developed which has been released by bioconductor

Bioconductor would not have your package on github. Bioconductor has your repository in a git server. If you already have a clone of your github repository you could follow the instructions here to add the remote to the Bioconductor repository you referenced here:

Re: [Bioc-devel] Few questions of maintaining a new bioconductor package

In Addition to Nitesh's comments: Please do not push the version to 1.0.0 yourself. This will be done at the time of release by the core team. Continue to increment z of verion x.y.z. For example 0.99.5. For now, you have to wait for a nightly build to view the results of the

Re: [Bioc-devel] Packagebuilder skips building of MsCoreUtils package

This seems to have resolved on today's build report. Lori Shepherd 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] "length(url) == 1 is not TRUE" error for vignette only on build system

To follow up on this: Please check the package code for adding/accessing resources in the netDx package. If the BiocFileCache options were used correctly there should not have been multiple entries added to the builders cache as Martin demonstrated below. Once the package has been updated to

Re: [Bioc-devel] Vignette examples

Did you export the function in the package? Lori Shepherd 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 Emilie

Re: [Bioc-devel] Build issues under macOS

of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Wednesday, September 9, 2020 11:29 AM To: McDavid, Andrew ; bioc-devel@r-project.org ; mst...@fredhutch.org Subject: Re: [Bi

Re: [Bioc-devel] Single Package Builder Updates

oc-devel on behalf of Shepherd, Lori Sent: Wednesday, September 9, 2020 12:40 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Single Package Builder Updates There have been some bugs reported for the MacOS Single Package Builder. We will begin running some tests and updates shortly which ma

[Bioc-devel] Single Package Builder Updates

There have been some bugs reported for the MacOS Single Package Builder. We will begin running some tests and updates shortly which may result in some downtime or unexpected ERROR's when trying to trigger build reports. We appreciate your understanding and hope to have the issue resolved

Re: [Bioc-devel] Build issues under macOS

Thanks everyone. I'm looking into the Single Package Builder issues with the build bin and hopefully will have a solution uploaded soon. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

[Bioc-devel] Bioconductor Release 3.12 Schedule Posted

The Bioconductor Release 3.12 Schedule has been posted and is tentatively scheduled for October 28th. Important deadlines can be found on the website and will be posted here and on the bioc-devel at r-project.org mailing list. As a quick summary: October 2: New package submission deadline

Re: [Bioc-devel] Hotfix rejected by git

Yes I can see the updates 1.17.1 on the master branch on git.bioconductor.org. We are looking into the RSS git ERROR. We only allow corrections to the current release (RELEASE_3_11) and devel (master) branches. We do not allow updates to past releases for legacy and reproducibility.

[Bioc-devel] List of Deprecated Packages for Bioc3.12

Please see the support site post for the current list of deprecated packages for release 3.12. These packages will be removed from Bioc3.13. It should be noted, we did try to reach out to these package maintainers multiple times and they were either unresponsive or had emails bounce. We

Re: [Bioc-devel] BiocViews error during build on macOS

This looks like an intermittent ERROR that probably occurred at the unlucky time of when we would try to reinstall the package biocViews. I'll kick off a manual build of your package in review to see if it clears up. If it does not we will investigate further on our side and you can ignore

Re: [Bioc-devel] Request package deprecation

Thank you for letting us know. I will begin the deprecation process for the package. Thank you for your contributions. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] New package Vignette

Thank you for reaching out. Since the package just became available please allow a few days for everything to populate on the builders and landing pages. We will keep an eye on it and if it is still not appearing by next week our team will follow up with an investigation. Thank you Lori

Re: [Bioc-devel] [Bioconductor/Contributions] New package: preciseTAD (#1553)

Hello, Thank you for your inquiry and we are sorry for any delays. We try to review packages within 2-3 weeks. Your reviewer is aware and should be in contact soon. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics &

[Bioc-devel] Fw: MultiAssayExperiment not found in docker devel image

Marcel or Nitesh? This was sent to the issue bot. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Joseph Gerrein Sent:

Re: [Bioc-devel] Bioc-issue-bot not acknowledging a submitted package

Could you try closing the issue and reopening a new issue. But before opening could you please changing the name of the repository. Your github repository location is HPAStainR_package But the package DESCRIPTION names the package is HPAStainR. The repository and DESCRIPTION Package name

Re: [Bioc-devel] networkBMA package

We will not update the CITATION file for you. You will have to push it up after we get the credentials issue straightened out. The email associated with your credentials account seems to be ka...@u.washington.edu . Please try logging in with that email to add ssh keys to your account.

