Re: [Bioc-devel] Submitting ssh key

It sometimes takes an hour or two after the build report is generated for the landing pages to be generated. The landing page is now visible. https://bioconductor.org/packages/3.12/bioc/html/preciseTAD.html There was an already reported issue for the badges at the top that I'm looking into toda

Re: [Bioc-devel] Help me check if I push my package to git bioconductor

As explained before... There is not a github location for packages on Bioconductor, only your personal github location. Bioconductor maintains a git server located at git.bioconductor.org NOT a copy of the repo in the Bioconductor/github. So the location of the package on Bioconductor is the fol

[Bioc-devel] Deadline for devel branch 3.12 to pass R CMD build and R CMD check

The deadline for packages to pass R CMD build/check without error is Friday October 23. This ensures a build report with the committed changes. The branch will be frozen Tuesday October 27th to branch for the Release of Bioconductor 3.12. Please see the release schedule for other important de

[Bioc-devel] Bioconductor Release 3.11 Code Freeze Deadline

The release 3.11 branch will be frozen October 12th All code changes should be committed by the morning of October 12th. After this date there will be no updates to Bioconductor 3.11 packages in Bioconductor. Please see the release schedule for other important deadlines. http://bioconductor.org

[Bioc-devel] Last Day to Submitted New Packages for Bioc 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 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 acce

Re: [Bioc-devel] ExperimentHub with AWS

Hello! Thank you for your interest in the hubs. We would agree that hosting on AWS would be better than a google drive. Firstly, there is an off-list h...@bioconductor.org email to direct future hub inquires and questions too. I will send the credentials in a private email follow this one t

[Bioc-devel] One week to RELEASE_3_11 freeze

Hello all, Just a friendly reminder that in one week (October 12th) the RELEASE_3_11 branch of Bioconductor will be frozen. At that time we will disable commits to the RELEASE_3_11 packages we have on Bioconductor and they will be frozen in time at this state. We encourage all package maintai

Re: [Bioc-devel] Issue when fetching upstream

I think you might be referring to the emails you received from github when going through the submission process. Once packages are accepted in Bioconductor we do not build on commit; there is single build per day. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center

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

We are encountering ERRORs with the Single Package Builder used for new package submission. Currently, build reports are not being produced on git push. We are aware of the issue and are working to have it resolved as soon as possible. We apologize for any inconvenience and will kick off manu

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

om: Bioc-devel on behalf of Kern, Lori Sent: Thursday, October 8, 2020 8:51 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Single Package Builder for New Package Submission We are encountering ERRORs with the Single Package Builder used for new package submission. Currently, build reports

Re: [Bioc-devel] Remove Windows support for a package

I would consider if your package really needs to depend on the dependent package or if there are alternative solutions. Not supporting on windows will make your package not useful for a large portion of the Bioconductor community. That said... You can add a hidden file to the top level of the

[Bioc-devel] Package Code Freeze for Release Bioconductor 3.11 Tuesday October 13th!

This is a reminder, The Release Bioc 3.11 Code Freeze will occur on this coming Tuesday October 13th. All changes to the Bioconductor versions of packages on the RELEASE_3_11 branch must be pushed up before the freeze. Bioconductor does not allow changes to past versions of packages so this wi

Re: [Bioc-devel] Question for scheduled release

The officially release will not be until October 28th. Today, commmits to release/ RELEASE_3_11 (1.4.0) will be frozen and there will be no more commits allowed to this branch every. You can still commit the the master/devel branch (1.5.0) . For version x.y.z , if you push to the devel you

Re: [Bioc-devel] Package sitePath check error is bound to an upper dependency package

Thank you for letting us know. We appreciate your contributions to the project and your continued maintenance of your package. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo,

Re: [Bioc-devel] Help for R package check

Hello, If the ERROR comes from a dependency there is nothing you can do. You could reach out to the ReactomePA package to encourage them to fix the issue. As you can see from their build report, its failing to build and why it is not available for your package bioconductor.org/checkResults/

Re: [Bioc-devel] A question about r package update

We apologize. It was announced on the Bioconductor slack but we forgot to post on the bioc-devel mailing list. There was an issue with the builders and there was no report generated yesterday Thursday October 15. The issue should be resolved and we expect a build report today. I do see 1.5.2 i

