Re: [Bioc-devel] monocle package on Bioconductor

where there is a community to help you. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute "I don’t expect you to respond to my email outside your work hours" > On Jun 7, 2022, at 7:17 PM, Brent G Ewing wr

Re: [Bioc-devel] MetaboSignal problems reported in the Multiple platform build/check report for BioC 3.15

Hi Andrea, Please try again, I’ve fixed your email in the system. Try to activate your account with this email "andrea.rodriguez-martine...@imperial.ac.uk”. The previous email for some reason had ‘@ic.ac.uk’. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Sc

Re: [Bioc-devel] Maintainer change pRolocGUI

Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On May 17, 2022, at 5:36 AM, Laurent Gatto wrote: > > Would it be possible to give Lisa Breckels write access to > the pRolocGUI git repo, as she will be

Re: [Bioc-devel] Add Maintainer to `tripr` package

update both and confirm with are reply. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On May 13, 2022, at 6:28 AM, Nikolaos Pechlivanis wrote: > > Dear Mrs. Kern, > > Thank you for your pr

Re: [Bioc-devel] Maintainer change for pairkat package

Hi Cameron and Max, Max should have access to the package with the registered BiocCredentials address. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Feb 10, 2022, at 1:06 PM, Cameron Severn wr

Re: [Bioc-devel] Git recognizes me but denies access

Is this resolved Philipp? ‘destiny’ seems to be failing on windows still http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Dec 19, 2

Re: [Bioc-devel] DeMixT Bioconductor maintainer

. Please change the maintainer once this happens on the DESCRIPTION file. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Dec 28, 2021, at 5:36 PM, Yang,Peng wrote: > > Hi Bioconductor team, >

Re: [Bioc-devel] No write permissions on PDATK

As far as password reset goes. Please check your spam as well. Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Dec 17, 2021, at 11:58 AM, Chris Eeles > wrote: > > Hello Core Team, > > I am trying to

Re: [Bioc-devel] No write permissions on PDATK

Hi, Should be fixed. Please check again now. Best Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Dec 17, 2021, at 11:58 AM, Chris Eeles > wrote: > > PDATK ___

Re: [Bioc-devel] Transfer Maintainership of GeoDiff

Hi, I’ve added Nicole. She should have maintainer access. Please change the DESCRIPTION file. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 15, 2021, at 1:59 PM, Nicole Ortogero wrote: > > Hi Bio

Re: [Bioc-devel] Activate account in Bioconductor Git Credentials

/developers/how-to/version-numbering/ http://bioconductor.org/developers/ Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 17, 2021, at 5:01 PM, Yihang Xin wrote: > > Hi Alex and Nitesh, > > I wo

Re: [Bioc-devel] Git recognizes me but denies access

Please activate your account flying-sh...@web.de for BiocCredentials. You should be good to go. Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 18, 2021, at 4:23 AM, Philipp A. wrote: > > My addresses are

Re: [Bioc-devel] Activate account in Bioconductor Git Credentials

. Ideally, Alex would make the final sync from Github to Bioconductor once all your development is done on Github. If you would like access to the package on git.bioconductor even now, please let me know and cc Alex. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor

Re: [Bioc-devel] Git recognizes me but denies access

Hi Philipp, The email address that is registered to BiocCredentials right now is 'philipp.ange...@gmail.com'. It doesn’t look like an institutional email address. Could you please confirm the email change to flying-sh...@web.de ?? Best, Nitesh Nitesh Turaga Scientist II, Department

Re: [Bioc-devel] Add or Transfer Maintainership of DecoupleR Package

to the account, please add your SSH keys and you’ll get access to the package. Best regards, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 5, 2021, at 12:44 PM, Jesús Vélez Santiago > wrote: > > Hi, >

Re: [Bioc-devel] Bioconductor Git Credentials

Hi Wubing, You would need to activate your account first, at https://git.bioconductor.org/BiocCredentials/account_activation. Then you are able to set your password. You have never activated your account. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor

Re: [Bioc-devel] Git recognizes me but denies access

as well, https://bioconductor.org/developers/how-to/git/faq/. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Nov 8, 2021, at 12:23 PM, Philipp A. wrote: > > Hi, > > My package (destiny) has