Re: [Bioc-devel] New version in tscR doesn't trigger new build

Please read the top of this page for timing. It can take up to 36-48 hours to appear on the build report depending on when you pushed your changes http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Based on the information you provided I would expect to see the changes on

Re: [Bioc-devel] Triggering a new build

Thank you for your inquiry. We have experienced some issues adding credentials for new packages. We are investigating and should have a solution shortly. We will comment on your open issue on the tracker when the issue is resolved. We apologize for any inconvenience this has caused.

[Bioc-devel] New Package Submission Workflow Updates!

Hello Bioconductor Development Community, The team has made a significant change to the single package builder process for submitting new packages to Bioconductor. Previously, when submitting a new package, the process was to submit on github, add a webhook for interactive building on version

Re: [Bioc-devel] Unable to replicate Windows build error on new package.

rk 14263 From: Erik Christensen Sent: Tuesday, July 7, 2020 3:10 PM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Unable to replicate Windows build error on new package. Thanks, Do I need to bump the version or do anything to trigger a rebuild or just wait fo

Re: [Bioc-devel] Unable to replicate Windows build error on new package.

Please ignore the build bin ERROR. I think this is an issue on the Bioconductor build system rather than directly related to your package. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

[Bioc-devel] single package builder updates

Hello, We will be performing some updates on the single package builder for new submissions today June 30. There will be a period of downtime while we run the updates. During this time packages on the tracker will not receive automatic builds. We apologize for any inconvenience and

Re: [Bioc-devel] Passing BiocCheck with roxygen2 tags.

I think it's looking for details on the return value for the functions. I believe the correct syntax is @return to add a return value section in roxygen Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton

Re: [Bioc-devel] Package mantenence QSutils

I see your commit on the Bioconductor git.bioconductor server. Your update however did not include a version bump. Without a version bump the builder does not recognize any changes. Please bump the version of the package to 1.7.1 For What Its Worth -- Please only use Authors@R and remove

Re: [Bioc-devel] Bioconductor package MEAT not updating

There is a RELEASE_3_11 branch and a master (devel 3.12) branch. You pushed to the master (devel) branch which has been updated to 1.1.0 http://bioconductor.org/packages/3.12/bioc/html/MEAT.html To push to release you would have to follow the instructions found here:

Re: [Bioc-devel] Bioconductor package devel site not updating

Elm & Carlton Streets Buffalo, New York 14263 From: Hoffman, Gabriel Sent: Friday, June 19, 2020 8:00 AM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: Bioconductor package devel site not updating Hi Lori, Thanks for your help. It looks like y

Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors)

rk 14263 From: Ahmed Mohamed Sent: Monday, June 22, 2020 2:18 AM To: Martin Morgan Cc: Vincent Carey ; Herv� Pag�s ; bioc-devel ; Shepherd, Lori Subject: Re: [Bioc-devel] lipidr: Unable to reproduce error (possibly from S4Vectors) Excellent catch Martin. I was able to confirm t

Re: [Bioc-devel] Problem installing sesameData on locked down server

Hope this helps. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Schneper, Lisa M. Sent: Wednesday, June 17, 2020 10:08 AM T

Re: [Bioc-devel] Bioconductor package devel site not updating

Hello, The message you sent appears blank. So I'll take my best guess at what you are referring to: Please see this post indicating that we are having trouble with our website and are in process of fixing it. We have located the issue and pushed a fix and once applied the landing pages