Re: [Bioc-devel] Package deprecation

Thank you for letting us know. We will take the necessary steps to deprecate the package. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ___

Re: [Bioc-devel] VERSO issue #1689

We are sorry for the delay. We try to get to package reviews within 2 weeks of submission. Package reviews are only part of the core team task and as you can imagine release time is busy. Nitesh will have a review for you shortly. Lori Shepherd Bioconductor Core Team Roswell Park Comprehens

Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update

___ From: Xiaowen Chen Sent: Saturday, October 17, 2020 2:40 PM To: Martin Morgan ; Kern, Lori ; bioc-devel@r-project.org Subject: Re: [Bioc-devel] [EXTERNAL]Re: A question about r package update Yes, the check report is the one I lately push, But the epihet on the website" bioconductor

Re: [Bioc-devel] MOFA package deprecation

Thank you for letting us know. Yes I can specialize the message to point users to MOFA2. I will take care of this later today. Does MOFA2 still use the accompanied data package MOFAdata or should that also be deprecated? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Canc

Re: [Bioc-devel] Can we still patch a broken package in 3_11

The RELEASE_3_11 branch is frozen and will not be updated. Please update in your current master branch so the changes will be included in the upcoming release. thank you. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformat

Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

We are sorry for the inconvenience. There was an issue generating the build report, again. We hope to have it resolved and have the new build report posted later today. I do see the 0.99.13 updates in our git repository so they were pushed up and should be reflected in the next posted build r

Re: [Bioc-devel] 3.12 builds

Please review this page on timing for build report and landing page updates. bioconductor.org/developers/how-to/troubleshoot-build-report/ The recent commit to 0.99.23 was only today. This would not have been in time for today's build report and should be reflected on tomorrow's build report.

Re: [Bioc-devel] MOGAMUN not available in the devel's repository

It normally takes a day or two from that point to be reflected in the build report. I can verify it was added to the software manifests for nightly builds two days ago. It probably was too late to make yesterdays build but should be present on today's build report (generally posted around 1 PM

[Bioc-devel] SUPPORT SITE UPGRADE TODAY -- PLEASE REFRAIN FROM POSTING

In roughly 30 minutes we will begin an update of support site (support.bioconductor.org) . The support site will temporarily be down and unreachable. Once the upgrade is complete, it will be back online and we will let you know when you can begin posting again. Thank you for your patience and

Re: [Bioc-devel] SUPPORT SITE UPGRADE TODAY -- PLEASE REFRAIN FROM POSTING

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of Kern, Lori Sent: Thursday, October 22, 2020 9:41 AM To: BioC-devel Subject: [Bioc-devel] SUPPORT SITE UPGRADE TODAY -- PLEASE REFRAIN FROM POSTING In ro

[Bioc-devel] Bioc 3.12 Feature Freeze and Deadline for passing R CMD build/check

Developers, The release of Bioconductor 3.12 is less than one week out. Please respect the 'feature freeze' of 3.12 where we ask that all commits are limited to bug fixes and documentation (no more API changes). The deadline to pass R CMD build and check on the daily builders is today. While

[Bioc-devel] Last day to make commit before the RELEASE_3_12

Hello Bioconductor developers, We are still on track for Bioconductor Release 3.12 for this Wednesday October 28th. This means that tonight is the last day to commit changes to the devel branch before creating of the RELEASE_3_12 versions of your packages. And any changes you make to your pac

Re: [Bioc-devel] NanoporeRNASeq not found in the devel Bioc3.12 package list

We are looking into the issue. This happens with a numer of packages and we think it has to do with multiple resources trying to access without an official locking mechanism in place. I'm investigating the Hubs issue and hope to have it resolved soon. There is nothing more you need to do on y

[Bioc-devel] Bioconductor 3.12 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_12_release/ The Bioconductor Core Team This email message may contain legally privileged and/or confidential information. If you are

Re: [Bioc-devel] skipped, ERROR

Is your package in the submission queue, I see it is. It is best to ask questions there so it can be tracked by your reviewer. Packages submitted at this phase will be officially released in spring and therefore should be tested against all devel versions of packages. The current Bioc devel 3.

