Re: [Bioc-devel] Add collaborator

I'll create one for you Pedro and send you a private email about access. Nitesh -- Nitesh Turaga Senior Programmer Analyst Bioconductor core team Roswell Park From: Pedro Russo Sent: Wednesday, December 11, 2019 6:00:48 AM To: Turaga, Nitesh Cc: Helder Nakaya

Re: [Bioc-devel] Add collaborator

Hi, I'll help you with this. Does Pedro have a Bioccredentials account already? Best Nitesh -- Nitesh Turaga Senior Programmer Analyst Bioconductor core team Roswell Park From: Bioc-devel on behalf of Helder Nakaya Sent: Wednesday, December 11, 2019 6:52:00

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

he best way to do it. Because this way I am rebasing 50 commits from GitHub, while on the bioc side it could only be a cherry pick or patch for the release and devel version bumps. Best, Alex On 9. Dec 2019, at 16:34, Alexander Gosdschan wrote: The package I am talking about is methylKit,

Re: [Bioc-devel] How to move package from workflow to software

changes which are better managed and reviewed via that process. Best, Nitesh > On Dec 5, 2019, at 4:39 PM, Turaga, Nitesh > wrote: > > Hi Julien, > > I've done a basic review of your package, BgeeCall as a software package. > > This is a very basic review o

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

Hi, Please let me know which package you are talking about. Also, give me your GitHub package name. Nitesh > On Dec 9, 2019, at 7:24 AM, Alexander Gosdschan wrote: > > Hi, > > Somehow I missed to push a large number of commits to the bloc git master > branch before the latest release

Re: [Bioc-devel] How to move package from workflow to software

a look. Nitesh > On Nov 15, 2019, at 12:44 PM, Turaga, Nitesh > wrote: > > Hi Julien, > > We have decided that it shouldn't go through a deprecation cycle. Instead, I > will do a quick review of the package(build + check, and the times for build > and check are

Re: [Bioc-devel] Changes not applied in bioc source

Hi Vinh, I checked the installation from BiocManager. It seems the same version 1.1.2 is being installed by BiocManager as well as from the Bioconductor git repo. Can you tell me how to test for this bug? I just ran the vignette but don't see an error. It will be more helpful for us to debug

Re: [Bioc-devel] Bioconductor package twilight

Hi, Your package was registered to stefanie.sch...@molgen.mpg.de. But this has been changed now. You should be able to activate your BiocCredentials account at stefanie.sch...@gmx.de Best, Nitesh > On Dec 4, 2019, at 10:42 PM, Stefanie Senger wrote: > > Hi Lori, > > > I just tried to

Re: [Bioc-devel] Activating git credentials

It's possible your university is blocking emails. But either way, I've set a password for you and reset your account. You should receive a private email. Once you add your SSH keys, you'll have access to your package. Best, Nitesh > On Dec 4, 2019, at 10:10 AM, Turaga, Nitesh >

Re: [Bioc-devel] Activating git credentials

; it and forgot about it. But it was not the case since I did not get any > emails, also not in the junk folder. > > Best, > Marc > > On 04/12/2019, 15:54, "Turaga, Nitesh" wrote: > >Hi Marc, > >Your email address is associated with your

Re: [Bioc-devel] Activating git credentials

Hi Marc, Your email address is associated with your package. "m.pagesgall...@umcutrecht.nl" You should be able to activate it from BiocCredentials. Have you tried checking in your spam folder or junk folder for the activation email? https://git.bioconductor.org/BiocCredentials It seems

Re: [Bioc-devel] [Bioconductor/Contributions] MBQN package (#1064)

://bioconductor.org/developers/how-to/git/ . I'll be sending you a private email with your credentials. Best, Nitesh > On Nov 27, 2019, at 1:29 PM, Eva Brombacher wrote: > > Yes, that would be great. Many thanks for your help. > > Best wishes, > > Eva > > Am 27.11.19 um 1