Re: [Bioc-devel] updating package on the development version

Please see this post indicating that we are having trouble with our website and are in process of fixing it. We have located the issue and pushed a fix and once applied the landing pages should generate properly. https://stat.ethz.ch/pipermail/bioc-devel/2020-June/016923.html Please check

Re: [Bioc-devel] Website Not Updating

rk 14263 From: Chengyang.Ji12 Sent: Thursday, June 18, 2020 9:11 PM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: RE: [Bioc-devel] Website Not Updating Hi, I added �Phylogenetics� and �SNP� to BiocViews of my package sitePath in both release and develop version

[Bioc-devel] Website Not Updating

Hello All, It was brought to our attention that our website was not updating over the last few days. You may see outdated or missing package landing pages. We are working on a fix that should be implemented by the end of the day today. Cheers, Lori Shepherd Bioconductor Core Team Roswell

Re: [Bioc-devel] Updates to Single Package Builder for submitting new packages

accepted into Bioconductor. Cheers, Lori Shepherd 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 Shepherd, Lor

[Bioc-devel] Updates to Single Package Builder for submitting new packages

Hello all, We are working on some updates to the Single package builder used for submitting new packages. This shouldn't affect any packages already in the submission queue only new incoming packages being submitted. The update should not take long and we will announce when we are finished.

Re: [Bioc-devel] Problem installing sesameData on locked down server

If the institution is behind a proxy there is a different ExperimentHub (and AnnotationHub) option for setting the proxy. try: setExperimentHubOption("PROXY", ) Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

rk 14263 From: Bhagwat, Aditya Sent: Friday, June 12, 2020 11:33 AM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: RE: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it Thankyou Lori, Is there a way to get a visual

Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker

alo, New York 14263 From: Shraddha Pai Sent: Friday, June 12, 2020 10:32 AM To: Bioc-devel ; Shepherd, Lori Subject: Fwd: [Bioc-devel] netDx: Build errors despite code working in BioC docker Forgot to cc the group. Also, this is the correct li

Re: [Bioc-devel] netDx: Build errors despite code working in BioC docker

A 404 ERROR generally has to do with accessing web resources. I looked at your vignette and it appears that this link http://baderlab.org/netDx/supporting_data/refGene.hg18.bed Does not exist. Resources accessed by Bioconductor should be publically available. If that location is not

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bhagwat, Aditya Sent: Thursday, June 11, 2020 3:07 PM To: Shepherd, Lori ; bioc-devel@r-pro

Re: [Bioc-devel] fatal: 'upstream/RELEASE_3_11' is not a commit and a branch 'RELEASE_3_11' cannot be created from it

Newly accepted packages are added into devel only. They will be a release branch as soon as the next scheduled Bioconductor release occurs. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

Re: [Bioc-devel] FEM package update and release

FEM was deprecated before the last release as shown in the release build report. http://bioconductor.org/checkResults/release/bioc-LATEST/FEM/ FEM will not be undeprecated and added to devel (master) until after it is building in the RELEASE_3_11 branch. The package has been broken for over

[Bioc-devel] List of Deprecated Packages for Bioc 3.12

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. The list will be updated monthly. This is the current list of deprecated packages for Bioc 3.12 : Maintainer requested

Re: [Bioc-devel] MotifDb missing some PWMs from FlyFactorSurvey database

Paul - On the support site, you can edit your profile and put package names as watchedtags. When a person posts to the support site and tags with the package name you would then be emailed. This assumes they tag the post correctly but also an option Lori Shepherd Bioconductor Core

Re: [Bioc-devel] Bioconductor package tidybulk

rk 14263 From: stefano Sent: Thursday, June 4, 2020 12:56 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re: Bioconductor package tidybulk Thanks Lori, I have to questions 1) I got versioning error ``` rstudio-1 267 % git push upstream master Counting objects: 3