Re: [Bioc-devel] Outdated Bioconductor's config.yaml

Yes. Thank you for pointing it out. I will update immediately. Expect the changes to propagate over the next hour or so. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] latest devel version of igvR - apparently not picked up by the build system

There are a number of things that could be the possible cause... Firstly, on the Bioconductor end, it looks like the devel build report has not been updated since Friday as indicated by the date at the top of this page: http://bioconductor.org/checkResults/3.13/bioc-LATEST/ This page gives so

Re: [Bioc-devel] Acceptable dataset origins besides ExperimentHub

Including this data should be okay. The benefit of the ExperimentHub package would be to allow broader use of the data beyond your package to the Bioconductor community at large.If you include the data from the site, I would strongly, strongly suggest implementing a caching mechanism (Exp

Re: [Bioc-devel] Issue when merging upstream current release branch

To recap: It seem like you have created the RELEASE_3_12 branch that will track from upstream (Bioconductor's RELEASE_3_12 branch) as the following you said worked: git checkout -b RELEASE_3_12 upstream/RELEASE_3_12 So the following fails: git merge origin/RELEASE_3_12 merge: origin/RELEASE_3_

Re: [Bioc-devel] Issue when merging upstream current release branch

formatics Elm & Carlton Streets Buffalo, New York 14263 From: H�l�ne Borges Sent: Thursday, November 12, 2020 1:00 PM To: Kern, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Issue when merging upstream current release branch Yes, I have exact

Re: [Bioc-devel] Problem with EnMCB

The packages are not available yet because they have not been able to build properly on the daily builder. There was a configuration ERROR on the windows builder preventing the dependencies of those packages to build and therefore also causing those packages to fail. We believe we have fixed th

Re: [Bioc-devel] How to Push a Bug Fix Live - MSstatsTMTPTM

There are a few issues. I see the pushed changes but only on the master branch. The email you received indicated it also was failing on the Release 3.12 (RELEASE_3_12) branch. Please see the instructions for pushing to both release and devel branches of Bioconductor: bioconductor.org/develope

[Bioc-devel] Single Package Builder Updates

Bioconductor Community, We will be switching the single package builder for new package submissions to build off the devel Bioc 3.13 builders shortly. During this time the single package builder will have intermittent connectivity and you will not receive automatic build reports on version bum

Re: [Bioc-devel] View package posts from its web page

Thank you for letting us know. We have recently updated the support site; I will check the end point API behind the link and make the necessary changes. I have opened a github issue for the website to keep track of this issue. https://github.com/Bioconductor/bioconductor.org/issues/77 Cheers

Re: [Bioc-devel] Maintainer change request -Phenogenranker

I will take care of this shortly and post on the issue when it is resolved. Thank you. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 F

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Your packages is failing in both release and devel of Bioconductor. You need to fix the package. You can see the ERROR on the build reports bioconductor.org/checkResults/devel/bioc-LATEST/epihet and bioconductor.org/checkResults/release/bioc-LATEST/epihet If you click on the ERROR on either

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

n Streets Buffalo, New York 14263 From: Xiaowen Chen Sent: Monday, November 23, 2020 3:29 PM To: Kern, Lori Cc: bioc-devel@r-project.org Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 Hi Kern, I built ep

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

halted 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 Kern, Lori Sent: Monday, November 23, 2020 4:01

Re: [Bioc-devel] CoxBoost

CoxBoost was removed from CRAN on 11-11-2020. https://cran.r-project.org/web/packages/CoxBoost/index.html We only allow dependencies that are on CRAN and Bioconductor. I would reach out to the CoxBoost maintainer to see if they will reinstate the package on CRAN. The other option is to fix

Re: [Bioc-devel] ExperimentHub package check fails on Windows

The allocation memory I don't believe has a solution besides decreasing the amount of data that is utilized. If that isn't possible there are ways to mark the package unsupported only on windows i386. We have seen some intermittent connectivity issues reported for the server and are investigat

Re: [Bioc-devel] Hi to Everyone

We are sorry you are having trouble signing up for the mailing list. We have signed you up manually, please be on the lookout for a confirmation email. Depending on institutional setting there is a chance it could be marked as spam so also look in your spam folder. Cheers, Lori Shepherd Bi

Re: [Bioc-devel] Illegal Version Bump after accidentally pushing Version Bump to 1.1.1

I answered on the support site too but please check out this documentation http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/ You need to push to the RELEASE_3_12 branch not the master branch. the RELEASE_3_12 is the Bioconductor release 3.12 branch while the master b