Re: [Bioc-devel] [Bioconductor/Contributions] MBQN package (#1064)

urg.de as well. > > Regarding your question, I don't have a BiocCredentials account yet and, > indeed, would like to have access to the Bioconductor repo if this is > possible. > > Best, > > Eva > > > Am 27.11.19 um 19:02 schrieb Turaga, Nitesh: >

Re: [Bioc-devel] [Bioconductor/Contributions] MBQN package (#1064)

Hi, That is because you are not listed as the maintainer of the package in the DESCRIPTION file. Author: Ariane Schad , Clemens Kreutz , Eva Brombacher Maintainer: Ariane Schad I'm cc-ing the maintainer of the package as well. Please let me know if there is an issue with contributing on

Re: [Bioc-devel] transfer maintainer status of gCrisprTools

Hi, Which email would Russ like to use as his email account with BiocCredentials? Best, Nitesh > On Nov 22, 2019, at 5:11 PM, Peter Haverty > wrote: > > I'd like to transfer gCrisprTools to Russ Bainer (russ.bai...@gmail.com, > rbai...@mazetx.com). How do I do that? > >

Re: [Bioc-devel] Submitting a package with heavy data and vignette

Hi, I think this is a good path forward. Please take a look at the link below which will provide further guidelines for you, http://bioconductor.org/developers/package-guidelines/#data https://bioconductor.org/developers/package-submission/#experPackage

Re: [Bioc-devel] BiocCredentials & transfer maintenance

Hi Renan, This has been fixed, you should get a private email about your new BiocCredentials account. You should see access to, pepDat PICS Gviz PING pepStat Pviz ImmuneSpaceR XCIR Best, Nitesh On 11/18/19, 1:29 PM, "Bioc-devel on behalf of Renan Sauteraud" wrote: I am trying to

Re: [Bioc-devel] New package submission : No reviewer communication.

is tedious and takes a lot of time. I just wanted to clarify with people with previous experience submitting packages as this is my first time. Thanks, Ashwath -Original Message- From: Turaga, Nitesh Sent: Tuesday, November 19, 2019 1:56 PM To: Kuma

Re: [Bioc-devel] New package submission : No reviewer communication.

Hi, Please be patient in this regard. The reviewer will get to your package as soon as they can. Each package takes time to review, and each reviewer is reviewing multiple packages. As far as asking for support regarding your package, it is best to ask your questions on the "Issue" which was

Re: [Bioc-devel] Git pushing problems for data package

, Nitesh On 11/18/19, 5:27 AM, "Bioc-devel on behalf of Turaga, Nitesh" wrote: Hi Tim, It seems like you may have had more than two usernames. I might have ended my search too early. I'll fix this. Just give me a little time.

Re: [Bioc-devel] Git pushing problems for data package

Hi Tim, I've standardized your user name across your packages. Firstly, please check https://git.bioconductor.org/BiocCredentials/permissions_by_user/, And tell me what you see? Nitesh On 11/18/19, 5:27 AM, "Bioc-devel on behalf of Turaga, Nitesh" wrote: Hi Tim,

Re: [Bioc-devel] Git pushing problems for data package

, Jr. Sent: Sunday, November 17, 2019 4:25:26 PM To: Turaga, Nitesh Cc: Hervé Pagès Subject: Re: [Bioc-devel] Git pushing problems for data package Followup: I changed my github username associated with my email address to my actual GitHub username (I am thinking that we will need to update

Re: [Bioc-devel] How to move package from workflow to software

ine them to create a workflow. It corresponds to a new > approach allowing to generate present/absent gene expression calls from > RNA-Seq libraries without using an arbitrary cutoff. > > I would be very happy if you can help me moving it to the software section. > > Best, >

Re: [Bioc-devel] Git pushing problems for data package

Hi Tim, That's because you have for some reason two different usernames with Bioconductor. I've corrected the issue. You are now universally "ttriche" only. You should have access now. Best Nitesh > On Nov 15, 2019, at 9:52 AM, Tim Triche, Jr. wrote: > > Hi all, > > How do I push