Re: [Bioc-devel] bumphunter 1.35.0 - GENCODE FTP Server File Download Error

Dear Selvi, It looks like a transient issue that happens on and off. I’m not sure there is any special insight I can offer here. I do not think any action is needed on your end. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber

Re: [Bioc-devel] Release 3.14 process - stop all commits

. To sync your packages, please follow http://bioconductor.org/developers/how-to/git/sync-existing-repositories/. If you have any questions, please send them to bioc-devel@r-project.org as a new email. Best regards, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team

[Bioc-devel] Release 3.14 process - stop all commits

allowing commits to be pushed to the Bioconductor git server again. Best regards, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute ___ Bioc-devel@r-project.org mailing list https

Re: [Bioc-devel] hypeR Bioconductor package

The release branch has been frozen. http://bioconductor.org/developers/release-schedule/ Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oct 25, 2021, at 10:28 AM, Federico, Anthony, Nicholas > wrote: &

[Bioc-devel] Release 3.13 is frozen

Hello, The release 3.13 branch of Bioconductor is now frozen. You will not be able to push to this RELEASE_3_13 branch of your package again. Please review the release schedule http://bioconductor.org/developers/release-schedule/ for more information. Best regards, Nitesh Turaga Scientist

Re: [Bioc-devel] Bioconductor Release 3.13 Code Freeze

Hi The release 3.13 branch will be frozen after the next 2 hours. After today, you will not be able push to this branch. Please refer to http://bioconductor.org/developers/release-schedule/. Best regards, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member

Re: [Bioc-devel] hypeR Bioconductor package

Hi, What is your upstream remote set as? git remote -v Please send results. It might just be you are using the wrong SSH key. A good solution is to try with a new SSH key on your BiocCredentials app. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor

Re: [Bioc-devel] Can't push to upstream for ToxicoGx

Hi Chris, Either way, this is a problem we have to solve post release. I’ve given the SSH key you are using access to that package as well. It should work now. Best Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oc

Re: [Bioc-devel] Can't push to upstream for ToxicoGx

Hi Can you just try with a new SSH key? This is again related to using the wrong account. benjamin.haibe.ka...@utoronto.ca is the email associated with the BiocCredentials account, and `ChristopherEeles` is the GitHub username / Bioc ID attached to it. Best, Nitesh Turaga Scientist II

Re: [Bioc-devel] Don't have git access to my newly submitted git package

I think point #2 is the bigger issue. We are pressed for time as far as reviews go, and I’m happy to try and get sparrow reviewed, but cannot promise time for sparrow.shiny. You are welcome to submit though, but there is no guarantee that I will be assigned to the package for review. Nitesh

Re: [Bioc-devel] regain access to git repository

/account_activation. If not I’ll change it to n...@u.washington.edu. Just let me know. Best Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oct 4, 2021, at 4:22 PM, Noah G. Hoffman wrote: > > Hello, >

Re: [Bioc-devel] Reset package

H Matineh, This is taken care of, and your package has been reset. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oct 5, 2021, at 9:14 AM, matine rb wrote: > > Dear Bioconductor community

Re: [Bioc-devel] Reset package

Hi, I’ve taken care of the resetting of the repo on Bioconductor from your GitHub location https://github.com/compbiomed/curatedTBData. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oct 5, 2021, at 5

Re: [Bioc-devel] Don't have git access to my newly submitted git package

Hi Steve, You are having it ;) I’m the one assigned to your package. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oct 4, 2021, at 5:42 PM, Steve Lianoglou wrote: > > Hi Nitesh, > > Tha

Re: [Bioc-devel] Don't have git access to my newly submitted git package

Hi Steve, This is resolved now. You should see access to your package. Waiting till the next cycle is fine if you think that is the best approach. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Oct 1, 2

Re: [Bioc-devel] access problems

/account_activation. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Sep 29, 2021, at 1:38 AM, Schalkwyk, Leonard wrote: > > I am the maintainer of the wateRmelon package. This message is coming from >

Re: [Bioc-devel] Add maintainer to scruff and celda

Hi, Joshua campbell is the maintainer of these two packages already. If that is not reflected in the description file of the package, it is up to Joshua to change it. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer

Re: [Bioc-devel] Submit a package via Gitlab

/importing-a-repository-with-github-importer which is quite helpful. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Sep 17, 2021, at 2:35 PM, Jiyuan Fang wrote: > > Dear Sir/Madam, > > May I

Re: [Bioc-devel] Regarding package IntramiRExploreR

Dear Surajit, You should have access now with the new email. Please add SSH keys in the BiocCredentials app, and you’ll gain access. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Sep 10, 2021, at 5:30

Re: [Bioc-devel] pre-receive hook won't let me fix (very) old merge conflict

the conflicts in your code were introduced in the ‘pre-git’ era. I can disable the hook for your package and we can resolve it. I’ll send you a private email to coordinate. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute

Re: [Bioc-devel] lessons learned: negative experiences with git log

nly” merge commits and the files that change with this command, git log --merges -m --name-only -n 5 Hope this helps. Best regards, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Aug 13, 2021, at 9

Re: [Bioc-devel] Best practices for joint release/update of BioC packages

ndependent development of two separate packages adding a lot of complexity. (We should not consider this method for the sake of good software engineering practices) I’m hoping other members on the team / community can provide better suggestions. Best, Nitesh Turaga Scientist II, Department of Da

Re: [Bioc-devel] Git lfs support

Hi, We don’t have LFS support on the Bioconductor git server. I would suggest finding an alternative. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Aug 24, 2021, at 6:18 PM, Anatoly Sorokin wrote: > &g

Re: [Bioc-devel] git: lost write access to some repos + what is my BiocCredentials email address?

Hi Henrik, You should have access to these packages again. Please try again. Best Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Aug 19, 2021, at 8:08 AM, Henrik Bengtsson > wrote: > > Hi, > > I

Re: [Bioc-devel] Pushing an update to already released package

check the RSS feed for our git server http://bioconductor.org/developers/gitlog/ There are other helpful FAQ here, http://bioconductor.org/developers/how-to/git/faq/. Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On

Re: [Bioc-devel] EXTERNAL: R: Bioconductor package DaMiRseq

there. If all else fails, generate a new SSH key and add it. Best Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Jul 29, 2021, at 3:20 AM, Mattia Chiesa wrote: > > Dear all, > sorry to keep asking but I d

Re: [Bioc-devel] pre-receive hook declined

Hi, This is because all commits to RELEASE_3_12 have been blocked during the release of Bioconductor 3.13. You can now only commit/push to RELEASE_3_13 and devel. Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Jul

Re: [Bioc-devel] Bioconductor package DaMiRseq

Please add your SSH keys and you’ll gain access to your package. Once you get access, change the maintainer email address in the DESCRIPTION file of the package. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On

Re: [Bioc-devel] Bioconductor package DaMiRseq

Hi Are you using mattia.chi...@cardiologicomonzino.it to activate your BiocCredentials account? It seems this email is not the same as the one on the maintainer on the DESCRIPTION file of the package. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core

Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor repositories

Hello, Please take a look at http://bioconductor.org/developers/how-to/git/faq/ #13 onwards to see if any of those issues fix your problem. There is nothing wrong on our end. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber

Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor repositories

Hi Nicole, Please sync your two repos now. You should be all set. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Jul 26, 2021, at 12:44 PM, Kramer, Nicole Emma > wrote: > > Hi Nitesh, > >

Re: [Bioc-devel] BentoBox and BentoBoxData git.bioconductor repositories

Hi Nicole, Thank you for cleaning the repos. I will do the force push for you, but you will have to re-sync the Github repo once it’s done. I’ll email you as soon as I’m done with the force push. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team

Re: [Bioc-devel] Maintainer change

Hi Mikhail, You now have access to both packages. Please remove the previous maintainer in the DESCRIPTION file and add yourself as the new maintainer. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On

Re: [Bioc-devel] Git credentials

Hi Ludwig, Could you please try to activate your account now? I’ve changed your email. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Jul 15, 2021, at 10:57 AM, Geistlinger, Ludwig > wrote: >

Re: [Bioc-devel] Updating stable release

Hi Margaret, Please follow the documentation on the website, http://bioconductor.org/developers/how-to/git/. http://bioconductor.org/developers/how-to/version-numbering/ Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer

Re: [Bioc-devel] Getting ready for package submission, running into a couple of errors/warnings that I can't figure out

Hi, I will try to answer a couple of the questions you asked. I am not able to help with your question on ‘qpdf'. > On Jul 12, 2021, at 5:58 PM, Wight, Andrew E. > wrote: > > Good evening all - I'm getting my first package ready for submission to > Bioconductor, and I'm running into a

Re: [Bioc-devel] lack of ability to push changes to new bioc repo via git

Hi Ben, Please activate your account at https://git.bioconductor.org/BiocCredentials/account_activation. Once you do that, you can add SSH keys and gain access to your package. Best, Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer

Re: [Bioc-devel] pre-receive hook declined

Hi Please try again. You should not see this error anymore. This was a mistake on our end. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Jul 1, 2021, at 1:49 AM, Michael Love wrote: > > I'

Re: [Bioc-devel] pre-receive hook declined

Hi, Can you please try again?? It seems a minor issue on our end, which I just fixed. Best, Nitesh Nitesh Turaga Scientist II, Department of Data Science, Bioconductor Core Team Member Dana Farber Cancer Institute > On Jun 30, 2021, at 1:41 PM, Victor Yuan wrote: > > Hi I ca

[Bioc-devel] Reg: Git hook update on Experiment Data and workflow packages

-the-command-line 2. https://www.atlassian.com/git/tutorials/using-branches/merge-conflicts 3. Bioconductor git hooks: https://github.com/Bioconductor/git-hooks If you have any questions, please reply to this thread. Best regards, Nitesh Nitesh Turaga Scientist II, Department of Data Science

Re: [Bioc-devel] Push bug fix to release branch

Hi Alan, What you have written below looks correct to me. A simpler way to remember this is how the versioning works - (X.Y.Z) or (major.minor.patch). You only every update the “patch” or the “Z” number in the versioning system. Best, Nitesh Nitesh Turaga Scientist II, Department

Re: [Bioc-devel] Help fixing version and resync existing package epidecodeR

Hi Kandarp, Please email the bioc-devel@r-project.org for questions on git. You can try to use the documentation we have on our website, http://bioconductor.org/developers/how-to/git/sync-existing-repositories/. The problem is to sync your Github repo with the Bioconductor git repo, hence

Re: [Bioc-devel] I don't have access to my package

Hi, Your email is listed for access on the package, but jh...@genetics.utah.edu is listed as the email. You also haven’t activated your account on BiocCredentials or added and SSH key to it. Please activate your account at https://git.bioconductor.org/BiocCredentials/account_activation

[Bioc-devel] RELEASE_3_13 is now available for bioconductor_docker

Hello Developers, The Bioconductor docker images have been updated to reflect the latest release. For more details on how to use the docker image, http://bioconductor.org/help/docker/ . - 'bioconductor/bioconductor_docker:RELEASE_3_13' is the new image (Bioc 3.13 and R version 4.1.0). -

Re: [Bioc-devel] Access to schex

intainer addresses), but none of > them seem to change anything. Could it be that there is a problem with the > email addresses registered to the package? It may be that a year ago we > changed these to make them the same between RUVcorr and schex. > > Cheers, > > Saskia &

Re: [Bioc-devel] Bioconductor git repository commits have resumed

You should also be able to see the RELEASE_3_13 branch on your package (example below is BiocGenerics) at, https://code.bioconductor.org/browse/BiocGenerics/RELEASE_3_13/ Best, Nitesh From: Nitesh Turaga Date: Wednesday, May 19, 2021 at 7:31 AM To: bioc-devel@r-project.org Subject

[Bioc-devel] Bioconductor git repository commits have resumed

should have access to the "master" (devel branch) and the RELEASE_3_13 branch of their packages. Thank you for your contributions, and we are looking forward to more. Best regards, Nitesh Turaga [[alternative HTML version deleted]] __

[Bioc-devel] Creating Bioconductor 3.13 branch on May 19th 2021 - 11 AM EDT

packages (software, data experiment, workflow, and books). The process will take about 2.5 - 3 hours once commits are stopped. If there are any issues in the meantime, please reply to this thread and c.c bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>. Best regards, Nitesh