Re: [Bioc-devel] Bioconductor package tidybulk

rk 14263 From: stefano Sent: Wednesday, June 3, 2020 4:29 AM To: Shepherd, Lori ; bioc-devel@r-project.org Subject: Re: Bioconductor package tidybulk Hello Again, I would be happy to submit the github master with the patch tonight if you could please confirm th

Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Tuesday, May 19, 2020 2:19 PM To: Mike Smith ; bioc-devel Subject: Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch Pand

[Bioc-devel] Single Package Builder for New Package Submission

Hello all, We will be updating the Single Package Builder to run on the devel version of Bioconductor 3.12 over the new few days. During the update the Single Package Builder may experience intermittent down time. We apologize for any inconvenience this may cause and hope to keep downtime to a

Re: [Bioc-devel] Vignette Building Latex Errors on Windows Release Branch

Pandoc 2.9.2 appears to be installed on tokay2 Lori Shepherd 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 Mike

Re: [Bioc-devel] Debugging not updated for coexnet package

There is lots of documentation on how to achieve this. Most specifically for pushing changes to the RELEASE_3_11 branch following the documentation http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive

Re: [Bioc-devel] BgeeCall package present twice

Yes looking at the links further it is a legacy version. The one that resolves to a workflow page if you look closely is when 3.11 was in development phase https://bioconductor.org/packages/release/workflows/html/BgeeCall.html While the software page is the current release. I'm not exactly

Re: [Bioc-devel] Debugging not updated for coexnet package

If you followed the instructions for syncing the repository to git.bioconductor.org found here http://bioconductor.org/developers/how-to/git/sync-existing-repositories/ you should follow the instructions for pushing to Bioconductor

Re: [Bioc-devel] The new version of the package 'cbaf' is not downloadable for BioC 3.11

We have encountered some problems with the build report since last Friday as reported here https://stat.ethz.ch/pipermail/bioc-devel/2020-May/016766.html It is possibly related to that. We are hopeful we have resolved the builder issues and once it returns to a normal state we are hopeful this

Re: [Bioc-devel] annotationhub troubleshooting

This is a known reported issue. See open issue: https://github.com/Bioconductor/AnnotationHub/issues/10 It actually is not coming from AnnotationHub but from interactiveDisplayBase package. I have reported the issue to those maintainers who have yet to make a fix. In the meantime there is

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

rk 14263 From: Charles Warden Sent: Monday, May 4, 2020 12:04 PM To: Herv�� Pag��s ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: RE: [Bioc-devel] Windows Development Build Error Message for COHCAP Hi Everybody, It looks like the error is now fixed (from

[Bioc-devel] Removal of Information in OrgDb generated from NCBI -- Feedback needed.

Hello Bioconductor maintainers The core team was made aware of an issue with one of the make orgDb functions in AnnotationForge: https://github.com/Bioconductor/AnnotationForge/issues/13 Investigating further, NCBI will no longer be updating the gene2unigene file. The url has moved to an

Re: [Bioc-devel] No build report

Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Cao, Quy Sent: Wednesday, April 29, 2020 11:48 AM To: Herv� Pag�s ; Shepherd, Lori ; Nitesh Turaga ; Bioc-devel Subject: RE: [Bioc-devel] No build re

Re: [Bioc-devel] Bioconductor 3.11 is Released!

of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: David Jimenez-Morales Sent: Wednesday, April 29, 2020 1:06 AM To: Shepherd, Lori Cc: Bioc-devel@r-project.org Subject: Re: [Bioc-devel] Bioconductor 3.11 is Released! Congrat

[Bioc-devel] Bioconductor 3.11 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_11_release/ The Bioconductor Core Team This email message may contain legally privileged and/or confidential information. If you

Re: [Bioc-devel] Checking that last commit made the cut

That is the correct location to check. Notice the date at the top of the page is still yesterday. Today's report has not posted yet. When today's report is posted check to see if it is updated. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Charles Warden Sent: Monday, April 27, 2020 12:27 PM To: Herv�� Pag��s ; Shepherd, Lori ; 'bioc-devel@r-project.org' Subject: RE: [Bioc-devel] Windows Development Bui