Re: [Bioc-devel] How to move package from workflow to software

Hi, Changing the BiocViews section in the DESCRIPTION file doesn't change your package from a workflow package to a software package. There are fundamental differences between workflow packages and software packages in the way we handle them within Bioconductor. Could you tell us why you'd

Re: [Bioc-devel] scPCA: Push Access Request

You should have access now. From: Nima Hejazi Date: Wednesday, November 13, 2019 at 11:01 AM To: "Turaga, Nitesh" Cc: Philippe Boileau , "bioc-devel@r-project.org" Subject: Re: [Bioc-devel] scPCA: Push Access Request Hi Nitesh — Thanks for the quick reply. Sure, I thin

Re: [Bioc-devel] scPCA: Push Access Request

Hi, I'll help you with this. Nima, I'm guessing the email you want is the same one? Best, Nitesh On 11/13/19, 10:45 AM, "Bioc-devel on behalf of Philippe Boileau" wrote: Hello BioC Team, This is to confirm that the Nima Hejazi and I are co-developers of this package,

Re: [Bioc-devel] Update maintainer for DeMixT

I have sent Peng Yang the credentials needed to activate the newly created BiocCredentials account (https://git.bioconductor.org/BiocCredentials). Once the account is activate and SSH keys are added, Peng should have access. Best, Nitesh On 11/4/19, 6:58 AM, "Turaga, Nitesh&qu

Re: [Bioc-devel] Update maintainer for DeMixT

Hi I'd like to bring to your attention a few things, 1. There can only be ONE maintainer in the DESCRIPTION file, http://bioconductor.org/developers/package-guidelines/#description. Please modify your DESCRIPTION file to reflect only one official maintainer. You can have multiple Authors.

Re: [Bioc-devel] Large file problem in git

Try BFG cleaner https://rtyley.github.io/bfg-repo-cleaner/ But I agree with what Herve says. You may use this on your own github repo if you'd like. But leaving it as is, is a good option. On 9/30/19, 10:57 PM, "Bioc-devel on behalf of Pages, Herve" wrote: Hi Jelena, The

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

issue here > https://github.com/Bioconductor/Contributions/issues/1247. > > Cheers, > > Tim > > On 23/8/19 3:46 am, Turaga, Nitesh wrote: >> Hi Tim, >> >> Based on what your have mentioned, it seems that DMRcatedata should become >> an experiment hub package

Re: [Bioc-devel] Reset to a previous commit

the code changes, and add a new version 1.9.3 to it. Step 3, You should be able to just do a regular push to Bioconductor here on out. Best, Nitesh > On Sep 10, 2019, at 8:51 AM, Turaga, Nitesh > wrote: > > Hi Simon, > > Bioconductor's git system doesn'

Re: [Bioc-devel] Reset to a previous commit

Hi Simon, Bioconductor's git system doesn't allow force push (This is a feature) . It only allows a force push by administrators (Bioconductor Core team). Please send me a link to your GitHub repo which is at 1.9.0, and I will sync it for you. I've updated the link where the instructions are

[Bioc-devel] Fwd: Update InterMineR maintainer

Begin forwarded message: From: ni41435_ca mailto:nitesh.tur...@roswellpark.org>> Subject: Re: Update InterMineR maintainer Date: September 10, 2019 at 8:08:40 AM EDT To: Rachel Lyne mailto:rac...@intermine.org>> Lower case 'i' vs upper case in the package name 'I'. It's a typo. "Git" is

[Bioc-devel] Fwd: Update InterMineR maintainer

Forwarding to Bioc-devel for issue tracking. Begin forwarded message: From: Rachel Lyne mailto:rac...@intermine.org>> Subject: Re: Update InterMineR maintainer Date: September 10, 2019 at 8:03:55 AM EDT To: "Turaga, Nitesh" mailto:nitesh.tur...@roswellpark.org>> git rem

Re: [Bioc-devel] Version number error

I suspect this was a Bioconductor hook rejecting the "version" number? Is that correct Chris? Please also reply with the exact error message. Best, Nitesh > On Sep 4, 2019, at 7:58 AM, Shepherd, Lori > wrote: > > Or perhaps just providing the git commands you tried and the ERROR that was