[Bioc-devel] List of Deprecated Packages for Bioc3.13

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 3.13 : User Requested Software: Bioc

Re: [Bioc-devel] Request access to EGSEA123

I believe you should have access now. Let us know if you do not. 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 be

Re: [Bioc-devel] updating released version of package

There is information on this page: http://bioconductor.org/developers/how-to/troubleshoot-build-report/ Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 __

Re: [Bioc-devel] Build errors due to 'usethis' package

We have installed the needed system dependency that should allow the packages needed by and the package usethis to be available for tonight's build. It should clear up on its own and you do not need to take any further actions. Get Outlook for iOS _

Re: [Bioc-devel] When I can see my package(PFP(#1669)) in the nigthly 'devel’ build?

It should appear it today's devel build report. http://bioconductor.org/checkResults/3.13/bioc-LATEST/ Today's report is not out yet but should be within the next few hours Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformat

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

The current Bioconductor release is 3.12 so you changed the commands below to reflect 3_12? (i.egit checkout RELEASE_3_12 ) Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New Y

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Xiaowen Chen Sent: Friday, December 18, 2020 3:13 PM To: Kern, Lori Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 Yes,

Re: [Bioc-devel] Problem with download count tables

Thank you for bringing it to our attention. We discovered this yesterday as well and are looking into the issues with the stats generation. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffa

[Bioc-devel] List of Deprecated Packages for Bioc3.13

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 3.13 : Maintainer requested deprecation

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

Did you 'git commit' the changes to the branch? Get Outlook for iOS<https://aka.ms/o0ukef> From: Xiaowen Chen Sent: Wednesday, December 23, 2020 2:56:01 PM To: Kern, Lori Cc: bioc-devel@r-project.org Subject: Re: [EXTERNAL]epihet problems

Re: [Bioc-devel] [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12

I think. Get Outlook for iOS<https://aka.ms/o0ukef> From: Xiaowen Chen Sent: Wednesday, December 23, 2020 4:19 PM To: Kern, Lori Subject: Re: [EXTERNAL]epihet problems reported in the Multiple platform build/check report for BioC 3.12 Hi Kern, The comma

Re: [Bioc-devel] credential not recognized when git clone my packages

Are you on a different computer? You could always create and add additional public keys for your package through the git credentials app. https://git.bioconductor.org/BiocCredentials/ If you have never activated the account, please activate first: https://git.bioconductor.org/BiocCredentials/acco

Re: [Bioc-devel] Bioconductor Package Error: LRcellTypeMarkers

Thank you for the detailed report. I will go on the builder to have a look. We recently updated the devel builders of R including the mac so I'm hoping it has resolved itself. I will post more on your open issue and have informed your reviewer to look at the package in the meantime. Cheers,

Re: [Bioc-devel] Change of package mantainer/manager

CTDquerier was removed in Bioconductor 3.12 after being deprecated in 3.11 as it had been failing across all OS platforms since at least 05/31/19 with no response or contact. The package is considered defunct and could be reinstated by re-submitting to the new package tracker. Cheers, Lori S

[Bioc-devel] List of Deprecated Packages for Bioc3.13   KL

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 3.13 : Maintainer requested deprecation

Re: [Bioc-devel] Re-submit defunct package

I took care of the database updates that needed to occur to allow it to be submitted. Please try resubmitting a new issue to the tracker. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo,

Re: [Bioc-devel] Updating a package due to reviewer comments and other questions

Additionally on the fread not being found: if you are using roxygen and devtools to develop you may need to run document() again for the changes to be made to the NAMESPACE. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinform

Re: [Bioc-devel] How to update an experiment data package

The instructions for updating an experiment data package are the same as software. They are located at git.bioconductor.org and have the same branch structuring for RELEASE_3_12 and master. As with software packages, only packages that push changes with a valid version bump will propagate to u

Re: [Bioc-devel] MOFA package deprecation

stics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Britta Velten Sent: Saturday, February 6, 2021 4:53 AM To: Kern, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] MOFA package deprecation Hi Lori, a quick follow up qu

[Bioc-devel] List of Deprecated Package Bioc 3.13

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 3.13 : Maintainer requested deprecation