Re: [Bioc-devel] Access to schex

Hi Saskia , Please try to add new keys. It�s possible you aren�t using the correct key pair to access your package. Best, Nitesh From: Bioc-devel on behalf of Saskia Freytag Date: Saturday, May 15, 2021 at 8:42 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] Access to schex Hi, I

Re: [Bioc-devel] MSstatsPTM Maintainer Change

Hi, You are already the maintainer of this package. I don�t understand your request here. Did you have a problem pushing to the package? Nitesh From: Devon Kohler Date: Wednesday, May 12, 2021 at 12:46 PM To: maintai...@bioconductor.org , bioc-devel@r-project.org Cc: Tsung-Heng Tsai

Re: [Bioc-devel] Problems while activating my bioconductor git account

Hi, I�ve changed the email to m...@sebastianbauer.info. You did used to have sebastian.ba...@charite.de. Please activate now, and add your SSH keys to gain access to the package. Best, Nitesh From: Bioc-devel on behalf of

Re: [Bioc-devel] BFG clean-up and reset for compartmap

cc-ing bioc-devel From: Nitesh Turaga Date: Tuesday, May 11, 2021 at 10:13 AM To: Johnson, Ben Subject: Re: BFG clean-up and reset for compartmap That is exactly right. I would also delete/archive non-bioconductor feature branches like dev, hg38 etc. Only master and RELEASE_X_Y branches

Re: [Bioc-devel] Maintainer change Bioconductor packages

on the package itself will be on your end to make. Change the maintainer email, subscribe to bioc-devel etc. Best, Nitesh From: Nitesh Turaga Date: Tuesday, May 11, 2021 at 7:59 AM To: Pablo Moreno Cc: Suhaib Mohammed , maintai...@bioconductor.org , bioc-devel@r-project.org , gene-express...@ebi.ac.uk

Re: [Bioc-devel] BFG clean-up and reset for compartmap

the branches and run BFG. Best, Nitesh From: Johnson, Ben Date: Tuesday, May 11, 2021 at 8:02 AM To: Nitesh Turaga , bioc-devel@r-project.org Subject: Re: BFG clean-up and reset for compartmap Hi Nitesh, It would be https://github.com/biobenkj/compartmap. Thanks! Best, Ben K Johnson Postdoctoral

Re: [Bioc-devel] BFG clean-up and reset for compartmap

Hi, What exactly is the github repo we have to pull from? Nitesh From: Bioc-devel on behalf of Johnson, Ben Date: Monday, May 10, 2021 at 3:11 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] BFG clean-up and reset for compartmap Hi all, We had a couple manifest files that were

Re: [Bioc-devel] Maintainer change Bioconductor packages

st, Nitesh From: Pablo Moreno Date: Sunday, May 9, 2021 at 10:32 PM To: Nitesh Turaga Cc: Suhaib Mohammed , maintai...@bioconductor.org , bioc-devel@r-project.org , gene-express...@ebi.ac.uk Subject: Re: Maintainer change Bioconductor packages Dear Nitesh, I think that in the rush of Suhaib

Re: [Bioc-devel] Transfer Maintainership of the Package NetSAM

Hi, This is now done. Please try to activate your account on BiocCredentials. https://git.bioconductor.org/BiocCredentials/account_activation and add SSH keys. You will gain access to the package then. Best, Nitesh From: Zhang, Bing Date: Sunday, May 9, 2021 at 5:07 PM To:

Re: [Bioc-devel] Force Package Update after Removing Large Files from .git History

Hi Gabriel, Thanks for taking the time to fix the package size to < 5MB. I�ve synced your package repo on git.bioconductor.org. You should be good to go now. If you have any further questions on this, please feel free to reply to this thread. Best, Nitesh From: Bioc-devel on behalf of

Re: [Bioc-devel] Maintainer for preciseTAD

Hi Mikhail, I�ve added you to have access to the package preciseTAD. You should be able to use your registered SSH keys with Bioconductor to access the package now. I cannot make you the maintainer directly. This is a discussion you should have with Spiro and make the change in the package