Re: [Bioc-devel] transfer maintainer

> On Aug 26, 2019, at 11:48 AM, zzric...@gmail.com wrote: > > Hi Nitesh, > > Thanks for your reply. The email to register is: > h...@georgetown.edu > > We will make changes to all documentations as well. > > Thanks > > On Mon, Aug 26, 2019 at 6:56 AM Turag

Re: [Bioc-devel] transfer maintainer

Hi, What email address would you like to register? Right now, kg...@georgetwon.edu is registered in the BiocCredentials website. Make sure you are changing the maintainer on the DESCRIPTION page of the package and everywhere else needed. We will take care of the BiocCredentials page Best,

Re: [Bioc-devel] DMRcate_2.0.0 and updated DMRcatedata

Hi Tim, Based on what your have mentioned, it seems that DMRcatedata should become an experiment hub package. https://bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html Please take a look that vignette. Let me know if you have any

Re: [Bioc-devel] mixOmics issue url

Please push to both branches "master" and "RELEASE_3_9" on the remote "git@git,bioconductor.org:packages/mixOmics". Do you have access to the Bioconductor git server? Have you followed this documentation and help page? http://bioconductor.org/developers/how-to/git/push-to-github-bioc/ Best,

Re: [Bioc-devel] Changing the Bioconductor package maintainer

Hi, You should be able activate your BiocCredentials account with the email address chuklina.jel...@gmail.com. Once you activate, you need to add your SSH keys. You should be able to then sync your package with the Github changes. Best, Nitesh > On Aug 8, 2019, at 8:16 AM, Jelena Chuklina

Re: [Bioc-devel] Bioc credentials

Please try again. I've changed your email address to the one leo.la...@iki.fi It was listed differently before. Thanks Nitesh > On Jul 31, 2019, at 2:08 PM, Leo Lahti wrote: > > Hello list. I maintain the microbiome R pkg in Bioconductor. > > While updating the devel version, I noticed

Re: [Bioc-devel] Please add my email to the Bioconductor server

Hi Theo, You have been added to our system. You should be able to access your package. Before that, you have to add your SSH keys to the BiocCredentials web app, so that your SSH key gets associated with the package. Please activate your account at

Re: [Bioc-devel] patch old releases? e.g. RELEASE_3_8

Hi, Dario is correct. Anything other than the current devel or RELEASE branch cannot be modified. Best, Nitesh On 7/12/19, 2:00 AM, "Bioc-devel on behalf of Dario Strbenac" wrote: Good day, No; anything older than the release branch at present is not modifiable.

Re: [Bioc-devel] Give person commit access to 'SBGNview'

Done > On Jul 11, 2019, at 10:59 AM, Luo Weijun wrote: > > Thanks Nitesh, > I also need commit access to SBGNview.data, which is part of the same > project. Can you add it? Thanks. > Weijun > > > > On Thursday, July 11, 2019, 10:38:43 AM EDT, Turaga, Ni

Re: [Bioc-devel] Give person commit access to 'SBGNview'

Please activate your BiocCredentials account to manage it. The email address is luo_wei...@yahoo.com. Once you do that, you can add specific SSH keys which give you access. Your GitHub ID is already added and access to the package should be managed with the same SSH key as your GitHub.

Re: [Bioc-devel] Biconductor Git Credentials

Please activate and update your account. I have made the needed fix. Best, Nitesh On 6/27/19, 7:16 PM, "Bioc-devel on behalf of Federico, Anthony, Nicholas" wrote: an...@bu.edu This email message may contain legally privileged and/or confidential information. If you are not the

Re: [Bioc-devel] updating package

Hi, It seems like the email is configured correctly on BiocCredentials app. It is because the account is not activated it doesn't work. You'd have to first activate your account before moving forward with setting a password. I've added your GitHub credentials to the account. Best, Nitesh

Re: [Bioc-devel] Github repo with multiple BioC packages

Hi Shraddha, The packages need to be in two separate GitHub repos. There is a way to submit the data package and the software package together. The data package can become an experiment hub package if you wish.