Re: [Bioc-devel] autonomics: warnings only on tokay2

It is suggested this has to do with the way we are running R CMD check . For now you may ignore the windows ERROR's. Your reviewer is aware of this as well. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Car

Re: [Bioc-devel] How to integrate code from a package not available on bioconductor

Have you reached out to the maintainer of the github package to see if they would plan on submitting to CRAN or Bioconductor? If they do not, you could see if they are okay with you including the code in your package and then clearly indicate their authorship in the man pages and by giving cont

Re: [Bioc-devel] How to integrate code from a package not available on bioconductor

ote%2F On Wed, Feb 10, 2021 at 2:51 PM Wolfgang Huber wrote: > > > > Il giorno 10feb2021, alle ore 14:31, Kern, Lori > ha scritto: > > > > Have you reached out to the maintainer of the github package to see if > they would plan on

Re: [Bioc-devel] EWCE Bioconductor package

When a package is defuncted and removed from Bioconductor, push access is no longer granted. The package has been out of Bioconductor for several releases and will have to be re-submitted and undergo a formal review through the submission tracker. github.com/Bioconductor/Contributions/issues A

Re: [Bioc-devel] Problem with my setters on Windows during the build and the check

Please ignore this for now. The reviewer is also aware to ignore. We think this is related to how we are building/checking the packages and are investigating a solution. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformati

Re: [Bioc-devel] What is the Timeout limit on R CMD check?

The page you have listed is for long tests. If long tests are implemented through the documented process, those checks have 40 minutes to run and are currently only run once per week. The daily builders do not give such a large time limit to packages. We build and check all packages so there i

Re: [Bioc-devel] MSstatsTMTPTM Bug Fix

The daily build system will build, check, and propagate packages only once per day. See the top of this page for some information on timing http://bioconductor.org/developers/how-to/troubleshoot-build-report/ >From the looks of the git.bioconductor.org repo, the changes were only pushed >yeste

[Bioc-devel] Single Package Builder

We are making some updates to the single package builder. While builds should not be affects, email notifications of events may be hindered. The update should be complete within the next 30 minutes. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Depa

Re: [Bioc-devel] About developing package

Others may chime in but it seems like a reasonable Bioconductor package. Please look in the Software biocViews. Probably StatsticalMethods and Classification sound appropriate. We can add additional biocViews if you proceed with the Bioconductor submission. It would also seem reasonable to ad

Re: [Bioc-devel] Reference ExperimentHub package in statistical package

In the review process, that is why we ask to submit related packages under the same issue. They will be installed in the same location and available for testing before being added to the official Bioconductor repositories (once officially added available through BiocManager::install) You can u

Re: [Bioc-devel] How to change the name of a package on Bioconductor

This should be taken care of. The page now displays : bioconductor.org/packages/devel/bioc/html/VaSP.html The badges at the top of the page should fill in, in the next day or so. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistic

[Bioc-devel] Rsync to Bioconductor

In the next few weeks we will be limiting the ability to rsync to Bioconductor resources. If you currently are using rsync please reach out to maintai...@bioconductor.org as we will need additional information to continue to allow rsync on your machines. Cheers, Lori Shepherd Bioconductor C

Re: [Bioc-devel] What should I do if I need to ask my package to be deprecated?

Thank you for letting us know. I will begin the deprecation process for the package. Cheers Get Outlook for iOS From: Bioc-devel on behalf of Kozo Nishida Sent: Thursday, February 25, 2021 5:00:18 PM To: bioc-devel@r-project.org Subject

Re: [Bioc-devel] Rsync to Bioconductor

& Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Henrik Bengtsson Sent: Thursday, February 25, 2021 3:50 PM To: Kern, Lori Cc: bioc-devel Subject: Re: [Bioc-devel] Rsync to Bioconductor FYI, I just sent an email to 'maintai...@bio

[Bioc-devel] Release build report

Please be advised, the Bioconductor RELEASE_3_12 build report has not been updated since Monday Feb 22. We have identified the issue and are working on the resolution. We appreciate your patience. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Depart

Re: [Bioc-devel] Formatting of ExperimentHub Data in package

I think because you specified: #' @usage all_mgi_wtEnsembl(metadata=FALSE) You would need to document the parameter metadata with: #' @param metadata Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Car

Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Please feel free to also comment directly on your issue for your reviewer to assist. The packages not being available on windows is likely on our end and you can ignore for now. System files should not be git tracked. They should be remove using git remove and then committed up. git rm git co

Re: [Bioc-devel] Remotes in DESCRIPTION not supported for BioC?