Re: [Bioc-devel] Log in to the BiocCredentials app

Hi Mauro, I just checked and you�ve never activated your account. You should try to activate it before you do anything else. Best, Nitesh From: mauro castro Date: Tuesday, May 4, 2021 at 1:31 PM To: Nitesh Turaga Cc: Bioc-devel Subject: Re: [Bioc-devel] Log in to the BiocCredentials app Hi

Re: [Bioc-devel] Log in to the BiocCredentials app

Hi Have you checked your Spam or junk mail? You should have received an email from maintai...@bioconductor.org - Bioconductor git credentials administrator. If it�s being filtered or something, could you please try to do the password reset again? I

Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

olving that, but there can only be so much progress when using daily builds as a gauge. Best regards, Waldir ma., 03.05.2021 kl. 17.07 +, skrev Nitesh Turaga: Today - May 3, 2021. My apologies. Nitesh From: Nitesh Turaga mailto:nturaga.b...@gmail.com>> Date: Monday, May 3, 2021 at 1:04

Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

Dear Maintainers, The RELEASE_3_12 branch is now frozen. Best, Nitesh From: Nitesh Turaga Date: Monday, May 3, 2021 at 1:08 PM To: bioc-devel@r-project.org Subject: Re: Bioconductor Release Announcement: RELEASE_3_12 branch freeze Today - May 3, 2021. My apologies. Nitesh From: Nitesh

Re: [Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

Today - May 3, 2021. My apologies. Nitesh From: Nitesh Turaga Date: Monday, May 3, 2021 at 1:04 PM To: bioc-devel@r-project.org Subject: Bioconductor Release Announcement: RELEASE_3_12 branch freeze Dear Maintainers, Please keep in mind that we are on schedule for our release as given

[Bioc-devel] Bioconductor Release Announcement: RELEASE_3_12 branch freeze

-experiment and workflow). After 2pm today, you will not be able to push to the RELEASE_3_12 branch. Best regards, Nitesh Turaga [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo

Re: [Bioc-devel] Bioc Git credentials

Hi Leonard, I�ve changed your email now, you should be able to activate your account. The email listed was to a gene.com email address. Add new SSH keys if you don�t have the old key pairs. Best, Nitesh From: Bioc-devel on behalf of Leonard Goldstein Date: Sunday, May 2, 2021 at 10:06 PM

Re: [Bioc-devel] issue with ssh public key

. This is a fail safe, we don�t want package maintainers to disappear and give us emails that aren�t valid. Best, Nitesh From: Martin, Tiphaine Date: Monday, May 3, 2021 at 9:39 AM To: Nitesh Turaga , bioc-devel@r-project.org Subject: RE: issue with ssh public key Hi, This was my previous email

Re: [Bioc-devel] issue with ssh public key

The email registered is tiphaine.mar...@kcl.ac.uk . If this is not correct, I will have to change it on my end. Best, Nitesh From: Bioc-devel on behalf of Martin, Tiphaine Date: Saturday, May 1, 2021 at 11:47 PM To: bioc-devel@r-project.org Subject:

Re: [Bioc-devel] upstream push error

Hi, Have you followed http://bioconductor.org/developers/how-to/git/faq/ points 14,15 ,16 ? It�s more likely your keys aren�t set up properly on your end. If it persists, just add a new SSH key. Best, Nitesh From: Bioc-devel on behalf of Lieven Clement Date: Wednesday, April 28, 2021 at

Re: [Bioc-devel] Error pushing upstream

Hi Pedro, There is no �main� branch on the Bioconductor repository. There is only the master branch. Try git push upstream master From: Bioc-devel on behalf of Pedro Baldoni Date: Wednesday, April 28, 2021 at 7:27 AM To: bioc-devel@r-project.org Subject: [Bioc-devel] Error pushing

Re: [Bioc-devel] unable to push to new package

27, 2021 at 3:56 AM To: Nitesh Turaga Cc: bioc-devel@r-project.org , Germain Pierre-Luc Subject: Re: unable to push to new package Dear Nitesh, Thanks so much! After we did as you suggested, pushing upstream worked fine. There is still a warning in the build report<http://bioconductor.