Re: [Bioc-devel] My address is not associated with a maintainer.

Hi Please activate your account in the BiocCredentials account, and then add your SSH keys for access https://git.bioconductor.org/BiocCredentials Username: email address Password: biocuser Best, Nitesh > On Jun 6, 2019, at 7:57 AM, Damian Szklarczyk wrote: > > Dear Bioconductor, > >

Re: [Bioc-devel] FW: BioC packages NuPoP and nuCpos

So there might be some settings under my current user account on my computer. > What could it be? Do you have an suggestions? > > On 5/28/19, 12:47 PM, "Turaga, Nitesh" wrote: > >I see, I based my assumption that you access Github via HTTP protocol as > per yo

Re: [Bioc-devel] FW: BioC packages NuPoP and nuCpos

d, but GitHub does not provide > shell access. > > > > On 5/28/19, 12:39 PM, "Turaga, Nitesh" wrote: > >At this point, I'd suggest two things, > >1. Create a new key, and try to use that new key by adding it in your > BiocCredentials accou

Re: [Bioc-devel] FW: BioC packages NuPoP and nuCpos

49B May 24 08:21 JWangNUGitHub.pub > -r 1 jon staff 3.4K May 24 08:21 JWangNUGitHub > > ~~~ > Here is my config file: > > host git.bioconductor.org > HostName git.bioconductor.org > IdentityFile ~/.ssh/id_rsa > User git > > On 5/28

Re: [Bioc-devel] FW: BioC packages NuPoP and nuCpos

Ok, now that we know that there remotes have been set up right, I'd like to also make sure that the private keys you are using correspond to the public keys we have on file. cat */j.wang* ssh-rsa

Re: [Bioc-devel] FW: BioC packages NuPoP and nuCpos

Hi, Can I see the output of your (inside your package repository, to check if you have correctly set up your remotes)? git remote -v http://bioconductor.org/developers/how-to/git/faq/ #14 is very important for me to help your trouble short. Best, Nitesh This email message may

Re: [Bioc-devel] Updating email for BiocCredentials

Hi, Please activate your account in the BiocCredentials app. You can use your new email to activate it and add SSH keys da...@bccrc.ca. Once you activate, and add SSH keys, you should have access to your package. Best, Nitesh This email message may contain legally privileged and/or

Re: [Bioc-devel] Add maintainer of synergyfinder

Hi Shuyu, The first SSH key you added in your BiocCredentials account is not a valid SSH key. The rest of your 3 keys seem to be valid, please try to use one of those. 1. Based on your logs, from `ssh -Tv g...@git.bioconductor.org` you are not using the keys which you have submitted. 2. I

Re: [Bioc-devel] Procedure for changing email

Hi Leo, If your old email is registered to the BiocCredentials app, then you'd have to change that too. If you reply with that email, a Bioc admin can change it for you (me). Best Nitesh Get Outlook for Android From: Bioc-devel on

Re: [Bioc-devel] FCBF git push to RELEASE_3_9 was denied

I'm actually unable to reproduce that error on my local machine. Since the data/ folder contains the scDengue.RData file. Try another version bump and see if it persists. I'm suspecting it might be something to do with with the .gitignore. I think maybe someone like Hervé or Martin might have

Re: [Bioc-devel] duplicate commits in preprocessCore

Hi Ben It seem from your git log that, the duplicate commits are from RELEASE_3_5. A good way to deal with this now is to just allow your incoming commits to get through. You should be able to send in your commits now. But, one thing to note is, make sure you don't have any duplicate commits

[Bioc-devel] Pre-receive hook on git.bioconductor.org to prevent merge conflict markers enabled

Dear Maintainers, A new "pre-receive hook" on git.bioconductor.org server has been enabled to keep the repositories in good shape. The new hook prevents "merge conflict markers". Please note that the hook is now enabled as of 11:45 AM May 10th 2019. Git merges sometimes result in conflicts

Re: [Bioc-devel] pushing changes to an existing package

Hi Simina, This is an issue with Github. So just to walk through what might be happening, this is a case when users set up 2FA (two factor authentication). You might want to to set up SSH keys for GitHub as well, and use the SSH protocol (given below instead of HTTPS) as your remote origin.