Currently the builders do not allow the user of remotes and you would have to wait for it to be submitted to CRAN or Bioconductor. All Bioconductor dependencies must be on CRAN or Bioconductor. Get Outlook for iOS From: Bioc-devel on beha

Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build

Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Oluwafemi OLUSOJI Sent: Tuesday, March 2, 2021 4:47 AM To: Kern, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Error on BiocCheckGitClone and Windows build Hello Lori

Re: [Bioc-devel] [Bioc-deve] Check package status / built report

Michael is right. Additionally there is some information on the timing of pushing / pulling of the build system on the top of this page: bioconductor.org/developers/how-to/troubleshoot-build-report/ While its possible you made the changes in time for today's report, Most likely the changes will

Re: [Bioc-devel] [Bioc-deve] Check package status / built report

propagate for availability to the end users. Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 ____ From: Kern, Lori Sent: Tuesday,

Re: [Bioc-devel] ClusterJudge problems reported in the build/check

Did you remember to do a version bump when submitting the changes? It does not appear so. The build machines will not recognize code changes without a valid version bump. You should increase from 1.13.0 to 1.13.1 for the new changes to propagate and be available through BiocManager::install

Re: [Bioc-devel] RegEnrich problems reported in the Multiple platform build/check report for BioC 3.12

Please remember there are always two branches of Bioconductor active at one time, a release and a devel branch. Pushing to master and changing to 1.1.1 was on the devel branch and is indeed building cleanly as indicated on the build report: http://bioconductor.org/checkResults/devel/bioc-LATEST/R

Re: [Bioc-devel] including package in github

-devel@r-project.org ; Kern, Lori Subject: including package in github Dear bioconductor team, Recently, I want to upgrade our package EnMCB and add some functions. However, the functions are based on a GitHub package ("Coxboost") This package has been removed from CRAN, but I can fi

[Bioc-devel] List of Deprecated Packages Bioc 3.13

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 3.13 : Maintainer requested deprecation

Re: [Bioc-devel] Bioconductor Permission denied (publickey).

You'll likely need to add keys to your account. https://git.bioconductor.org/BiocCredentials/login/?next=/BiocCredentials/ If this is your first time accessing the BiocCredentials app you will have to activate the account first: https://git.bioconductor.org/BiocCredentials/account_activation/

Re: [Bioc-devel] Methods to speed up R CMD Check

If your data is using ExperimentHub, it should already be caching the downloaded data. Once it is downloaded once, it should be using the cached download for subsequent calls to the hub. We will investigate to ensure that the caching mechanism is functioning properly on all of our Bioconducto

Re: [Bioc-devel] Recently accepted package not appearing in nightly builds

Your package was identified as a workflow package based you the biocViews you selected. The workflow packages did not build last Friday and next run is today. You should check the following page for your workflow package build results: http://bioconductor.org/checkResults/3.13/workflows-LATES

Re: [Bioc-devel] No updates on Bioconductor landing page after making changes to package and bumping package version

On git.bioconductor.org there it is showing no associated version bump. I still see 1.1.0 . The build system will only recognize package changes associated with a version bump in this case to 1.1.1. Please push this change in the DESCRIPTION. Lori Shepherd Bioconductor Core Team Roswell P

Re: [Bioc-devel] Adding new "DifferentialDNA3DStructure" to biocViews

DifferentialDNA3DStructure has been added to the devel list of biocViews terms and will be carried through in future releases. It will be available once biocViews version 1.59.3 propagates on the build system Cheers, Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Cen

[Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

We are in process of making some major updates to the caching in BiocFileCache, AnnotationHub, and ExperimentHub. Namely, the default caching location will change from using rappdirs::user_cache_dir to using tools::R_user_dir eventually relieving the dependency on rappdirs. To avoid confli

Re: [Bioc-devel] Updates to BiocFileCache, AnnotationHub, and ExperimentHub

plicable to those two packages as well. -A On 4/5/21 6:41 AM, Kern, Lori wrote: > We are in process of making some major updates to the caching in > BiocFileCache, AnnotationHub, and ExperimentHub. Namely, the default caching > location will change from using rappdirs::user_cac

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