Re: [Bioc-devel] CGEN package maintainer change request

Hi, Please check http://bioconductor.org/developers/how-to/git/ From: Nilotpal Sanyal Date: Friday, April 23, 2021 at 12:04 PM To: Nitesh Turaga , Wheeler, Bill (IMS) , maintai...@bioconductor.org , bioc-devel@r-project.org Cc: Summer S Han , nilan...@jhu.edu Subject: Re: CGEN package

Re: [Bioc-devel] CGEN package maintainer change request

Hi, I�ve created a new account for Nilotpal in the BiocCredentials platform. Nilotpal would have to activate the account first, and then add SSH keys to gain access to the package. Once access is gained, please change the maintainer field in the DESCRIPTION file of the package. Best, Nitesh

Re: [Bioc-devel] Bioconductor Package Version

on the slack channel or on the bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> mailing list. Best, Nitesh From: AJ Kinstlick Date: Thursday, April 22, 2021 at 6:37 PM To: Nitesh Turaga Cc: Kern, Lori Subject: Re: [Bioc-devel] Bioconductor Package Version Hi Nitesh and L

Re: [Bioc-devel] unable to push to new package

Hi, You do not have write privileges to the package because only the maintainer (cre) is given write access. The submission is a little messy here, because 1. It�s submitted from a lab account (this is ok in general) 2. You are not listed as maintainer, but want to maintain the package.

Re: [Bioc-devel] unable to push to new package

it to your account after you activate it https://git.bioconductor.org/BiocCredentials/account_activation . I would also recommend deleting your Github SSH key, because it matches Pierre�s. This is the wrong way to do it. Both of you should delete that key. Best, Nitesh From: Nitesh Turaga

Re: [Bioc-devel] New maintainer for BASiCS

Hi, I've added Allan to have access to the package BASiCS. It is up to you to update the maintainer record on the DESCRIPTION file of the package, this is not something Bioconductor does for you. Remember there can only be 1 active maintainer of the package listed in the DESCRIPTION file, but

Re: [Bioc-devel] Update maintainer of nucleR package

Hi Diego, We have added the new maintainer for the package as requested. Hi Alba, You have to activate your BiocCredentials account at https://git.bioconductor.org/BiocCredentials/account_activation with the email you gave us. Once you activate, please add SSH keys and you�ll gain access to

Re: [Bioc-devel] Bioconductor package InterMineR

: Kern, Lori Date: Thursday, April 15, 2021 at 8:27 AM To: rac...@intermine.org , Nitesh Turaga Subject: Re: Bioconductor package InterMineR Looping one of our better git experts in for an opinion on this. Nitesh, advise on reverting to previous version that won't cause conflicting issues

Re: [Bioc-devel] BFG repo cleanup for package under review

Hi Spencer, I�ve fixed the issue please try now. Best, Nitesh From: Nitesh Turaga Date: Wednesday, April 7, 2021 at 1:31 PM To: Spencer Nystrom , bioc-devel@r-project.org Subject: Re: [Bioc-devel] BFG repo cleanup for package under review Hi Spencer, I�ll take a look at this today and get

Re: [Bioc-devel] BFG repo cleanup for package under review

Hi Spencer, I�ll take a look at this today and get back to you Thanks for the reminder. Best, Nitesh From: Bioc-devel on behalf of Spencer Nystrom Date: Wednesday, April 7, 2021 at 1:24 PM To: bioc-devel@r-project.org Subject: [Bioc-devel] BFG repo cleanup for package under review Sorry

Re: [Bioc-devel] BFG cleanup on `spiky` repo (under submission)

Hi Tim, This package should be fixed now. I've synced your github repo with the one on git.bioconductor.org. Please check to make sure everything is as expected including the size. Best, Nitesh On 4/1/21, 6:22 AM, "Bioc-devel on behalf of Triche, Tim" wrote: Hi all,

Re: [Bioc-devel] Bioconductor Git Credentials error

Hi Ashish, I replied to your email yesterday, let�s stick to the same thread there. From: Ashish Jain Date: Friday, April 2, 2021 at 1:02 PM To: Nitesh Turaga Cc: raman sethi , Chen Jinmiao , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] Bioconductor Git Credentials error

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