Re: [Bioc-devel] FCBF git push to RELEASE_3_9 was denied

Hi Tiago, Let's take a look at the commit history you have, /t/FCBF ❯❯❯ git log commit

Re: [Bioc-devel] pushing changes to an existing package

No idea Simina. Maybe a typo? Best, Nitesh This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby

Re: [Bioc-devel] pushing changes to an existing package

Once your access works you should see yourself as maintainer with Read and Write access on MultiMed and CancerMutationAnalysis. Best Nitesh This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent

Re: [Bioc-devel] pushing changes to an existing package

ductor<mailto:git@git.bioconductor>.org:packages/MultiMed.git (push) You can try first by resetting your upstream, git remote set-url upstream git@git.bioconductor<mailto:git@git.bioconductor>.org:packages/MultiMed.git Let me know if this works. Best, Nitesh On May 2, 2019,

[Bioc-devel] Access to Bioc git server resumed

Dear Maintainers, Access to Bioc git server is now active again. Maintainers will now have access to RELEASE_3_9 and master branch. Make sure you sync your packages with the latest release changes before making any updates.

Re: [Bioc-devel] pushing changes to an existing package

own hosts. R packages/MultiMed Cheers, Simina On Tue, Apr 30, 2019 at 11:01 AM Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Hi Simina, http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a little more please. Best, Nitesh On Apr 30,

Re: [Bioc-devel] Bioconductor version 3.9 branching today

Minor typo, we'll be creating the Bioconductor 3.9 branch (RELEASE_3_9) starting at 11AM. > On May 2, 2019, at 9:28 AM, Turaga, Nitesh > wrote: > > Dear Bioc developers, > > Today we'll be creating the Bioconductor 3.8 branch (RELEASE_3_9) starting at >

[Bioc-devel] Bioconductor version 3.9 branching today

Dear Bioc developers, Today we'll be creating the Bioconductor 3.8 branch (RELEASE_3_9) starting at 11am EST. All commits to git.bioconductor.org will be blocked for a few hours starting at 11AM. We'll post back when push access is restored and you can resume

Re: [Bioc-devel] Deleting a branch on Bioconductor git

Hi Kevin, I'm actually surprised you were able to push a branch at all. I'll delete this branch. Best, Nitesh > On May 2, 2019, at 7:52 AM, Kevin Wang wrote: > > Hi all, > I accidentally pushed a branch called “RELEASE_3_9” to the “scMerge" package > that I am maintaining on

Re: [Bioc-devel] pushing changes to an existing package

Hi Simina, http://bioconductor.org/developers/how-to/git/faq/ #14 to help us out a little more please. Best, Nitesh On Apr 30, 2019, at 10:45 AM, Simina Boca mailto:smb...@georgetown.edu>> wrote: Hello, I am trying to update my package MultiMed

Re: [Bioc-devel] Access to Bioconductor Git Credentials

Hi Frank, We have reset your email to the new one. Please take a look and activate the account now, and add your SSH keys. I will your credentials to activate in a private email. Thanks, Nitesh > On Apr 30, 2019, at 7:22 AM, Dondelinger, Frank > wrote: > > Hi, > > I am trying to update

Re: [Bioc-devel] RankProd package update

Hi, You are not listed on the package as a maintainer, even though the DESCRIPTION page shows it. Fangxin Hong http://jimmy.harvard.edu>> is listed as maintainer. I will change the maintainer to you at the email your provided. I will send your a new BiocCredentials app account details

Re: [Bioc-devel] failing package nucleoSim

ote: Hi Nitesh, The repo is: https://github.com/ArnaudDroitLab/nucleoSim Thanks, Astrid ________ De : Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> Envoyé : 23 avril 2019 12:23 À : Astrid Deschenes Cc : Shepherd, Lori Objet : Re: failing package nucleoSim Hi