Re: [Bioc-devel] No build report

It looks like you had merge conflicts with the version bump to 1.1.1 until late Sat night: commit 199ad444e10c81c472deefe5dff5e32dff977b41 Author: Quy Xuan Cao Date: Sat Apr 25 23:33:03 2020 -0400 Bump up to version 1.1.1 on github This would be too late to be picked up on Sunday's

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Buffalo, New York 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Thursday, April 23, 2020 8:00 AM To: Charles Warden ; 'bioc-devel@r-project.org' Subject: Re: [Bioc-devel] Windows Development Build Error Message for COHCAP Thank you for your in

Re: [Bioc-devel] Windows Development Build Error Message for COHCAP

Thank you for your inquiry R 4.0.0 can be downloaed from the following page. This patched page exists a few weeks out from the official R release for the patched version of R windows: https://cran.r-project.org/bin/windows/base/rpatched.html 2. Landing pages can have different versions of

Re: [Bioc-devel] Resubmitting additional packages as separate issues

I will assist you with this tomorrow and contact you in a private email when you can resubmit. Get Outlook for Android From: Bioc-devel on behalf of Chris Eeles Sent: Wednesday, April 22, 2020 7:23:17 PM To: Bioc-devel@r-project.org

Re: [Bioc-devel] Package CNVPanelizer needs my attention

I'm sorry I don't see any question or response to this? Was there something you had a question about? The package CNVPanelizer is failing on the builders across all platforms and needs attention. http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVPanelizer/ The ERROR has to do with

Re: [Bioc-devel] Author name displayed incorrectly in package landing page

You might have better luck updating the Author and Maintainer fields in the DESCRIPTION to Authors@R syntax. It should also be noted there should only be one maintainer for the package. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of

[Bioc-devel] Bioc 3.11 Feature Freeze

Developers, The release of Bioconductor 3.11 is one week out. Today marks the 'feature freeze' of 3.11 where we ask that all commits are limited to bug fixes and documentation (no more API changes). Thanks you for your cooperation. Lori Shepherd Bioconductor Core Team Roswell Park

Re: [Bioc-devel] version inconsistence in the development version page and the build page of a bioconductor package, cogena

We don't update the pages with broken versions of packages. 3.21.1 as you showed has an ERROR so it will not propagate and the landing page will keep the last working version in this case 3.21.0. Please see the follow page that not only explains this but also has advice on the length 1 vector

Re: [Bioc-devel] Unable to reproduce vignette build error

I am able to reproduce this locally. Make sure you are using R 4.0.0 and have updated versions of all Bioconductor packages BiocManager::valid() BiocManager::install() I did an "R CMD Stangle Installing_and_Using_BrainSABER.Rmd" to produce an R file of code for the vignette and also tried to

[Bioc-devel] Important Upcoming Release 3.11 Deadlines This Week!!

Some Important Release Deadlines are fast approaching. See also the release schedule online The last day for any NEW package to be accepted and released under Bioc 3.11 is this Wed. April 22th. Packages accepted after this day will remain in Bioconductor devel and included in the Bioc 3.12

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

rk 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Friday, April 17, 2020 1:37 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Nominations for Bioconductor Awards! Bioconductor is excited to announce an opportunity to recognize those making sig

[Bioc-devel] Nominations for Bioconductor Awards!

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

Re: [Bioc-devel] regarding imports github R packages, in new R package's description file

This mailing list is for Bioconductor package development and Bioconductor submissions not CRAN. Bioconductor only allows dependencies from CRAN or Bioconductor and does not allow github only repositories. If you indeed meant to submit to CRAN you should check with CRAN's submission policies

Re: [Bioc-devel] Question for building error

The current ERROR "polygon edge not found" is a Bioconductor builder issue having to do with fonts not being found. We are working on a solution but for now you can ignore. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics &

Re: [Bioc-devel] HiCBricks Bioc 3.11 Mac build is failing

Firstly, macv2 is R devel so to accurately test you should be using R 4.0.0 with Bioc 3.11 packages. However, this ERROR is a Bioconductor builder issue having to do with fonts not being found. We are working on a solution but for now you can ignore. Lori Shepherd Bioconductor Core Team

Re: [Bioc-devel] Cairo error in Windows server

of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Yue Zhao (Jason) Sent: Monday, April 13, 2020 5:14 PM To: Shepherd, Lori Cc: bioc-devel Subject: Re: [Bioc-devel] Cairo error in Windows server Hi Lori, Thanks for the

Re: [Bioc-devel] Warning in tokay2

Please see this post: https://stat.ethz.ch/pipermail/bioc-devel/2019-April/014999.html Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Unit tests pass locally but fail on Bioconductor machines

There are many changes to base R hence the switch from 3.6 to 4.0. I would highly suggest using R 4.0. There is a R-alpha version now available for all platforms with the R - 4.0 release schedule for later this month. Please use the R-alpha version . on CRAN.r-project.org you should see a

Re: [Bioc-devel] Request to undeprecate MANOR

Yes we will undeprecated the MANOR package. Are you working on the ERROR's in the devel report? These cannot be ignored. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York

Re: [Bioc-devel] R Dependency Warning

If you have compressed data it can be ignored. 4.0.0 is what the package would be released under so I recommend that. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Last Day to Submit New Packages for Bioconductor Release 3.11

The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.11 release is TODAY 5 PM EST! Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be

Re: [Bioc-devel] CNORfeeder building error

When I look at the git.bioconductor.org checkout of your package, There are no R functions and no man functions for those exports. Your commit on Mar 30 only updated the NAMESPACE and vignette. base) lori@lori-HP-ZBook-15-G2:~/b/Rpacks/CNORfeeder(master)$ grep -r "buildFeederObjectDynamic" *

Re: [Bioc-devel] Development branch build error from celda

I think this is an intermittent connectivity issue and is safe to ignore. While today's build report has not yet officially posted, I check the report for you package and it seems to be all OK. Thank you for your diligence on investigating package ERRORs. Cheers, Lori Shepherd Bioconductor

Re: [Bioc-devel] Help with tokay2 errors

On quick glance into the logs on tokay2 it looks like it may be an issue with MotifDb and not your package. In merge_motif it doesn't get to evaluating the code as it is hung up on trying to load the MotifDb library. Once this library is called, There are numerous: *** recursive gc invocation

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

rk 14263 ____ From: Shepherd, Lori Sent: Monday, March 30, 2020 11:36 AM To: bioc-devel@r-project.org Subject: Final List of Deprecated Packages for Bioc3.11 The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor c

[Bioc-devel] Devel Builder Updates

We will be updating the devel builders to the lastest R 4.0.0 later today. This should not affect the daily builder but may interrupt the Single Package Builder for new submission. Build report status for a platform on the single package builder may be missing during the update period. The

[Bioc-devel] connectivity to hubs

There has been an issue reported that there is some connectivity / timeout issues happening to experimenthub and annotationhub. It seems to be intermittent but we are aware and investigating the issue. Thank you Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11

rk 14263 From: Bioc-devel on behalf of Shepherd, Lori Sent: Monday, March 30, 2020 11:36 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Final List of Deprecated Packages for Bioc3.11 The Bioconductor Team is continuing to identify packages that will be deprecated in

[Bioc-devel] Bioc2020 - Call for BOF/HAK/FAQ Sections

Bioc2020 is proceeding with planning for the conference to be held July 29-31, with contingency planning for an online-only conference if necessary. https://bioc2020.bioconductor.org/ As part of the program we want to encourage community involvement and interactive projects. This may take the

Re: [Bioc-devel] The errror from build report of ASpediaFI

For What Its Worth --- I can reproduce this on my linux machine. I would suggest making sure you are using R-4.0.0 and all the latest package versions as there have been recent updates to S4Vectors and possibly others that you depend/import. # if the following suggests updating packages

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