Re: [Bioc-devel] Adding maintainer to mzID

Hi Thomas, You found the right place. Please issue the change on the package as well (in the devel version), change the maintainer to Laurent Gatto. Laurent should now have access to this package. Best regards, Nitesh > On Apr 23, 2019, at 2:46 PM, Thomas Lin Pedersen wrote: > > Hi > >

Re: [Bioc-devel] update maintainer or nucleR package

Hi, If you want to change the maintainer on your package, please make the change in the DESCRIPTION file. This is something you need to do. I can make the change on the Bioconductor end, and change the access rights to your package with the new email address. It looks like Diego needs a

Re: [Bioc-devel] failing package seq2pathway

Hi Jennifer, It seems that you are not following the instructions accurately as given on the link you sent. You notice that you are only interacting with your Github repository and not the git.bioconductor.org private git server. You have to add both the "remote"

Re: [Bioc-devel] BiocCredentials say my email is not a maintainer

Hi, The email you registered is ines.desanti...@cruk.cam.ac.uk. We can add your gmail address. But you’d have to activate it as a new account on the BiocCredentials app. In the next email, I will send you a temp password for the new account. Once you

Re: [Bioc-devel] Adding maintainer for ‘singscore’

As a follow up and closure to this Bioc-devel thread. The user bhuvad was added to singscore. Best, Nitesh On Mar 14, 2019, at 11:54 PM, Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> wrote: Hi, We can add him as a collaborator on the git repo, but you can have only one of

Re: [Bioc-devel] Package build failure on RELEASE_3_8. Please fix.

are errors caused because of the GCC complier version being used on the image. Sorry for the confusion. Please note, this is not related to the errors on the build machine. Best, Nitesh > On Mar 8, 2019, at 12:55 PM, Turaga, Nitesh > wrote: > > Hello Bioconductor

Re: [Bioc-devel] Package missing in BiocCredentials app

Hi Markus, How about now, I just gave you permissions. You should be able to see it in the app, and get access to it. Best, Nitesh > On Mar 11, 2019, at 6:38 PM, Markus Riester wrote: > > Hi, > > an old data package of mine (curatedBladderData) is not showing up in my > BiocCredentials

[Bioc-devel] Package build failure on RELEASE_3_8. Please fix.

Hello Bioconductor Maintainers, The following packages have issues which need to be fixed by maintainers. The issues are listed below, if you are getting a direct email it means your package is one of the broken ones. Please take time to fix them as soon as possible. The packages are, 1.

Re: [Bioc-devel] Cannot reset credentials password

Hi Sergi, I’ve tested our system and it seems like the email activation system is working fine. It’s possible that your “upc.edu” is filtering the email before it reaches you. A lot of institutions do a spam filter before they even get to your inbox. Can you give me another

Re: [Bioc-devel] How to change the name of R package that is already published on Bioconductor?

ommits both today and yesterday. If you have further issues, please let me know. Thanks. Regards, Junpeng Zhang School of Engineering, Dali University Website: https://www.researchgate.net/profile/Junpeng_Zhang3 On Wednesday, March 6, 2019, 4:11:52 AM GMT+8, Turaga, Nitesh mailto:nitesh.tur...@roswe

Re: [Bioc-devel] How to change the name of R package that is already published on Bioconductor?

Hi Junpeng, Yes it is possible to do this. 1. We will first deprecate your package miRsponge in the devel version of Bioconductor. a) You will need to add .onLoad function, which points users to the new package ‘miRspongeR’. The .onLoad function goes in the zzz.R file, and it will throw a

Re: [Bioc-devel] Suggestion for "sync-existing-repositories" instructions

Thanks Alejandro. I’ll add your suggestion. > On Mar 5, 2019, at 12:14 PM, Alejandro Reyes > wrote: > > Hi all, > > Ran into troubles sync-ing the repositories of a package. End up solving it > and wanted to suggest adding a note to the instructions on "Sync an existing > GitHub

Re: [Bioc-devel] failed to access github, how to push updated package to the Github repository

e? Thank you, Holly From: Turaga, Nitesh mailto:nitesh.tur...@roswellpark.org>> Sent: Monday, March 4, 2019 10:26:35 AM To: Xinan Yang Cc: bioc-devel@r-project.org<mailto:bioc-devel@r-project.org>; Jennifer Sun Subject: Re: [Bioc-devel] failed to ac

Re: [Bioc-devel] failed to access github, how to push updated package to the Github repository

Hi, Firstly, you are not admin on the web app to be able to login with an “admin” account. Please try https://git.bioconductor.org/BiocCredentials/. You have an account under the email, mailto:xya...@uchicago.edu>>. Please try to log in and activate your account first using that email

Re: [Bioc-devel] How critical is package style for bioconductor?

As long as it’s consistent, you can use another style. Consistency helps reviewers read the code easily. Most people generally use “camelCase" or “snake_case" for variable names and function names. But keep in mind that class names need to be “CamelCase" as that is the R style of doing

Re: [Bioc-devel] Warning about the size of git pack file

Hi Vinh, See in line replies, On Feb 22, 2019, at 2:30 PM, Vinh Tran mailto:t...@bio.uni-frankfurt.de>> wrote: Dear all, I am planning to submit a package into Bioconductor. But BiocCheck() gave a warning about the size of the git pack file: $warning [1] "The following files are over 5MB

Re: [Bioc-devel] sg...@kumc.edu is not associated with a maintainer of a Bioconductor package

Hi, You do not need to submit your keys to Bioconductor if you are just submitting a package. BiocCredentials is an app which is used by package maintainers only, for packages which have already been accepted into Bioconductor. Please follow the regular submission process

Re: [Bioc-devel] Maintainer email change

The content of your email was not visible before you sent us this. Your package has been updated with the latest email. Be sure to change the DESCRIPTION file as well, to reflect where users can contact the maintainer. Best, Nitesh > On Feb 14, 2019, at 11:13 AM, Khadija El Amrani wrote: >

Re: [Bioc-devel] Maintainer email change

We need more information here. > On Feb 12, 2019, at 6:14 PM, Khadija El Amrani wrote: > > > ___ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or

Re: [Bioc-devel] update bioconductor package

> the "Minoo-AShtiani" profile. > Would please help get through this? I have no idea how to fix. > > All the best, > Minoo > > > > Sender notified by > Mailtrack 02/08/19, 12:29:23 PM > > On Sun, Jan 27, 2019 at 7:07 PM Turaga, Nitesh

Re: [Bioc-devel] Bioconductor git credentials

Hi Mike, I will take care of this for you. Jake would need to login to the BiocCredentials app (https://git.bioconductor.org/BiocCredentials) and authenticate himself with a username and password which I will send to his email directly. Jake should then add his SSH keys to his account, and

Re: [Bioc-devel] Submission of packages located at within a repository

Hi Britta, You could use submodules in git. I took some time to create an example use case for you, at https://github.com/nturaga/main_repository The “main_repository” contains a README.md file which you might find useful to go about creating the submodule for your packages/ The

Re: [Bioc-devel] error pushing changes

, > Best, > > Marta > > Marta Hidalgo > > De: Turaga, Nitesh > Enviado: miércoles, 30 de enero de 2019 18:27 > Para: Marta Hidalgo > Cc: Bioc-devel; Morgan, Martin > Asunto: Re: [Bioc-devel] error pushing changes > > Hi Marta, > > I have fixed y

Re: [Bioc-devel] error pushing changes

Hi Marta, I have fixed your repository in the Bioconductor repo. g...@git.bioconductor.org:packages/hipathia.git Please follow this document exactly as is, to sync your GitHub repository (http://bioconductor.org/developers/how-to/git/sync-existing-repositories/). If you are having issues with

Re: [Bioc-devel] update bioconductor package

You need to have access to your repository at git.bioconductor.org. http://bioconductor.org/developers/how-to/git/ You should find all of your documentation in that link. Nitesh > On Jan 27, 2019, at 2:50 AM, minoo ashtiani wrote: > > Hello everyone, > > I would like to update my

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